@@ Line 1: / Line 1: @@
-<div class="nonumtoc">__TOC__</div>
-====2.4.5 Antigen tests====
-An antigen is a substance—often a protein but may also be an environmental like a virus—that provokes the immune system to produce an antibody against it.<ref name="MPAntigen">{{cite web |url=https://medlineplus.gov/ency/article/002224.htm |title=Antigen |work=MedlinePlus |publisher=U.S. National Library of Medicine |accessdate=07 August 2020}}</ref> As such, another approach to testing for the presence of a virus in a specimen is to test for the antigen rather than the antibody. An antigen test is useful as a repeated surveillance test, but it has drawbacks as a one-time diagnostic test.<ref name="Anderson5Invest20">{{cite web |url=https://www.wcvb.com/article/5-investigates-concerns-about-current-use-of-rapid-antigen-tests-for-covid-19/33538332 |title=5 Investigates: Concerns about current use of rapid antigen tests for COVID-19 |author=Anderson, K. |work=WCVB 5 ABC |date=06 August 2020 |accessdate=07 August 2020}}</ref><ref name="ServiceRadical2020">{{cite journal |title=Radical shift in COVID-19 testing needed to reopen schools and businesses, researchers say |journal=Science |author=Service, R.F. |year=2020 |doi=10.1126/science.abe1546}}</ref><ref name="KremerUWSys20">{{cite web |url=https://urbanmilwaukee.com/2020/08/07/uw-system-orders-350000-covid-19-tests/ |title=UW System Orders 350,000 COVID-19 Tests |author=Kremer, R. |work=Urban Milwaukee |date=07 August 2020 |accessdate=07 August 2020}}</ref> For COVID-19 and other viral infections, an antigen test has the advantage that specimen collection can typically be done with a simple nasal swab rather than a more invasive [[nasopharyngeal swab]]. Another advantage, on one hand, is that antigen testing is more rapid and convenient because the extraction and amplification steps of PCR are not used. On the other, antigen testing is less sensitive for the same reason: you test only what's there (rather than amplifying the amount for greater sensitivity).<ref name="ServiceRadical2020" /><ref name="GuglielmiTheExp20">{{cite journal |title=The explosion of new coronavirus tests that could help to end the pandemic |journal=Nature |author=Guglielmi, G. |volume=583 |pages=506–09 |year=2020 |doi=10.1038/d41586-020-02140-8}}</ref>
-A theory increasingly gaining traction, however, is that "[a] higher frequency of testing makes up for poor sensitivity.”<ref name="ServiceRadical2020" /><ref name="KremerUWSys20" /><ref name="ClarkCOVID20">{{cite web |url=https://www.medpagetoday.com/infectiousdisease/covid19/87930 |title=COVID Antigen Tests: Coming to Case Counts Near You? |author=Clark, C. |work=MedPage Today |date=06 August 2020 |accessdate=07 August 2020}}</ref> Several researchers have shared pre-print and published research suggesting this outcome<ref name="ServiceRadical2020" />:
-<blockquote>Larremore and his colleagues have modeled the benefits of more frequent tests, even ones that are less accurate than today’s. Fast tests repeated every three days, with isolation of people who test positive, prevents 88% of viral transmission compared with no tests; a more sensitive test used every two weeks reduced viral transmission by about 40%, they report in a 27 June preprint on medRxiv. Paltiel and his colleagues reached much the same conclusion when they modeled a variety of testing regimes aimed at safely reopening a 5000-student university. In a 31 July paper in JAMA Network Open, they found that, with 10 students infected at the start of the semester, a test that identified only 70% of positive cases, given to every student every two days, could limit the number of infections to 28 by the end of the semester. Screening every seven days allowed greater viral spread, with the model predicting 108 infections.</blockquote>
-As such, the utility of antigen testing, despite its lower sensitivity, appears to be surveillance situations where a large group of individuals who are at risk can be screened at regularly scheduled intervals of two to four days. The end result, in theory, would be few people who are target-positive would be missed, positives could be isolated and verified with a more sensitive test, and more target-positive people would be identified and isolated before reaching peak infectivity.<ref name="ServiceRadical2020" /><ref name="CourageCovid20">{{cite web |url=https://www.vox.com/2020/7/31/21336212/covid-19-test-results-delays |title=Should we be testing fewer people to stop the spread of Covid-19? |author=Courage, K.H. |work=Vox |date=31 July 2020 |accessdate=05 August 2020}}</ref> To be clear, it's not a perfect solution, but as Harvard epidemiologist Michael Mina and Boston University economist Laurence Kotlikoff suggest, "[w]e need the best means of detecting and containing the virus, not a perfect test no one can use."<ref name="CourageCovid20" /> A coalition of six U.S. state governors has bought into that concept and agreed to work together with the Rockefeller Foundation, as well as the Quidel Corporation and Becton, Dickinson and Company, which have received FDA EUAs to market antigen tests for SARS-CoV-2.<ref name="ClarkCOVID20" /><ref name="MervoshItsLike20">{{cite web |url=https://www.nytimes.com/2020/08/04/us/virus-testing-delays.html |title=‘It’s Like Having No Testing’: Coronavirus Test Results Are Still Delayed |author=Mervosh, S.; Fernandez, M. |work=The New York Times |date=04 August 2020 |accessdate=05 August 2020}}</ref> However, it's not clear how those six states will best put the tests to use despite 1. their moderate sensitivity (and thus a greater chance of false negatives<ref name="ClarkCOVID20" />) and 2. the question of whether or not the two companies can produce enough test kits for repeat testing in those states.<ref name="ServiceRadical2020" /> As of August 2020, three total vendors have FDA EUAs for antigen tests: the two mentioned, plus LumiraDx UK Ltd.<ref name="FDAEmerg20" />
-==3. Adding COVID-19 and other virus testing to your laboratory==
-Maybe you've been running an environmental health laboratory and want to expand into clinical health testing. Perhaps you're in charge of an academic research lab but want to expand to the clinical diagnostic side. Or maybe you're running a [[physician office laboratory]] (POL) and are wondering if it's even possible to expand your waived testing efforts to COVID-19. Where the previous chapter discussed the "what" of COVID-19 and viral testing, this chapter aims to help you with the "how" of adding it to your laboratory offerings.
-Naturally, many questions come with the "how":
-* Does using one method make the most sense, or will your lab turn to multiple methods for virus testing? This may be determined by current equipment, space considerations, and budget.
-* What type of lab are you running? A POL is going to have fewer options available than a CLIA moderate- or high-complexity lab.
-* How interoperable are you existing laboratory and clinical informatics solutions? Research laboratories face more challenges in integrating their systems with EHRs and other clinical systems.
-* What vendors and consultants are out there to help get equipped? Some vendors have very specific solutions, whereas others may have a broader range of offerings.
-These questions and more are addressed this chapter.
-===3.1 What methodologies will you use?===
-====3.1.1 PCR====
-In the previous chapter, the most common testing methodologies for [[COVID-19]] and other [[Coronavirus|coronaviruses]] were discussed in detail. The prevailing method (often called the "gold standard") among them all is real-time reverse-transcription [[polymerase chain reaction]] (rRT-PCR) assays for testing. Broadly speaking, PCR is useful in pharmaceutical, biotechnology, and genetic engineering endeavors, as well as clinical diagnostics. As such, labs in those industries that already have PCR infrastructure in place have a theoretical step-up over a lab that doesn't.
-PCR technology has advanced to the point where it is more efficient and user-friendly than prior, yet "the high cost of the instruments, servicing contracts, and reagents pose major challenges for the market, especially to the price-sensitive academics."<ref name="MWPoly20">{{cite web |url=https://www.marketwatch.com/press-release/polymerase-chain-reaction-market-sector-analysis-report-regional-outlook-competitive-share-forecast---2023-2020-06-23 |title=Polymerase Chain Reaction Market Sector Analysis Report, Regional Outlook & Competitive Share & Forecast - 2023 |author=Kenneth Research |work=MarketWatch |date=23 June 2020 |accessdate=06 August 2020}}</ref> Writing about the thirty-fifth anniversary of PCR in 2018, science writer Alan Dove not only highlighted these cost issues but also the size and energy requirements for running the equipment. "As a result, one of the defining techniques of modern molecular biology has remained stubbornly inaccessible to educators and unusable in many remote locations."<ref name="DovePCR18">{{cite journal |title=PCR: Thirty-five years and counting |journal=Science |author=Dove, A. |volume=360 |issue=6389 |pages=670–672 |year=2018 |doi=10.1126/science.360.6389.673-c}}</ref> Various efforts have been made over the years to bring costs down by modifying how heating and temperature control are performed<ref name="WongARapid15">{{cite journal |title=A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings |journal=PLoS One |author=Wong, G.; Wong, I. Chan, K. et al. |volume=10 |issue=7 |at=e0131701 |year=2015 |doi=10.1371/journal.pone.0131701}}</ref><ref name="KuznetsovDIYbio15">{{cite journal |title=DIYbio Things: Open Source Biology Tools as Platforms for Hybrid Knowledge Production and Scientific Participation |journal=Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems |author=Kuznetsov, S.; Doonan, C.; Wilson, N. et al. |pages=4065–68 |year=2015 |doi=10.1145/2702123.2702235}}</ref><ref name="NortonPhila16">{{cite web |url=https://www.bizjournals.com/philadelphia/news/2016/05/11/government-contract-biomeme-hiring-med-tech.html |title=Phila. med tech startup working on multimillion dollar government contract |author=Norton, D. |work=Philadelphia Business Journal |date=11 May 2016 |accessdate=06 August 2020}}</ref><ref name="AnLow20">{{cite journal |title=Low-Cost Battery-Powered and User-Friendly Real-Time Quantitative PCR System for the Detection of Multigene |journal=Micromachines |author=An, J.; Jiang, Y.; Shi, B. et al. |volume=11 |at=435 |year=2020 |doi=10.3390/mi11040435}}</ref>, but many of those system aren't typically optimal during a pandemic when turnaround time is critical.
-Amidst the pandemic, additional challenges also exist to those wanting to conduct PCR testing for COVID-19 and other viruses. As was discussed at the end of the previous chapter, supplies of reagents and consumables are not particularly robust mid-pandemic, with shortages being reported since March 2020.<ref name="HerperShortage20">{{cite web |url=https://www.statnews.com/2020/03/10/shortage-crucial-chemicals-us-coronavirus-testing/ |title=Shortage of crucial chemicals creates new obstacle to U.S. coronavirus testing |work=STAT |author=Herper, M.; Branswell, H. |date=10 March 2020 |accessdate=10 April 2020}}</ref><ref name="HaleQiagen20">{{cite web |url=https://www.fiercebiotech.com/medtech/qiagen-aims-to-more-than-quadruple-its-covid-19-reagent-production-6-weeks |title=Qiagen aims to more than quadruple its COVID-19 reagent production in 6 weeks |work=Fierce Biotech |author=Hale, C. |date=18 March 2020 |accessdate=10 April 2020}}</ref><ref name="MehtaMystery20">{{cite web |url=https://www.chemistryworld.com/mystery-surrounds-uk-claim-of-covid-19-test-reagent-shortage/4011457.article |title=Mystery surrounds UK claim of Covid-19 test reagent ‘shortage’ |work=Chemistry World |author=Mehta, A. |date=03 April 2020 |accessdate=10 April 2020}}</ref><ref name="RocheIrish20">{{cite web |url=https://www.irishtimes.com/news/science/irish-scientists-develop-reagent-in-effort-to-ease-covid-19-testing-delays-1.4223897 |title=Irish scientists develop reagent in effort to ease Covid-19 testing delays |work=The Irish Times |author=Roche, B. |date=08 April 2020 |accessdate=10 April 2020}}</ref><ref name="PadmaEfforts20">{{cite web |url=https://www.chemistryworld.com/news/efforts-to-combat-covid-19-in-india-hit-by-imported-reagent-shortages/4011718.article#/ |title=Efforts to combat Covid-19 in India hit by imported reagent shortages |author=Padma, T.V. |work=Chemistry World |date=13 May 2020 |accessdate=19 May 2020}}</ref><ref name="DavidSurvey20">{{cite web |url=https://abcnews.go.com/Health/survey-shows-resources-covid-19-diagnostic-testing-limited/story?id=71341885 |title=Survey shows resources for COVID-19 diagnostic testing still limited months later |author=David, E.; Farber, S.E. |work=ABC News |date=20 June 2020 |accessdate=08 July 2020}}</ref><ref name="JohnsonNCLabs20">{{cite web |url=https://patch.com/north-carolina/charlotte/nc-labs-facing-shortages-covid-19-testing-chemicals |title=NC Labs Facing Shortages In COVID-19 Testing Chemicals |author=Johnson, K. |work=Patch |date=02 July 2020 |accessdate=08 July 2020}}</ref><ref name="MervoshItsLike20">{{cite web |url=https://www.nytimes.com/2020/08/04/us/virus-testing-delays.html |title=‘It’s Like Having No Testing’: Coronavirus Test Results Are Still Delayed |author=Mervosh, S.; Fernandez, M. |work=The New York Times |date=04 August 2020 |accessdate=05 August 2020}}</ref><ref name="CourageCovid20">{{cite web |url=https://www.vox.com/2020/7/31/21336212/covid-19-test-results-delays |title=Should we be testing fewer people to stop the spread of Covid-19? |author=Courage, K.H. |work=Vox |date=31 July 2020 |accessdate=05 August 2020}}</ref> These shortages may eventually work themselves out, but they highlight the need for other varying methods that don't necessarily depend on the same reagents and consumables that are in short supply.
-For those labs wishing to adopt PCR testing of viruses—particularly COVID-19—into their workflow while providing reasonable turnaround times, all is not lost. However, careful planning is required. For example, you'll want to keep in mind that some PCR machines require vendor-specific reagents. If you're going to acquire a particular instrument, you'll want to do due diligence by verifying not only the supported reagents but also those reagents' overall availability (real and projected). You'll also want to consider factors such as anticipated workload (tests per day), what your workflow will look like, and how to balance overall investment with the need for reasonable turnaround times.
-As of August 2020, an increasing body of research is being produced suggesting ways to improve turnaround times with PCR testing for COVID-19, with many research efforts focusing on cutting out RNA extraction steps entirely. Alcoba-Florez ''et al.'' [[Journal:Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples|propose]] direct heating of the sample-containing nasopharyngeal swab at 70 °C for 10 minutes in place of RNA extraction.<ref name="Alcoba-FlorezFast20">{{cite journal |title=Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples |journal=International Journal of Infectious Diseases |author=Alcoba-Florez, J.; González-Montelongo, R.; Íñigo-Campos, A.; García-Martínezde Artola, D.; Gil-Campesino, H.;<br />The Microbiology Technical Support Team; Ciuffreda, L.; Valenzuela-Fernández, A.; Flores, C. |volume=97 |pages=66–68 |year=2020 |doi=10.1016/j.ijid.2020.05.099}}</ref> Adams ''et al.'' have proposed an "adaptive PCR" method using a non-standard reagent mix that skips RNA extraction and can act "as a contingency for resource‐limited settings around the globe."<ref name="ShapiroStream20">{{cite web |url=https://news.vanderbilt.edu/2020/07/29/streamlined-diagnostic-approach-to-covid-19-can-avoid-potential-testing-logjam/ |title=Streamlined diagnostic approach to COVID-19 can avoid potential testing logjam |author=Shapiro, M. |work=Research News @ Vanderbilt |date=29 July 2020 |accessdate=06 August 2020}}</ref><ref name="AdamsCOVID20">{{cite journal |title=COVID‐19 diagnostics for resource‐limited settings: Evaluation of “unextracted” qRT‐PCR |journal=Journal of Medical Virology |author=Adams, N.M.; Leelawong, M.; Benton, A. et al. |year=2020 |doi=10.1002/jmv.26328}}</ref> Wee ''et al.'' skip RNA extraction and nucleic acid purification by using a single-tube homogeneous reaction method run on a lightweight, portable thermocycler.<ref name="MeharImproving20">{{cite web |url=https://www.techexplorist.com/improving-speed-gold-standard-covid-19-diagnostic-test/34069/ |title=Improving the speed of gold-standard COVID-19 diagnostic test |author=Mehar, P. |work=Tech Explorist |date=27 July 2020 |accessdate=06 August 2020}}</ref><ref name="WeeRapid20">{{cite journal |title=Rapid Direct Nucleic Acid Amplification Test without RNA Extraction for SARS-CoV-2 Using a Portable PCR Thermocycler |journal=Genes |author=Wee, S.K.; Sivalingam, S.P.; Yap, E.P.H. |volume=11 |issue=6 |at=664 |year=2020 |doi=10.3390/genes11060664}}</ref> Other innovations include tweaking reagents and enzymes to work with one step, skipping the reverse transcription step,<ref name="CSIRFaster20">{{cite web |url=https://www.engineeringnews.co.za/article/faster-local-covid-19-test-kits-could-be-ready-by-year-end-2020-07-30/ |title=Faster, local COVID-19 test kits could be ready by year-end |author=Council for Scientific and Industrial Research |work=Engineering News |publisher=Creamer Media |date=30 July 2020 |accessdate=07 August 2020}}</ref> and using saliva-based molecular testing that skips RNA extraction.<ref name="RanoaSaliva20">{{cite journal |title=Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction |journal=bioRxiv |author=Ranoa, D.R.E.; Holland, R.L.; Alnaji, F.G. et al. |year=2020 |doi=10.1101/2020.06.18.159434}}</ref><ref name="ThomasFast20">{{cite web |url=https://www.news-medical.net/news/20200806/Fast-cheap-and-easy-COVID-19-test-from-Yale.aspx |title=Fast, cheap and easy COVID-19 test from Yale |author=Thomas, L. |work=News Medical - Life Sciences |date=06 August 2020 |accessdate=16 August 2020}}</ref>
-'''Saliva as a specimen'''
-The saliva molecular tests in particular are intriguing. Talk of the potential utility of using saliva as a specimen for COVID-19 was occurring as early as April<ref name="XuSaliva20">{{cite journal |title=Saliva: Potential diagnostic value and transmission of 2019-nCoV |journal=International Journal of Oral Science |author=Xu, R.; Cui, B.; Duan, X. et al. |volume=12 |at=11 |year=2020 |doi=10.1038/s41368-020-0080-z}}</ref><ref name="GreenwoodSaliva20">{{cite web |url=https://news.yale.edu/2020/04/24/saliva-samples-preferable-deep-nasal-swabs-testing-covid-19 |title=Saliva samples preferable to deep nasal swabs for testing COVID-19 |author=Greenwood, M. |work=YaleNews |date=24 April 2020 |accessdate=01 May 2020}}</ref>, and the first saliva-based COVID-19 test, produced by Spectrum Solutions in cooperation with RUCDR Infinite Biologics Laboratory<ref name="SSFirst20">{{cite web |url=https://spectrumsolution.com/fda-authorized-covid-19-updates/ |title=First saliva collection device FDA EUA authorized for COVID-19 testing |publisher=Spectrum Solutions |date=2020 |accessdate=16 August 2020}}</ref> and Vault Health<ref name="VHVault20">{{cite web |url=https://www.prnewswire.com/news-releases/vault-health-launches-first-of-its-kind-saliva-based-fda-eua-approved-test-for-covid-19-301039633.html |title=Vault Health Launches First-of-its-Kind Saliva-based FDA EUA Approved Test for COVID-19 |author=Vault Health |work=PR Newswire |date=14 April 2020 |accessdate=01 May 2020}}</ref>, was given an FDA EUA in April. On August 15, Yale School of Public Health was given an EUA for it SalivaDirect molecular test. Although still PCR-based (and a CLIA high-complexity test), SalivaDirect is being touted as a means to improve specimen collection safety, consume fewer reagents, prove compatible with high-throughput workflow, and cut overall turnaround time. Not only is saliva easier to collect and safer for healthcare staff, the test is essentially "open sourced," not requiring proprietary equipment from Yale, making the test more flexible by being validated to reliably function with a wider array of reagents and instruments.<ref name="GallagherFDA20">{{cite web |url=https://www.contagionlive.com/news/fda-grants-emergency-covid19-authorization-yale-open-source-method-saliva-testing |title=FDA Grants Emergency COVID-19 Authorization to Yale's Open Source Method of Saliva Testing |author=Gallagher, G.M. |work=ContagionLive |date=15 August 2020 |accessdate=16 August 2020}}</ref><ref name="ZillgittFDA20">{{cite web |url=https://www.usatoday.com/story/sports/nba/2020/08/15/fda-approves-covid-19-saliva-test-developed-yale-nba-nbpa-aid/5590452002/ |title=FDA approves COVID-19 saliva test developed at Yale in partnership with the NBA, NBPA |author=Zillgitt, J. |work=USA Today |date=15 August 2020 |accessdate=16 August 2020}}</ref> When compared to using a nasopharyngeal swab specimen using the ThermoFisher Scientific TaqPath COVID-19 combo kit, results were comparable 94.1% of the time.<ref name="ThomasFast20" /> While sensitivity and specificity may be slightly less comparable to other PCR options<ref name="WeisslederCOVID20">{{cite web |url=https://csb.mgh.harvard.edu/covid |title=COVID-19 Diagnostics in Context |author=Weissleder, R.; Lee, H.; Ko, J. et al. |publisher=Harvard Center for Systems Biology |date=15 August 2020 |accessdate=16 August 2020}}</ref>, the overall advantages during reagent shortages and a definitive need for broader testing likely outweigh the slightly lesser sensitivity and specificity.
-====3.1.2 Pooled testing====
-Another method some labs are taking to speed up turnaround time is using pooled testing. The general concept involves placing two or more test specimens together and testing the pool as one specimen. The most obvious advantage to this is that the process saves on reagents and other supplies, particularly when supply chains are disrupted. This methodology is best used "in situations where disease prevalence is low, since each negative pool test eliminates the need to individually test those specimens and maximizes the number of individuals who can be tested over a given amount of time."<ref name="RohdeCOVID20">{{cite web |url=https://asm.org/Articles/2020/July/COVID-19-Pool-Testing-Is-It-Time-to-Jump-In |title=COVID-19 Pool Testing: Is It Time to Jump In? |author=Rohde, R. |publisher=American Society for Microbiology |date=20 July 2020 |accessdate=06 August 2020}}</ref> However, it's best left to situations where expectations are that less than 10 percent of the population being tested is affected by what's being tested for.<ref name="RohdeCOVID20" /><ref name="MashaPooled20">{{cite web |url=https://asiatimes.com/2020/08/pooled-virus-tests-help-stretched-health-services/ |title=Pooled virus tests help stretched health services |author=Masha, M.; Chau, S. |work=Asia Times |date=04 August 2020 |accessdate=06 August 2020}}</ref><ref name="CitronerHowPool20">{{cite web |url=https://www.healthline.com/health-news/how-pooled-testing-can-help-us-fight-spread-of-covid-19 |title=How Pooled Testing Can Help Us Fight Spread of COVID-19 |author=Citroner, G. |work=Healthline |date=03 August 2020 |accessdate=06 August 2020}}</ref>
-The downside of pooled testing comes with the issues of dilution, contamination, and populations with 10 or more percent infected. A target-positive specimen that comingles with other target-free specimens is itself diluted and in some cases may cause issues with the limit of detection for the assay. Additionally, if the pool tests positive, target-free specimens may become contaminated by a target-positive specimen. This may cause issues with any individual specimen assays that get ran. And the workflows involving pooling must be precise, as a technician working with multiple specimens at the same time increases the chance of lab errors.<ref name="RohdeCOVID20" /><ref name="MashaPooled20" /><ref name="CitronerHowPool20" /> Finally, at least in the U.S., a Food and Drug Administration (FDA) emergency use authorization (EUA) for a validated pooled testing method is required.<ref name="RohdeCOVID20" /> (Validation of pooled methods may differ in other countries.<ref name="MashaPooled20" />) The U.S. Centers for Disease Control and Prevention (CDC) has published [https://www.cdc.gov/coronavirus/2019-ncov/lab/pooling-procedures.html interim guidance] on pooled testing strategies for [[SARS-CoV-2]].
-====3.1.3 Rapid antigen testing====
-As mentioned in the previous chapter, the benefits of antigen testing For COVID-19 and other viral infections are 1. specimen collection can typically be done with a simple nasal swab rather than a more invasive [[nasopharyngeal swab]], 2. testing is more rapid and convenient, and 3. it takes some pressure off the PCR supply chain. However, antigen testing only tests what's there, rather than amplifying the amount, resulting in generally lower sensitivities.<ref name="ServiceRadical2020">{{cite journal |title=Radical shift in COVID-19 testing needed to reopen schools and businesses, researchers say |journal=Science |author=Service, R.F. |year=2020 |doi=10.1126/science.abe1546}}</ref><ref name="GuglielmiTheExp20">{{cite journal |title=The explosion of new coronavirus tests that could help to end the pandemic |journal=Nature |author=Guglielmi, G. |volume=583 |pages=506–09 |year=2020 |doi=10.1038/d41586-020-02140-8}}</ref> As such, the real utility of antigen testing, despite its lower sensitivity, appears to be surveillance situations where a large group of individuals who are at risk can be screened at regularly scheduled intervals of two to four days. If your lab is able to support this sort of testing, then this type of testing may be an option. However, as of August 2020, only three vendors have EUAs for antigen diagnostic tests: Quidel Corporation; Becton, Dickinson and Company; and LumiraDx UK Ltd.<ref name="FDAEmerg20">{{cite web |url=https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas |title=In Vitro Diagnostics EUAs |publisher=U.S. Food and Drug Administration |date=11 August 2020 |accessdate=12 August 2020}}</ref> With six U.S. states already contracted to purchase hundreds of thousands of two of those companies' test kits<ref name="ClarkCOVID20">{{cite web |url=https://www.medpagetoday.com/infectiousdisease/covid19/87930 |title=COVID Antigen Tests: Coming to Case Counts Near You? |author=Clark, C. |work=MedPage Today |date=06 August 2020 |accessdate=07 August 2020}}</ref><ref name="MervoshItsLike20">{{cite web |url=https://www.nytimes.com/2020/08/04/us/virus-testing-delays.html |title=‘It’s Like Having No Testing’: Coronavirus Test Results Are Still Delayed |author=Mervosh, S.; Fernandez, M. |work=The New York Times |date=04 August 2020 |accessdate=05 August 2020}}</ref>, it's not clear how well they'll manage to meet demand.
-====3.1.4 LAMP and CRISPR====
-Early on in the pandemic, while PCR was getting most of the attention, reverse transcription loop-mediated isothermal amplification (RT-LAMP), an isothermal [[Nucleic acid test|nucleic acid amplification]] technique that allows for RNA amplification, was also quietly being discussed<ref name="LambRapid20">{{cite journal |title=Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification |journal=medRxiv |author=Lamb, L.E.; Barolone, S.N.; Ward, E. et al. |year=2020 |doi=10.1101/2020.02.19.20025155}}</ref><ref name="Schmid-BurgkLAMP20">{{cite journal |title=LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding |journal=bioRxiv |author=Schmid-Burgk, J.L.; Li, D.; Feldman, D. et al. |year=2020 |url=https://www.biorxiv.org/content/10.1101/2020.04.06.025635v2.article-info |doi=10.1101/2020.04.06.025635}}</ref>, and it has since gained more attention.<ref name="YuRapid20">{{cite journal |title=Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform |journal=Clinical Chemistry |author=Yu, L.; Wu, S.; Hao, X. et al. |volume=66 |issue=7 |pages=975–77 |year=2020 |doi=10.1093/clinchem/hvaa102 |pmid=32315390 |pmc=PMC7188121}}</ref><ref name="ParkDevelop20">{{cite journal |title=Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) |journal=Journal of Molecular Diagnostics |author=Park, G.-S.; Ku, K.; Baek, S.-H. et al. |volume=22 |issue=6 |pages=729–35 |year=2020 |doi=10.1016/j.jmoldx.2020.03.006 |pmid=32276051 |pmc=PMC7144851}}</ref><ref name="KellnerARapid20">{{cite journal |title=A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing |journal=bioRxiv |author=Kellner, M.J.; Ross, J.J.; Schnabl, J. et al. |year=2020 |doi=10.1101/2020.06.23.166397}}</ref><ref name="ThiAColor20">{{cite journal |title=A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples |journal=Science Translational Medicine |author=Thi, V.L.D.; Herbst, K.; Boerner, K. et al. |at=eabc7075 |year=2020 |doi=10.1126/scitranslmed.abc7075 |pmid=32719001}}</ref><ref name="EsbinOver20">{{cite journal |title=Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection |journal=RNA |author=Esbin, M.N.; Whitney, O.N.; Chong, S. et al. |volume=26 |issue=7 |pages=771–83 |year=2020 |doi=10.1261/rna.076232.120 |pmid=32358057 |pmc=PMC7297120}}</ref><ref name="HaleOxford20">{{cite web |url=https://www.fiercebiotech.com/medtech/oxford-researchers-develop-portable-covid-19-test-costing-less-than-25 |title=Oxford researchers develop portable COVID-19 test costing less than $25 |author=Hale, C. |work=Fierce Biotech |date=09 July 2020 |accessdate=07 August 2020}}</ref> The University of Oxford, for example, is in the process of getting a rapid, affordable, clinically-validated RT-LAMP test approved for the European market. Oxford also notes that "[a]n advantage of using LAMP technology is that it uses different reagents to most laboratory-based PCR tests."<ref name="HaleOxford20" /> Thi ''et al.'' have tested a two-color RT-LAMP assay with an N gene primer set and diagnostic validation using LAMP-sequencing, concluding that the pairing of the two "could offer scalable testing that would be difficult to achieve with conventional qRT-PCR based tests."<ref name="ThiAColor20" /> And California-based Color Genomics have set up their own proprietary RT-LAMP system, capable of handling up to 10,000 tests per day.<ref name="SheridanThisCal20">{{cite web |url=https://www.statnews.com/2020/08/06/better-simpler-faster-covid-19-test/ |title=This California company has a better version of a simpler, faster Covid-19 test |author=Sheridan, K. |work=STAT |date=06 August 2020 |accessdate=08 August 2020}}</ref>
-In most cases, LAMP-based testing is much simpler than PCR, lacking the requirement of specialized instruments. Despite LAMP generally being thought of as less sensitive than PCR<ref name="SheridanThisCal20" /><ref name="GuglielmiTheExp20">{{cite journal |title=The explosion of new coronavirus tests that could help to end the pandemic |journal=Nature |author=Guglielmi, G. |volume=583 |pages=506–09 |year=2020 |doi=10.1038/d41586-020-02140-8}}</ref><ref name="HeidtSaliva20">{{cite web |url=https://www.the-scientist.com/news-opinion/saliva-tests-how-they-work-and-what-they-bring-to-covid-19-67720 |title=Saliva Tests: How They Work and What They Bring to COVID-19 |author=Heidt, A. |work=The Scientist |date=09 July 2020 |accessdate=08 August 2020}}</ref>, the recent explosion of research into RT-LAMP methods for testing for the presence of SARS-CoV-2 seems to gradually indicate that "under optimized conditions," RT-LAMP methods may actually be able to rival the sensitivity and specificity of many RT-PCR COVID-19 tests.<ref name="EsbinOver20" /> Esbin ''et al.'' add<ref name="EsbinOver20" />:
-<blockquote>These methods allow for faster amplification, less specialized equipment, and easy readout. LAMP methods also benefit from the ability to multiplex targets in a single reaction and can be combined with other isothermal methods, like &#91;[[recombinase polymerase amplification]]&#93; in the RAMP technique, to increase test accuracy even more. These techniques may be particularly useful for rapid, point-of-care diagnoses or for remote clinical testing without the need for laboratory equipment.</blockquote>
-CRISPR methods are also being used in conjunction with RT-LAMP.<ref name="GuglielmiTheExp20" /><ref name="EsbinOver20" /><ref name="BroughtonCRISPR20">{{cite journal |title=CRISPR–Cas12-based detection of SARS-CoV-2 |journal=Nature Biotechnology |author=Broughton, J.P.; Deng, X.; Yu, G. et al. |volume=38 |pages=870–74 |year=2020 |doi=10.1038/s41587-020-0513-4 |pmid=32300245}}</ref> RT-LAMP creates complementary double-stranded DNA (cDNA) from specimen RNA and then copies (amplifies) it. Then CRISPR methods are used to detect a predefined coronavirus sequence (from a cleaved molecular marker) in the resulting amplified specimen. Though as of August 2020 approved assays using CRISPR-based detection of SARS-CoV-2 are limited to a handful of companies<ref name="GuglielmiTheExp20" /><ref name="GDHCRISPR20">{{cite web |url=https://www.medicaldevice-network.com/comment/crispr-biotechnology-disrupt-covid-19-testing-market/ |title=CRISPR biotechnology set to disrupt Covid-19 testing market |author=GlobalData Healthcare |work=Verdict Medical Devices |date=14 July 2020}}</ref>, the technology has some promise as an alternative testing method. It has the additional advantage of being readily coupled with lateral flow assay technology to be deployed in the point-of-care (POC) setting.<ref name="EsbinOver20" /><ref name="GDHCRISPR20" />
-====3.1.5 Point-of-care and other alternative testing====
-On August 5, 2020, the WHO published a draft blueprint for what they call Target Product Profiles (TPP), which "describe the desirable and minimally acceptable profiles" for four difference COVID-19 test categories.<ref name="WHOCOVIDTarget20">{{cite web |url=https://www.who.int/publications/m/item/covid-19-target-product-profiles-for-priority-diagnostics-to-support-response-to-the-covid-19-pandemic-v.0.1 |title=COVID-19 Target product profiles for priority diagnostics to support response to the COVID-19 pandemic v.0.1 |author=World Health Organization |publisher=World Health Organization |date=05 August 2020 |accessdate=12 August 2020}}</ref> Addressing POC testing, the WHO recommends that such assays<ref name="WHOCOVIDTarget20" /><ref name="PeplowRapid20">{{cite web |url=https://cen.acs.org/analytical-chemistry/diagnostics/Rapid-COVID-19-testing-breaks/98/web/2020/08 |title=Rapid COVID-19 testing breaks free from the lab |author=Peplow, M. |work=Chemical & Engineering News |date=10 August 2020 |accessdate=12 August 2020}}</ref>:
-* have a sensitivity (true positive rate) or at least 70 percent;
-* have a specificity (true negative rate) of at least 97 percent;
-* provide results in less than 40 minutes;
-* require diagnostic machines that cost less than $3,000 U.S.;
-* individually cost less than $20 for the patient;
-* be simple enough that only a few hours of training are required to run the test; and
-* operate reliably outside a clean laboratory environment.
-While few of the available test systems can meet all these requirements, it's clear the push to expand COVID-19 testing to the point of care is accelerating.<ref name="PeplowRapid20" /><ref name="KriegerCorona20">{{cite web |url=https://www.mercurynews.com/2020/08/10/coronavirus-how-to-test-everyone-all-the-time/ |title=Coronavirus: How to test everyone, all the time |author=Krieger, L.M. |work=The Mercury News |date=10 August 2020 |accessdate=12 August 2020}}</ref><ref name="KriegerCorona20">{{cite web |url=https://www.mercurynews.com/2020/08/10/coronavirus-how-to-test-everyone-all-the-time/ |title=Coronavirus: How to test everyone, all the time |author=Krieger, L.M. |work=The Mercury News |date=10 August 2020 |accessdate=12 August 2020}}</ref><ref name="BrownPoint20">{{cite web |url=https://www.mcknights.com/news/point-of-care-testing-could-be-biggest-advance-in-covid-19-fight/ |title=Point-of-care testing could be ‘biggest advance’ in COVID-19 fight |author=Brown, D. |work=McKnight's |date=10 August 2020 |accessdate=12 August 2020}}</ref><ref name="WissonCOVID20">{{cite web |url=https://www.healtheuropa.eu/covid-19-and-effective-cohorting-rapid-point-of-care-triage-testing/101696/ |title=COVID-19 and effective cohorting: Rapid point of care triage testing |author=Wisson, J. |work=Health Europa |date=28 July 2020 |accessdate=12 August 2020}}</ref> The U.S. National Institutes of Health's Rapid Acceleration of Diagnostics (RADx) funding program has sought to speed up innovation in COVID-19 testing and promote "truly nontraditional approaches for testing that have a slightly longer horizon."<ref name="TrombergRapid20">{{cite journal |title=Rapid Scaling Up of Covid-19 Diagnostic Testing in the United States — The NIH RADx Initiative |journal=New England Journal of Medicine |author=Tromberg, B.J.; Schwetz, T.A.; Pérez-Stable, E.J. et al. |year=2020 |doi=10.1056/NEJMsr2022263}}</ref> As of August 2020, RADx has chosen to fund seven biomedical diagnostic companies making new lab-based and POC tests that could significantly ramp up overall testing in the U.S. into September 2020. Four offerings are lab-based (from Ginkgo Bioworks, Helix OpCo, Fluidigm, and Mammoth Biosciences) and three are POC tests (from Mesa Biotech, Quidel, and Talis Biomedical), all using varying technologies and methods such as next-generation sequencing, CRISPR, microfluidic chips, nucleic acid testing, antigen testing, and saliva testing.<ref name="NIHDelivering20">{{cite web |url=https://www.nih.gov/news-events/news-releases/nih-delivering-new-covid-19-testing-technologies-meet-us-demand |title=NIH delivering new COVID-19 testing technologies to meet U.S. demand |author=National Institutes of Health |publisher=National Institutes of Health |work=News Releases |date=31 July 2020 |accessdate=12 August 2020}}</ref> Both Mesa Biotech's rapid, cartridge-based RT-PCR Accula System and Quidel's rapid Sofia SARS Antigen FIA test are already EUAed and CLIA-waived<ref name="FDAEmerg20" />, with Talis' Talis One LAMP-based lateral flow immunoassay kit still awaiting EUA and CLIA status approval. Whether or not these POC and lab-based tests make it to the average [[physician office laboratory]] remains to be seen, however.
-Outside the RADx program, enterprising researchers in other parts of the world are also attempting non-traditional approaches to improving COVID-19 testing options. Examples include<ref name="EsbinOver20" /><ref name="WissonCOVID20" /><ref name="Leichman10Ways20">{{cite web |url=https://www.israel21c.org/how-israeli-scientists-are-improving-corona-testing/ |title=10 ways Israeli scientists are improving corona testing |author=Leichman, A.K. |work=Isael21c |date=27 July 2020 |accessdate=11 August 2020}}</ref>:
-* a method of DNA nanoswitch detection of virus particles;
-* a dual biomarker-based finger-stick test for acute respiratory infections;
-* a rapid breath test to detect volatile organic chemicals from the lungs;
-* an affordable, hand-held spectral imaging device to detect virus in blood or saliva in seconds;
-* an ultrahigh frequency spectroscopic scanning device to see virus particles resonating;
-* a method that combines optical devices and magnetic particles to detect virus RNA;
-* an RNA extraction protocol that uses magnetic bead-based kits;
-* the additional use of an [[artificial intelligence]] (AI) application to better scrutinize test results; and
-* the miniaturization of PCR technology to make it more portable and user-friendly.
-Of course, most of these are largely experimental technologies, and realistically getting them into the lab may be far out. But they represent out-of-the-box ideas that have some kind of chance at playing a greater role in the clinical laboratory or in point of care settings in the future.
-===3.2 What kind of space, equipment, and supplies will you need?===
-====3.2.1 Laboratory space arrangements====
-'''PCR considerations'''
-Whether adding PCR to your existing laboratory, modifying existing PCR workflows, or starting from scratch, preventing contamination is a top priority. As PCR can effectively amplify even the tiniest of quantities of DNA and RNA, the risk of amplifying a contaminant and ruining the validity of an assay is very real.<ref name="MifflinSetting03">{{cite book |url=http://www.biosupplynet.com/pdf/01_pcr_primer_p.5_14.pdf |format=PDF |chapter=Chapter 1: Setting Up a PCR Laboratory |title=PCR Primer |author=Mifflin, T.E. |editor=Dieffenbach, C.; Dveksler, G. |edition=2nd |publisher=Cold Spring Harbor Laboratory Press |pages=5–14 |year=2003 |isbn=9780879696542 |accessdate=13 August 2020}}</ref><ref name="RochePCR06">{{cite book |url=https://www.gene-quantification.de/ras-pcr-application-manual-3rd-ed.pdf |format=PDF |chapter=Chapter 2: General Guidelines |title=PCR Applications Manual |editor=Degen, H.-J.; Deufel, A.; Eisel, D. et al. |edition=3rd |publisher=Roche Diagnostics GmbH |pages=19–38 |year=2006 |accessdate=13 August 2020}}</ref><ref name="AhmedSetting14">{{cite book |url=http://grcpk.com/wp-content/uploads/2014/10/12.-Setting-up-PCR-Lab.pdf |format=PDF |chapter=Chapter 12: Setting-up a PCR Lab |title=Manual of PCR |author=Ahmed, S. |publisher=Genetics Resource Centre |year=2014 |accessdate=13 August 2020}}</ref><ref name="RedigTheDevil14">{{cite web |url=https://bitesizebio.com/19880/the-devil-is-in-the-details-how-to-setup-a-pcr-laboratory/ |title=The Devil is in the Details: How to Setup a PCR Laboratory |author=Redig, J. |work=BiteSizeBio |date=01 August 2014 |accessdate=13 August 2020}}</ref><ref name="BioChekTheBasics18">{{cite web |url=https://www.biochek.com/wp-content/uploads/2018/05/BioChek-E-book-The-basics-of-PCR.pdf |format=PDF |title=The basics of PCR: Detecting viruses and bacteria red-handed |publisher=BioChek BV |date=May 2018 |accessdate=13 August 2020}}</ref><ref name="DasMitig18">{{cite journal |title=Mitigating PCR /Amplicon Contamination in a High Risk High Burden Mycobacterial Reference Laboratory in a Resource Limited Setting |journal=Mycobacterial Diseases |author=Das, P.K.; Ganguly, S.B.; Mandal, B. |volume=8 |issue=2 |at=261 |year=2018 |doi=10.4172/2161-1068.1000261}}</ref><ref name="WHODos18">{{cite web |url=https://www.who.int/malaria/areas/diagnosis/molecular-testing-dos-donts/en/ |title=Dos and Don'ts for molecular testing |author=World Health Organization |publisher=World Health Organization |date=31 January 2018 |accessdate=14 August 2020}}</ref> Contamination typically comes from non-amplified environmental substances such as aerosols, and from carryover contamination of amplicons from earlier PCR cycles. As such, not only do best-practice processes and procedures (P&P) need to be followed (e.g., unidirectional workflow, thorough cleaning procedures, proper preparation and disposal), but also where to place PCR-related equipment must be carefully considered.<ref name="MifflinSetting03" /><ref name="RochePCR06" /><ref name="RedigTheDevil14" /><ref name="DasMitig18" />
-When possible, separate rooms for sample preparation, PCR setup, and post-PCR activities, each with their own airflow control, are encouraged.<ref name="MifflinSetting03" /><ref name="RochePCR06" /><ref name="BioChekTheBasics18" /><ref name="DasMitig18" /><ref name="WHODos18" /> However, the laboratory attempting to add PCR to an already small clinical diagnostic lab may not have the luxury of having multiple rooms. In that case, a single-room setup may suffice, if the workflow areas remain demarcated or physically partitioned. Additionally, a single-room setup must also have stricter P&P and design controls to offset the space constraints. For example, the sample preparation area of the room should have a laminar flow hood with UV light that is regularly cleaned, and post-PCR analysis may need to occur later in the day after cleanup from prior steps.<ref name="MifflinSetting03" /><ref name="AhmedSetting14" /><ref name="WHODos18" /> Of course, always maintaining unidirectional workflow—regardless of number of rooms—is also critical to minimizing contamination. For example, technicians shouldn't be transporting amplified materials into the DNA extraction area.
-Although dated, Roche Diagnostics' 2006 ''[https://www.gene-quantification.de/ras-pcr-application-manual-3rd-ed.pdf PCR Applications Manual]''<ref name="RochePCR06" /> provides a detailed breakdown of setting up the laboratory for PCR. [https://www.longdom.org/open-access/mitigating-pcr-amplicon-contamination-in-a-high-risk-high-burden-mycobacterial-reference-laboratory-in-a-resource-limited-setting-2161-1068-1000261.pdf Das ''et al.'']<ref name="DasMitig18" />  and [https://bitesizebio.com/19880/the-devil-is-in-the-details-how-to-setup-a-pcr-laboratory/ Dr. Jennifer Redig]<ref name="RedigTheDevil14" /> provide additional valuable insight. The World Health Organization (WHO) also provides [https://www.who.int/malaria/areas/diagnosis/molecular-testing-dos-donts/en/ guidance] for setting up molecular testing in the lab.<ref name="WHODos18" />
-'''Isothermal amplification considerations'''
-Similarly, because DNA and RNR amplification is involved, contamination concerns exist with isothermal amplification techniques. Multiple pipetting steps and repeated freezing and thawing of reagents can still lead to cross-contamination<ref name="DiegoProgress19">{{cite journal |title=Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: Towards a ready-to-use test |journal=Scientific Reports |author=Diego, J. G.-B.; Fernández-Soto, P.; Crego-Vicente, B. et al. |volume=9 |at=14744 |year=2019 |doi=10.1038/s41598-019-51342-2 |pmid=31611563 |pmc=PMC6791938}}</ref>, as does opening the reaction chamber after reaction is completed.<ref name="MartzyChall19">{{cite journal |title=Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis |journal=Analytical and Bioanalytical Chemistry |author=Martzy, R.; Kolm, C.; Krska, R. et al. |volume=411 |pages=1695–1702 |year=2019 |doi=10.1007/s00216-018-1553-1 |pmid=30617408 |pmc=PMC6453865}}</ref> However, the advent of microfluidics and lateral flow technologies in isothermal amplification processes has seen the development of "fully enclosed microstructured devices into which performing the isothermal amplification reduces the risk of sample contamination and allows integration and portable device realization."<ref name="ZanoliIsotherm13">{{cite journal |title=Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices |journal=Biosensors |author=Zanoli, L.M.; Spoto, G. |volume=3 |issue=1 |pages=18–43 |year=2013 |doi=10.3390/bios3010018 |pmid=25587397 |pmc=PMC4263587}}</ref><ref name="RoskosSimple13">{{cite journal |title=Simple System for Isothermal DNA Amplification Coupled to Lateral Flow Detection |journal=PLoS One |author=Roskos, K.; Hickerson, A.I.; Lu, H.-W. et al. |volume=8 |issue=7 |at=e69355 |year=2013 |doi=10.1371/journal.pone.0069355 |pmid=23922706 |pmc=PMC3724848}}</ref> Even more cutting-edge techniques to reduce contamination such as the CUT-LAMP technique of Bao ''et al.''<ref name="BaoCUT20">{{cite journal |title=CUT-LAMP: Contamination-Free Loop-Mediated Isothermal Amplification Based on the CRISPR/Cas9 Cleavage |journal=ACS Sensors |author=Bao, Y.; Jiang, Y.; Xiong, E. et al. |volume=5 |issue=4 |pages=1082–91 |year=2020 |doi=10.1021/acssensors.0c00034 |pmid=32242409}}</ref> or the dUTP/UDG system for COVID-19 RT-LAMP reactions of Kellner ''et al.''<ref name="KellnerARapid20" /> hold further promise in making isothermal amplification processes in the laboratory easier to manage. That said, labs running isothermal amplification processes such as LAMP requiring analysis with agarose gel electrophoresis or a method requiring the opening of reaction vessels will preferably have a secondary area set up for analysis steps so as to minimize the chances of contamination.<ref name="NEBLoop14">{{cite web |url=https://www.neb.com/protocols/2014/06/17/loop-mediated-isothermal-amplification-lamp |title=Loop-mediated Isothermal Amplification (LAMP) |publisher=New England BioLabs |date=17 June 2014 |accessdate=14 August 2020}}</ref><ref name="Fernández-SotoDevelop14">{{cite journal |title=Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of ''Loa loa'' |journal=PLoS One |author=Fernández-Soto, P.; Mvoulouga, P.O.; Akue, J.P. et al. |volume=9 |issue=4 |at=e94664 |year=2014 |doi=10.1371/journal.pone.0094664 |pmid=24722638 |pmc=PMC3983228}}</ref>
-====3.2.2 Instruments and assays====
-[[File:Eppendorf Mastercycler Pro S.jpg|right|400px|thumb|Eppendorf Mastercycler Pro S, a thermal cycler for PCR and other applications]]
-'''High- and moderate-complexity CLIA testing'''
-Thermal cyclers are the standard instruments for PCR testing. Today, real-time or quantitative (qPCR) systems largely fill this niche. However, [[Digital polymerase chain reaction|digital and droplet digital PCR]] systems are emerging, and they have the benefit of producing even more rapid, precise, sensitive, accurate, and reproducible results, and they are capable of direct quantification and multiplexing. Other instruments and accessories for PCR workflows include proper power supplies, analytical balances, electrophoresis chambers, water and/or dry baths, and mini/micro centrifuges. However, if you're considering the addition of PCR workflow to your laboratory, the thermal cycler is typically where the largest up-front cost will be. As such, it's important to ask yourself critical questions to help guide your acquisition decisions.
-As part of their June 2018 survey on PCR equipment, ''Lab Manager'' poses five questions potential buyers should ask before making PCR purchases<ref name="KerkhofPCR18">{{cite web |url=https://www.labmanager.com/surveys/what-to-look-for-in-a-pcr-system-2154 |title=PCR Equipment Survey Results |author=Kerkhof, J. |work=Lab Manager |date=13 June 2018 |accessdate=14 August 2020}}</ref>:
-# Do your current and long-term needs require basic PCR systems, qPCR systems, or digital PCR systems?
-# What sample formats do you anticipate using?
-# What throughput requirements do you have now and anticipate in the near future?
-# What are you willing to sacrifice in regards to temperature ramp up and cool down times and accuracies?
-# Do you anticipate needing to run more than one independent PCR at the same time (multiblock PCR)?
-Given the considerable investment that goes into these and other life science instruments, you may want to seek vendors who have a strong track record of supporting and supplying parts for instruments they manufacture and distribute years after the instruments are introduced.<ref name="LMResults20">{{cite web |url=https://www.labmanager.com/surveys/results-from-the-lab-manager-life-science-technology-survey-22257 |title=Results from the Lab Manager Life Science Technology Survey |author=Lab Manager |work=Lab Manager |date=07 April 2020 |accessdate=14 August 2020}}</ref>
-As for PCR-based assays, the U.S. FDA has issued EUAs for more than 100 of them. The most up-to-date listing is of course found at the [https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas FDA website]. However, sorting through the extra details can be tedious. The Center for Systems Biology at Harvard has been maintaining a [https://csb.mgh.harvard.edu/covid contextual PDF chart] of the various COVID-19 diagnostic tests, which includes information such as run time, manufacturer-supplied data, and published clinical data (when available). This may prove useful in deciding on one or more particular tests. As with many aspects of this pandemic, other factors that may influence your choice of test kit include overall availability, cost, reagents included with the assay, and reagents separately required and their availability.
-Isothermal amplification techniques have the advantage of not requiring an expensive thermal cycler.<ref name="ThiAColor20" /> Instrument-appropriate reaction vessels, baths, heating units, turbidimeters, thermocyclers, etc. may be required, depending on what type of amplification you're doing. Companies like Meridian Bioscience offer LAMP-based molecular platforms, though they may not offer a specific COVID-19 assay to run on the platform.<ref name="MBAlethia">{{cite web |url=https://www.meridianbioscience.com/platform/molecular/alethia/ |title=Alethia |publisher=Meridian Bioscience |accessdate=14 August 2020}}</ref> As can be seen in Table 1, two isothermal amplification assays that run on their own proprietary instrument have received EUAs and are CLIA-waved, with a third potentially on the way. Using these systems and their COVID-19 assays at the point of care provides a somewhat more attractive option for laboratories wanting to add COVID-19 or even multiplex viral assays to their offerings.
-'''CLIA-waived testing'''
-If you're running a POL, or attempting to provide COVID-19 testing at the point of care, you'll be looking at the following assay and instrument options shown in Table 1:
-{|
- | STYLE="vertical-align:top;"|
-{| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="80%"
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;" colspan="7"|'''Table 1.''' CLIA-waived COVID-19-related ''in vitro'' diagnostic tests receiving U.S. FDA Emergency Use Authorizations (EUAs)
- |-
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Date EUA issued
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Manufacturer
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Name of test or assay
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Required instrument
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Technology (method)
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|RADx-funded?
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Additional comments
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|20 March 2020
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Cepheid
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.cepheid.com/coronavirus Xpert Xpress SARS-CoV-2 test]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.cepheid.com/en_US/systems/GeneXpert-Family-of-Systems/GeneXpert-Xpress GeneXpert Xpress System (Tablet and Hub Configurations)]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Molecular (RT-PCR)
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|No
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Has largely received positive review of sensitivity and specificity<ref name="MoranDetect20">{{cite journal |title=Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays |journal=Journal of Clinical Microbiology |author=Moran, A.; Beavis, K.G.; Matushek, S.M. et al. |volume=58 |issue=8 |at=e00772-20 |year=2020 |doi=10.1128/JCM.01072-20 |pmid=32303565 |pmc=PMC7383516}}</ref><ref name="LoeffelholzMulti20">{{cite journal |title=Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test |journal=Journal of Clinical Microbiology |author=Loeffelholz, M.J.; Alland, D.; Butler-Wu, S.M. et al. |volume=58 |issue=8 |at=e00926-20 |year=2020 |doi=10.1128/JCM.00926-20 |pmid=32366669 |pmc=PMC7383535}}</ref><ref name="GoldenbergerBrief20">{{cite journal |title=Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay |journal=Journal of Virological Methods |author=Goldenberger, D.; Leusinger, K.; Sogaard, K.K. et al. |volume=284 |at=113925 |year=2020 |doi=10.1016/j.jviromet.2020.113925 |pmid=32659240 |pmc=PMC7351036}}</ref>; company is reportedly working on a multiplex assay for SARS-CoV-2, Flu A, Flu B, and RSV<ref name="PRNCepheidAnn20">{{cite web |url=https://www.prnewswire.com/news-releases/cepheid-announces-development-of-four-in-one-combination-test-for-sars-cov-2-flu-a-flu-b-and-rsv-301072489.html |title=Cepheid Announces Development of Four-in-One Combination Test for SARS-CoV-2, Flu A, Flu B and RSV |author=Cepheid |work=PR Newswire |date=09 June 2020 |accessdate=13 August 2020}}</ref>
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|23 March 2020
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Mesa Biotech Inc.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.mesabiotech.com/coronavirus Accula SARS-CoV-2 test]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.mesabiotech.com/products Accula Dock] or [https://www.sekisuidiagnostics.com/product-category/point-of-care-testing/?wpv_view_count=5737&wpv_post_search=silaris Silaris Dock]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Molecular (RT-PCR)
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Yes
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Has received only minor scrutiny<ref name="HoganComp20">{{cite journal |title=Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens |journal=Journal of Clinical Microbiology |author=Hogan, C.A.; Garamani, N.; Lee, A.S. et al. |volume=58 |issue=8 |at=e01072-20 |year=2020 |doi=10.1128/JCM.01072-20 |pmid=32461285 |pmc=PMC7383558}}</ref>, with no formal FDA complaints<ref name="FDAMAUDE">{{cite web |url=https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfMAUDE/TextSearch.cfm |title=MAUDE - Manufacturer and User Facility Device Experience |publisher=U.S. Food and Drug Administration |accessdate=13 August 2020}}</ref>
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|27 March 2020
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Abbott Diagnostics Scarborough, Inc.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.globalpointofcare.abbott/en/product-details/id-now-covid-19.html ID NOW COVID-19]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.globalpointofcare.abbott/en/product-details/id-now.html ID NOW]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Molecular (isothermal amplification)
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|No
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Targets "a unique region of the RNA-dependent RNA polymerase (RdRP) gene"<ref name="RaviDiag20">{{cite journal |title=Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscape |journal=Biosensors and Bioelectronics |author=Ravi, N.; Cortade, D.L.; Ng, E. et al. |volume=165 |at=112454 |year=2020 |doi=10.1016/j.bios.2020.112454 |pmid=32729549 |pmc=PMC7368663}}</ref>; as of August 2020, the sensitivity of the test is still under scrutiny<ref name="DevineCorona20">{{cite web |url=https://www.cnn.com/2020/07/03/politics/coronavirus-white-house-test-abbott/index.html |title=Coronavirus test used by White House has questionable accuracy |author=Devine, C. |work=CNN Politics |date=03 July 2020 |accessdate=08 July 2020}}</ref><ref name="PerroneFDA20">{{cite web |url=https://apnews.com/c8ab010e8e02dfe7beb34a5e5df11279 |title=FDA probes accuracy issue with Abbott’s rapid virus test |author=Perrone, M. |work=Associated Press |date=14 May 2020 |accessdate=19 May 2020}}</ref><ref name="BasuPerform20">{{cite journal |title=Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution |journal=Journal of Clinical Microbiology |author=Basu, A.; Zinger, T.; Inglima, K. et al. |volume=58 |issue=8 |at=e01136-20 |year=2020 |doi=10.1128/JCM.01136-20 |pmid=32471894 |pmc=PMC7383552}}</ref><ref name="MitchellEval20">{{cite journal |title=Evaluation of the COVID19 ID NOW EUA assay |journal=Journal of Clinical Virology |author=Mitchell, S.L.; St. George, K. |volume=128 |at=104429 |year=2020 |doi=10.1016/j.jcv.2020.104429 |pmid=32425657 |pmc=PMC7227587}}</ref>
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|08 May 2020
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Quidel Corporation
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.quidel.com/immunoassays/rapid-sars-tests/sofia-sars-antigen-fia Sofia SARS Antigen FIA]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.quidel.com/immunoassays/sofia-tests-kits/sofia-2-analyzer Sofia 2]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Antigen
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Yes
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|With a comparatively lower specificity, best used as surveillance, repeat screening tool<ref name="ServiceRadical2020" /><ref name="GuglielmiTheExp20" />
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|10 June 2020
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Cue Health Inc.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.cuehealth.com/covid-19 Cue COVID-19 Test Cartridge]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.cuehealth.com/covid-19 Cue Health Monitoring System]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Molecular (isothermal amplification)
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|No
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|"Test primers amplify the nucleocapsid (N) region of the gene"<ref name="CueCOVID19Inst">{{cite web |url=https://www.cuehealth.com/s/IN9100003-1_10_IFU-Cue-COVID-19-Test-Cartridge-Pack-Professional.pdf |format=PDF |title=Cue COVID-19 Test Instructions for Use |publisher=Cue Health, Inc |date=June 2020 |accessdate=13 August 2020}}</ref>
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|02 July 2020
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Becton, Dickinson and Company
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.bd.com/en-us/offerings/capabilities/microbiology-solutions/point-of-care-testing/bd-veritor-plus-system-for-rapid-covid-19-sars-cov-2-testing BD Veritor System for Rapid Detection of SARS-CoV-2]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.bd.com/en-us/offerings/capabilities/microbiology-solutions/point-of-care-testing/veritor-plus-system BD Veritor Plus]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Antigen
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|No
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|With a comparatively lower specificity, best used as surveillance, repeat screening tool<ref name="ServiceRadical2020" /><ref name="GuglielmiTheExp20" />
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|N/A (Anticipated)
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Talis Biomedical
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://talis.bio/technology/ Talis One Cartridge]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://talis.bio/technology/ Talis One Instrument]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Molecular (RT-LAMP)
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Yes
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Expectations are that it will receive an FDA EUA and be CLIA-waived<ref name="TalisOne">{{cite web |url=https://talis.bio/technology/ |title=The Talis Advantage |publisher=Talis Biomedical |accessdate=13 August 2020}}</ref>, but yet to be determined.
- |-
-|}
-|}
-====3.2.3 Reagents====
-'''High- and moderate-complexity CLIA testing'''
-Reagent shortages since April have hampered efforts to expand testing in parts of the world, including the United States. As such, your reagent choices will likely be closely tied to both the assays you choose to implement and how reliably the supplier can get them to you. This in turn is likely driven by whether you're using a lab-developed test or a test kit. In some cases, e.g., the Xiamen Zeesan Biotech SARS-CoV-2 Test Kit (Real-time PCR), all but the Virus RNA Extraction Kit is included.<ref name="FDAXiamenSARS20">{{cite web |url=https://www.fda.gov/media/140717/download |format=PDF |title=SARS-CoV-2 Test Kit (Real-time PCR) Instructions for Use |publisher=Xiamen Zeesan Biotech |date=July 2020 |accessdate=14 August 2020}}</ref> On the other hand, Biomeme's SARS-CoV-2 Real-Time RT-PCR Test requires the separate acquisition of PCR buffer and external controls other than the exogenous RNA Process Control that comes with the kit.<ref name="FDABiomemeSARS20">{{cite web |url=https://www.fda.gov/media/141052/download |format=PDF |title=Biomeme SARS-CoV-2 Real-Time RT-PCR Test Instructions for Use |publisher=Biomeme, Inc |date=2020 |accessdate=14 August 2020}}</ref> Yale's SalivaDirect is a more flexible test, validated for use with multiple instruments and reagents that are not proprietary to Yale.<ref name="GallagherFDA20" /><ref name="ZillgittFDA20" /> Pay close attention to what comes with the assay, typically by reviewing the instructions for use (IFU; found on the FDA's EUA page).
-For PCR, the five basic reagents are template DNA, PCR primers, nucleotides, PCR buffer, and thermostable DNA polymerase. Some of these components can be acquired pre-mixed as a "master mix." For example, Thermo Fisher's PCR Master Mix contains a thermostable DNA polymerase called ''Taq'', nucleotides called deoxynucleotide triphosphates (dNTPs), and a buffer, which "saves time and reduces contamination due to a reduced number of pipetting steps."<ref name="TFSPCRMaster">{{cite web |url=https://www.thermofisher.com/order/catalog/product/K0171#/K0171 |title=PCR Master Mix (2X) |publisher=Thermo Fisher Scientific |accessdate=16 August 2020}}</ref>
-Reagent cost and usage for isothermal amplification methods such as LAMP are similar, though buffers and primers specific to the method are required.<ref name="DiegoProgress19" /><ref name="NEBLoop14" /><ref name="OGIsoth">{{cite web |url=http://www.optigene.co.uk/isothermal-reaction-guide/ |title=Isothermal Reaction Guide |publisher=OptiGene Limited |accessdate=16 August 2020}}</ref><ref name="KashirLoop20">{{cite journal |title=Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19 |journal=Medical Hypotheses |author=Kashir, J.; Yaqinuddin, A. |volume=141 |at=109786 |year=2020 |doi=10.1016/j.mehy.2020.109786 |pmid=32361529 |pmc=PMC7182526 |quote=Reagent-wise, the costs would be similar to that of real time RT-PCR ...}}</ref>
-'''CLIA-waived testing'''
-The FDA EUA devices (Table 1) all come with the necessary reagents, with the exception of any controls or references you may require. Refer to the IFU for the waived test kit to determine what additional consumables you'll require.
-====3.2.4 Consumables====
-'''High- and moderate-complexity CLIA testing'''
-Non-reagent consumables for high- and moderate-complexity CLIA testing include PCR tubes and plates; pipettes and tips; films, foils, and sealing mats; swabs; and viral transport media, among others. Some like Kellner ''et al.'' have experimented with methods to make isothermal amplifications methods more approachable in resource-poor environments by, for example, developing a pipette-free version of LAMP.<ref name="KellnerARapid20" />
-'''CLIA-waived testing'''
-The FDA EUA devices (Table 1) may require a few extra consumables. For example, the Accula SARS-CoV-2 test kit comes with swabs<ref name="MBAccula20">{{cite web |url=https://www.fda.gov/media/136355/download |format=PDF |title=Accula Test |publisher=Mesa Biotech, Inc |date=April 2020 |accessdate=16 August 2020}}</ref> and the Xpert Xpress SARS-CoV-2 kit comes with disposable transfer pipettes.<ref name="MBAccula20">{{cite web |url=https://www.fda.gov/media/136315/download |format=PDF |title=Xpert Xpress SARS-CoV-2 |publisher=Cepheid |date=March 2020 |accessdate=16 August 2020}}</ref> Refer to the IFU for the waived test kit to determine what additional consumables you'll require.
-====3.2.5 Software and services====
-A June 2020 report by Weemaes ''et al.'' in the ''Journal of the American Medical Informatics Association'' describes the bottlenecks they encountered in their test workflows at the Belgian National Reference Center, and how they updated their [[laboratory information system]] (LIS) with functionality to resolve those bottlenecks.<ref name="WeemaesLab20">{{cite journal |title=Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center |journal=JAMIA |author=Weemaes, M.; Martens, S.; Cuypers, L. et al. |at=ocaa081 |year=2020 |doi=10.1093/jamia/ocaa081 |pmid=32348469 |pmc=PMC7197526}}</ref> In addition to adding a COVID-19–specific order set into the [[computerized physician order entry]] (CPOE) module integrated with both their LIS and [[electronic health record]] (EHR), they included an up-to-date triage criteria component, a tool for optimizing sampling and packaging, a COVID-19 status button, and improved reporting modules for automating reference testing and epidemiological reporting. They also added extra database and data mining functionality to facilitate research and insights into epidemiologies and treatments. Their conclusion: "Rapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turnaround time of SARS-CoV-2 testing."<ref name="WeemaesLab20" /> The Association of Public Health Laboratories comes to a similar conclusion in regard to laboratory informatics solutions and public health laboratories' COVID-19 testing.<ref name="APHLLIMS20">{{cite web |url=https://www.aphl.org/aboutAPHL/publications/Documents/INFO-2020-LIMS.pdf |format=PDF |title=LIMS (Laboratory Information Management System) |author=Association of Public Health Laboratories |publisher= Association of Public Health Laboratories |date=2020 |accessdate=18 August 2020}}</ref>
-As such, adding COVID-19 and other respiratory illness testing to your workflow may necessitate an information management system, or an upgrade of your existing software systems. You may experience many of the same bottlenecks the Belgian National Reference Center experienced, especially if you're still working primarily with paper-based test ordering. Those researchers found that paper-based COVID-19 test requests often<ref name="WeemaesLab20" />:
-* omitted critical clinical status and contact information;
-* slowed down epidemiological and research studies;
-* hindered proper preanalytical biosafety procedures; and
-* impeded rapid response to evolving test criteria and clinical insights through test ordering protocols.
-How interoperable your laboratory software solution is with other systems such as EHRs is also worth consideration. The next chapter addresses system interoperability in greater detail, but it's worth mentioning it here in the context of adding software to improve testing workflows for SARS-CoV-2 and other respiratory viruses. Broadly speaking, improving interoperability among [[clinical informatics]] systems—whether at the point of care or within a specific laboratory—is recognized as an important step towards improving health outcomes.<ref name="KunImprov08">{{cite journal |title=Improving outcomes with interoperable EHRs and secure global health information infrastructure |journal=Studies in Health Technology and Informatics |author=Kun, L.; Coatrieux, G.; Quantin, C. et al. |volume=137 |pages=68–79 |year=2008 |pmid=18560070}}</ref><ref name="GCHIImproving">{{cite web |url=http://s3.amazonaws.com/rdcms-himss/files/production/public/Improving-Patient-Carethrough-Interoperability.pdf |format=PDF |title=Improving Patient Care through Interoperability |author=Global Center for Health Innovation |publisher=Global Center for Health Innovation |date=n.d. |accessdate=16 August 2020}}</ref> However, while developers of EHRs and other clinical informatics systems have intended to improve their software's interoperability, the COVID-19 pandemic has unfortunately shown the inadequacies still inherent in that software's overall design.<ref name="GlaserItsTime20">{{cite web |url=https://hbr.org/2020/06/its-time-for-a-new-kind-of-electronic-health-record |title=It’s Time for a New Kind of Electronic Health Record |author=Glaser, J. |work=Harvard Business Review |date=12 June 2020 |accessdate=18 August 2020}}</ref><ref name="LimoliPhys20">{{cite web |url=https://medcitynews.com/2020/07/physicians-deserve-better-software-covid-19-has-shown-why-medical-records-need-to-adapt/ |title=Physicians deserve better software: Covid-19 has shown why medical records need to adapt |author=Limoli, C.; Papathomas, G. |work=MedCity News |date=07 July 2020 |accessdate=18 August 2020}}</ref><ref name="JasonEHR20">{{cite web |url=https://ehrintelligence.com/news/ehr-optimization-health-it-projects-needed-after-covid-19-surge |title=EHR Optimization, Health IT Projects Needed After COVID-19 Surge |author=Jason, C. |work=EHR Intelligence |date=23 July 2020 |accessdate=18 August 2020}}</ref> As such, any research into acquiring a [[laboratory information management system]] (LIMS), LIS, or other clinical information management solution should take into account how well that solution is able to integrate with your other clinical systems, as well as any other third-party systems like physician or hospital EHRs. And it's not just the software solutions you'll want to consider. Will the new instruments you add to get you rolling with clinical respiratory illness testing integrate with your software?
-Finally, although rare, you may find you don't have the in-house expertise to fully implement a COVID-19 testing line to your laboratory. In such a case, you may need to turn to a laboratory services consultancy with experience in SARS-CoV-2 test method validation, instrument procurement and implementation, and legal matters. (See the next section for a representative example of consultants advertising COVID-19 testing knowledge and services for labs.)
-====3.2.6 Major vendors and consultants====
-Table 2 lists the major vendors developing and selling PCR, isothermal amplification, and NGS supplies, instruments, and software for both clinical diagnostics and life science research. "Research use only" equipment like Siemens Healthcare's Fast Track Cycler was ignored for completing the table. The vendor list was largely compiled from vendors identified in a handful of online market reports on PCR, with an added sprinkling of a few additional reagent vendors (e.g., Jena Bioscience, LGC, and New England BioLabs) who address isothermal amplification supplies in addition to PCR. Note that this is not an endorsement for any particular vendor.
-{|
- | STYLE="vertical-align:top;"|
-{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0" width="90%"
- |-
-  ! style="background-color:white; text-align:left; font-weight: normal; padding-left:10px; padding-right:10px;" colspan="13"|'''Table 2.''' Major players operating in the global diagnostic PCR, isothermal amplification, and NGS market
- |-
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Vendor
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Shop all products
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|PCR machines
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Nucleic acid extraction<br />and purification machines
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Immunoassay analyzers<br />and assays
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|PCR and qPCR assays
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|PCR and qPCR enzymes<br />and master mixes
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|DNA/RNA purification,<br />quantitation, and<br />amplification supplies
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|LAMP assays
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Isothermal amplification<br />enzymes and <br />master mixes
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|NGS supplies
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Supporting labware<br />and supplies
-  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Software
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Abbott
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.molecular.abbott/us/en/offerings/products Abbott products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Agilent Technologies
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.agilent.com/en-us/products Agilent products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Becton, Dickinson and Company
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.bd.com/en-us/offerings/capabilities BD products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Bio-Rad Laboratories, Inc.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.bio-rad.com/en-us/life-science-research/products Bio-Rad products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|bioMérieux SA
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.biomerieux-usa.com/az bioMérieux products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Danaher Corporation and its companies
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.cepheid.com/ Cepheid products],<br />[https://www.beckmancoulter.com/en/products Beckman Coulter products], and<br />[https://www.beckman.com/ Beckman Life Sciences products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|F. Hoffmann-La Roche AG
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.roche.com/products/diagnostics-portfolio.htm Roche Diagnostics products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Jena Bioscience GmbH
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.jenabioscience.com/ Jena Bioscience products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|LGC Limited and its companies
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.lucigen.com/products.html Lucigen products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Merck KGaA
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.sigmaaldrich.com/covid-19.html Sigma-Aldrich products] and<br />[https://www.emdmillipore.com/US/en/products/vMqb.qB.GdEAAAE_Mhd3.Lxj,nav Millipore Sigma products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|New England BioLabs, Inc.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.neb.com/products NEB products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Promega
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.promega.com/products/ Promega products] and [https://www.promega.com/products/catalog/ catalog]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|QIAGEN N.V.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.qiagen.com/us/products/ QIAGEN products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Siemens Healthcare GmbH
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.siemens-healthineers.com/products-services Siemens Healthcare products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|Thermo Fisher Scientific, Inc.
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.thermofisher.com/us/en/home/order.html Thermo Fisher products] and<br />[https://www.fishersci.com/us/en/browse/90217008/pcr-equipment-and-supplies Fisher Scientific products]
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
-  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
- |-
-|}
-|}
-Table 2's "Software" column represents whether or not the vendor offers laboratory informatics software such as a LIMS or LIS. Those vendors' solutions may or may not be tailored to handle the specific requirements of a clinical diagnostic or virology lab handling COVID-19 and other viruses. (See the next chapter for more in-depth information about working an informatics solution into COVID-19 and other viral testing workflow.) A non-endorsed, representative example of vendors who do include:
-* [[AgileBio]] - [https://www.labcollector.com/lp-covid19-pack/ COVID-19 LC]
-* [[BioSoft Integrators, LLC]] - [https://biosoftintegrators.com/covid-19/ LabOptimize LIMS for COVID-19]
-* [[CloudLIMS.com, LLC]] - [https://cloudlims.com/industries/covid-19-lims-software.html CloudLIMS for COVID-19]
-* [[Common Cents Systems, Inc.]] - [https://resources.apollolims.com/blog/covid-19-testing-and-the-important-role-of-a-lims Apollo LIMS for COVID-19]
-* [[Comp Pro Med, Inc.]] - [https://www.comppromed.com/covid-19-rapid-deployment-lis/ COVID-19 Rapid Deployment LIS]
-* [[Illumina, Inc.]] - [https://blog.software.illumina.com/2020/04/14/efficient-accurate-lab-management-for-covid-19-research/ BaseSpace Clarity LIMS for COVID-19]
-* [[LabLynx, Inc.]] - [https://www.covidlims.com/ COVIDLiMS]
-* [[LabVantage Solutions, Inc.]] - [https://www.labvantage.com/your-lab-type/labvantage-covid-19-lims/ LabVantage COVID-19 LIMS]
-* [[Physion, LLC]] - [https://www.ovation.io/covid-19-testing/ Ovation LIMS for COVID-19]
-* [[Sunquest Information Systems, Inc.]] - [https://www.sunquestinfo.com/docs/sunquest-covid19-mitogen-lims-product-focus.pdf Mitogen LIMS for COVID-19] (PDF)
-Additionally, when in-house knowledge is lacking, a consultant may be required. These consultants are meant to be representative examples of those laboratory consulting firms indicating they have the knowledge to help a laboratory with COVID-19-related testing and other issues. This list is not an endorsement for any particular consultant:
-* [https://www.aruplab.com/consulting ARUP Laboratories] (Utah)
-* [https://www.colaborate.com/covid-19-lab-consulting/ Colaborate] (Florida)
-* [https://elitediagnostics.com/verticals/infectious-disease/ Elite Diagnostics] (North Carolina)
-* [https://www.freedassociates.com/service/covid-19-response/ Freed Associates] (California)
-* [https://www.lighthouselabservices.com/infectious-disease/ Lighthouse Lab Services] (North Carolina)
-* [https://www.optimumhit.com/services/covid-19-support/ Optimum Healthcare IT] (Florida)
-* [https://www.triumvirate.com/coronavirus Triumverate Environmental] (Massachusetts)
-===3.3 What other considerations should be made?===
-====3.3.1 U.S. regulatory compliance====
-In the previous chapter, the regulatory hurdles of the [[Health Insurance Portability and Accountability Act]] (HIPAA) and the [[Clinical Laboratory Improvement Amendments]] (CLIA) were addressed. For those laboratories that are already operating in the clinical laboratory sphere, it should be relatively simple to address the additional considerations and pandemic-specific changes to those two regulations as described previously. In addition to that information, you can always periodically check the U.S. Department of Health & Human Services' (HHS') [https://www.hhs.gov/hipaa/for-professionals/special-topics/hipaa-covid19/index.html Office for Civil Rights] and their COVID-19 announcements and guidance, as well as the Centers for Medicare & Medicaid Services (CMS) [https://www.cms.gov/About-CMS/Agency-Information/Emergency/EPRO/Current-Emergencies/Current-Emergencies-page emergencies page].
-If for some reason you're not a clinical lab—or want to start a new lab—and want to take on COVID-19 and other clinical testing, you're going to need to get fast tracked into the CLIA program, for starters. Fortunately, CMS has already displayed a willingness to help labs wanting to perform COVID-19 testing receive their CLIA certificate rapidly. [https://www.cms.gov/Medicare/CMS-Forms/CMS-Forms/Downloads/CMS116.pdf Form CMS-116] will need to be completed and submitted to your [https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/Downloads/CLIASA.pdf state survey agency contact]. Of course, while you're waiting, you'll also want to become familiar with the trappings of CLIA by tapping into resources like the [https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/index?redirect=/CLIA/05_CLIA_Brochures.asp CMS page for CLIA], [https://www.cdc.gov/clia/quick-tips.html CDC page for CLIA], and resources available from professional organizations like the [https://www.aafp.org/family-physician/practice-and-career/managing-your-practice/clia.html American Academy of Family Physicians]. If all goes as plan, and directions are followed, you should have your CLIA certificate in no time. CMS adds<ref name="CMSFAQ">{{cite web |url=https://www.cms.gov/files/document/clia-laboratory-covid-19-emergency-frequently-asked-questions.pdf |format=PDF |title=Frequently Asked Questions (FAQs), CLIA Guidance During the COVID-19 Emergency |author=Centers for Medicare and Medicaid Services |accessdate=20 August 2020}}</ref>:
-<blockquote>We want to ensure that laboratories located in the United States applying for a CLIA certificate are able to begin testing for COVID-19 as quickly as possible. Once the laboratory has identified a qualified laboratory director and has provided all required information on the CMS-116 application, a CLIA number will be assigned. Once the CLIA number has been assigned, the laboratory can begin testing as long as applicable CLIA requirements have been met (e.g., establishing performance specifications).</blockquote>
-On the HIPAA side of things, you'll want to tap into resources such as the HHS' [https://www.hhs.gov/hipaa/for-professionals/training/index.html HIPAA training materials and resources], as well as their previously mentioned COVID-19 announcements and guidance.
-Other considerations include<ref name="PaulAGuide20">{{cite web |url=https://www.clinicallabmanager.com/insight/a-guide-to-setting-up-a-coronavirus-covid-19-clinical-diagnostic-testing-laboratory-22850 |title=A Guide to Setting up a Coronavirus (COVID-19) Clinical Diagnostic Testing Laboratory |author=Paul, S. |work=Clinical Lab Manager |date=29 May 2020 |accessdate=20 August 2020}}</ref><ref name="BuchanInterim19">{{cite web |url=https://asm.org/ASM/media/Policy-and-Advocacy/Biosafety-white-paper-2019.pdf |format=PDF |title=Interim Clinical Laboratory Guideline for Biological Safety |author=Buchan, B.W.; Mahlen, S.D.; Relich, R.F. |publisher=The American Society for Microbiology |date=January 2019 |accessdate=20 August 2020}}</ref><ref name="CDCFrequently20">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/faqs.html |title=Frequently Asked Questions about Coronavirus (COVID-19) for Laboratories |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=15 August 2020 |accessdate=20 August 2020}}</ref><ref name="OSHACOVID20">{{cite web |url=https://www.osha.gov/SLTC/covid-19/laboratory.html |title=COVID-19 - Control and Prevention /Laboratory Workers and Employers |publisher=Occupational Safety and Health Administration |accessdate=20 August 2020}}</ref>:
-* taking the time to get accredited to ISO 15189:2012 Medical laboratories — Requirements for quality and competence, "used by medical laboratories in developing their quality management systems and assessing their own competence"<ref name="ISO15189">{{cite web |url=https://www.iso.org/standard/56115.html |title=ISO 15189:2012 Medical laboratories — Requirements for quality and competence |publisher=International Organization for Standardization |date=August 2014 |accessdate=20 August 2020}}</ref>;
-* understanding and training on packaging (e.g., UN3373 Biological Substance, Category B) and shipping COVID-19 specimens (e.g., International Air Transport Association (IATA) Dangerous Goods Regulations), if you will be conducting such activities;
-* understanding the significance of and validating workflow procedures to at least Biosafety Level 2 (note there is no single U.S. government entity which has total responsibility for enforcing biosafety levels<ref name="NASNRCBiosec12">{{cite book |url=https://www.ncbi.nlm.nih.gov/books/NBK196149/ |chapter=Appendix E - Country and Region Overviews |title=Biosecurity Challenges of the Global Expansion of High-Containment Biological Laboratories: Summary of a Workshop |author=National Academy of Sciences and National Research Council |publisher=National Academies Press |pages=193–204 |year=2012 |isbn=9780309225786 |doi=10.17226/13315}}</ref>); and
-* understanding and training on Occupational Safety and Health Administration (OSHA) requirements for laboratory workers and employers for COVID-19.
-====3.3.2 Reporting====
-The topic of reporting COVID-19 results to local and regional health departments—as well as any internal medical reporting—is covered in detail in the next chapter. You'll want to be sure you and your team understand your state's health department reporting requirements, as well as what code sets ([[LOINC]], [[SNOMED CT|SNOMED]], [[International Statistical Classification of Diseases and Related Health Problems|ICD]], and [[Current Procedural Terminology|CPT]]) to use. The success of epidemiologists' response to outbreaks and pandemics depends on quality data reporting, and using the correct code sets helps labs meet reporting requirements, as well as ensure proper payment. The U.S. Centers for Disease Control and Prevention provides guidance on how to [https://www.cdc.gov/coronavirus/2019-ncov/lab/reporting-lab-data.html report COVID-19 laboratory data], which also makes for necessary reading.
-====3.3.3 Billing, Medicare, and Medicaid====
-The COVID-19 pandemic has unquestionably put the U.S. health care system in a tough spot. That health care system, with all its warts<ref name="PreskittHealth08">{{cite journal |title=Health care reimbursement: Clemens to Clinton |journal=Baylor University Medical Center Proceedings |author=Preskitt, J.T. |volume=21 |issue=1 |pages=40–4 |year=2008 |doi=10.1080/08998280.2008.11928358 |pmid=18209755 |pmc=PMC2190551}}</ref><ref name="FiferHealth16">{{cite web |url=https://www.asha.org/Articles/Health-Care-Economics-The-Real-Source-of-Reimbursement-Problems/ |title=Health Care Economics: The Real Source of Reimbursement Problems |author=Fifer, R. |publisher=American Speech-Language-Hearing Association |date=July 2016 |accessdate=21 August 2020}}</ref><ref name="HuckmanWhat20">{{cite web |url=https://hbr.org/2020/04/what-will-u-s-health-care-look-like-after-the-pandemic |title=What Will U.S. Health Care Look Like After the Pandemic? |author=Huckman, R.S. |work=Harvard Business Review |date=07 April 2020 |accessdate=21 August 2020}}</ref>, has arguably not done well to handle so many unanticipated health issues from a broad portion of the population.<ref name="HuckmanWhat20" /><ref name="DorsettPoint20">{{cite journal |title=Point of no return: COVID-19 and the U.S. healthcare system: An emergency physician’s perspective |journal=Science Advances |author=Dorsett, M. |volume=6 |issue=26 |at=eabc5354 |year=2020 |doi=10.1126/sciadv.abc5354 |pmid=32637627 |pmc=PMC7319747}}</ref><ref name="SlotkinHow20">{{cite web |url=https://hbr.org/2020/06/how-one-health-system-is-transforming-in-response-to-covid-19 |title=How One Health System Is Transforming in Response to Covid-19 |author=Slotkin, J.R.; Murphy, K.; Ryu, J. |work=Harvard Business Review |date=11 June 2020 |accessdate=21 August 2020}}</ref><ref name="MendelsonProvid20">{{cite web |url=https://www.forbes.com/sites/danielmendelson/2020/06/30/the-impact-of-covid-19-on-providers-risk-recession-and-reimbursement/ |title=The Impact Of COVID-19 On Providers: Risk, Recession And Reimbursement |author=Mendelson, D. |work=Forbes |date=30 June 2020 |accessdate=21 August 2020}}</ref> From a provider side, proper reimbursement for COVID-19 testing is among the many issues that must be addressed. One key aspect of ensuring proper reimbursement in a reasonable time frame is first making sure a clear preregistration process that captures critical patient and facility information is conducted. (This can be facilitated and made easier as a first-step process in a clinical informatics solution, for example.) Critical patient and facility information includes (but is not limited to):
-* name, date of birth, and gender
-* race and ethnicity
-* demographic information such as full address and phone number
-* ordering physician or attending health care provider for test (if applicable)
-* facility's National Provider Identifier (NPI)
-* patient insurance company name, policy ID, group ID, insured's name, and insured relationship to patient (if insured)
-* whether or not it's the patient's first test (federal reporting requirement)
-* whether or not the patient is a resident of a congregate care setting (federal reporting requirement; also, e.g., additional Medicaid reimbursement may be available in some states<ref name="FlinnStates20">{{cite web |url=https://www.leadingage.org/regulation/states-leverage-medicaid-provide-nursing-homes-lifeline-through-covid-19 |title=States Leverage Medicaid to Provide Nursing Homes a Lifeline through COVID-19 |author=Flinn, B. |work=LeadingAge |date=12 June 2020 |accessdate=21 August 2020}}</ref>)
-* whether or not the patient is a healthcare worker (federal reporting requirement; also, e.g., may affect the patient's worker's compensation claim<ref name="DOLClaimsUnder20">{{cite web |url=https://www.dol.gov/owcp/dfec/InfoFECACoverageCoronavirus.htm |title=Claims under the Federal Employees' Compensation Act due to the 2019 Novel Coronavirus (COVID-19) |author=Division of Federal Employees' Compensation |publisher=U.S. Department of Labor |date=2020 |accessdate=21 August 2020}}</ref><ref name="MichiganWorkers20">{{cite web |url=https://www.michigan.gov/ag/0,4534,7-359-98784_98791-523085--,00.html |title=Worker's Compensation for First Responders |author=Department of Attorney General |publisher=State of Michigan |date=2020 |accessdate=21 August 2020}}</ref>)
-* whether or not the patient is pregnant (federal reporting requirement; also, e.g., Medicare will ''only'' accept a COVID-19 code as secondary if the primary diagnosis code is viral disease complicating pregnancy, childbirth, or puerperium<ref name="HSRACOVID20">{{cite web |url=https://www.hrsa.gov/CovidUninsuredClaim |title=COVID-19 Claims Reimbursement to Health Care Providers and Facilities for Testing and Treatment of the Uninsured |publisher=Health Resources & Services Administration |date=May 2020 |accessdate=21 August 2020}}</ref><ref name="ACEPCoding20">{{cite web |url=https://www.acep.org/administration/reimbursement/covid-19/ |title=Coding Guidance for COVID-19 |publisher=American College of Emergency Physicians |date=2020 |accessdate=21 August 2020}}</ref>)
-Secondarily, it's also important to have a plan in place for testing the uninsured. While the Families First and Coronavirus Relief Act (FFCRA) and the National Disaster Management System (NDMS) provide legal mechanisms for reimbursement for what should otherwise be free patient testing for SARS-CoV-2 and the associated visit, ambiguities of these mechanisms and how they are enforced are still creating problems.<ref name="AdlerTheLaws20">{{cite web |url=https://www.brookings.edu/blog/usc-brookings-schaeffer-on-health-policy/2020/07/13/the-laws-governing-covid-19-test-payment-and-how-to-improve-them/ |title=The laws governing COVID-19 test payment and how to improve them |author=Adler, L.; Young, C.L. |work=USC-Brookings Schaeffer Initiative for Health Policy |publisher=Brookings Institution |date=13 July 2020 |accessdate=21 August 2020}}</ref> For example, while providers can turn to the NDMS (until funds run out) to pay uninsured claims at 110% of Medicare rates—with states' opting to cover those costs through their Medicaid program—providers are not obligated by the law to seek reimbursement from those entities and can optionally bill the uninsured patient directly, which is against the spirit of the FFCRA.<ref name="AdlerTheLaws20" /><ref name="DawsonTheNat20">{{cite web |url=https://www.kff.org/coronavirus-covid-19/issue-brief/the-national-disaster-medical-system-ndms-and-the-covid-19-pandemic/ |title=The National Disaster Medical System (NDMS) and the COVID-19 Pandemic |author=Dawson, L. |work=KFF |date=22 April 2020 |accessdate=21 August 2020}}</ref><ref name="CRSHealth20">{{cite web |url=https://crsreports.congress.gov/product/pdf/R/R46316 |title=Health Care Provisions in the Families First Coronavirus Response Act, P.L. 116-127 |author=Congressional Research Service |date=17 April 2020 |accessdate=21 August 2020}}</ref> As such, it's important to know what your lab's policy will be on managing uninsured patient claims. How will you get reimbursed if you're accepting uninsured patients? Resources that may help with these decisions include the [https://www.phe.gov/Preparedness/responders/ndms/definitive-care/Pages/default.aspx NDMS Definitive Care Reimbursement Program portal] and the Health Resources & Services Administration's [https://www.hrsa.gov/CovidUninsuredClaim information page] and [https://www.hrsa.gov/coviduninsuredclaim/frequently-asked-questions associated FAQ].
-For Medicare, Medicaid, and otherwise insured patients, the lab will likely have (or presumably acquire) someone on hand with billing experience. The preregistration information previously mentioned will still be important to implement. For further guidance on billing issues, you may wish to consult with CMS' [https://www.cms.gov/files/document/03092020-covid-19-faqs-508.pdf extensive document] titled ''COVID-19 Frequently Asked Questions (FAQs) on Medicare Fee-for-Service (FFS) Billing''. Also, the next chapter addresses code sets for reporting and billing, which may prove useful.
-==References==
-{{Reflist|colwidth=30em}}

Difference between revisions of "User:Shawndouglas/sandbox/sublevel36"

Latest revision as of 13:14, 6 September 2021

Navigation menu

Search