Difference between revisions of "User:Shawndouglas/sandbox/sublevel36"
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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> | 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''' | '''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. | |||
====3.2.4 Consumables==== | ====3.2.4 Consumables==== | ||
'''High and moderate CLIA testing''' | '''High and moderate 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''' | '''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 withs 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 consumbales you'll require. | |||
https://www. | |||
====3.2.5 Software and services==== | ====3.2.5 Software and services==== | ||
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> | |||
====3.2.6 Major vendors==== | ====3.2.6 Major vendors==== | ||
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https://www.fishersci.com/us/en/browse/90217014/thermal-cyclers | https://www.fishersci.com/us/en/browse/90217014/thermal-cyclers | ||
https://www.biocompare.com/PCR-Real-Time-PCR/6482-PCR-Equipment/ | https://www.biocompare.com/PCR-Real-Time-PCR/6482-PCR-Equipment/ | ||
https://www.biocompare.com/PCR-Real-Time-PCR/6731-PCR-Consumables/ | |||
https://www.sigmaaldrich.com/labware/labware-products.html?TablePage=9577275 | |||
===3.3 What other considerations should be made?=== | ===3.3 What other considerations should be made?=== |
Revision as of 18:53, 16 August 2020
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.[1] 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.[2][3][4] 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).[3][5]
A theory increasingly gaining traction, however, is that "[a] higher frequency of testing makes up for poor sensitivity.”[3][4][6] Several researchers have shared pre-print and published research suggesting this outcome[3]:
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.
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.[3][7] To be clear, it's not a perfect solution, but as Harvard epidemioligist 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."[7] 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.[6][8] 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[6]) and 2. the question of whether or not the two companies can produce enough test kits for repeat testing in those states.[3]
3. Adding COVID-19 and other virus testing to your laboratory
Does using one method make the most sense, or will your lab turn to multiple methods for virus testing?
What type of lab are you running? A physician office laboratory (POL) is going to have fewer options available than a CLIA moderate- or high-complexity lab.
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 coronaviruses were discussed in detail. The prevailing method (often called the "gold standard") among them all was 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 ifrastructure 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."[9] 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 requirments 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."[10] Various efforts have been made over the years to bring costs down by modifying how heating and temperature control are performed[11][12][13][14], 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.[15][16][17][18][19][20][21][8][7] 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 investent 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. propose direct heating of the sample-containing nasopharyngeal swab at 70 °C for 10 minutes in place of RNA extraction.[22] 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."[23][24] Wee et al. skip RNA extraction and nucleic acid purification by using a single-tube homogeneous reaction method run on a lightweight, portable thermocycler.[25][26] Other innovations include tweaking reagents and enzymes to work with one step, skipping the reverse transcription step,[27] and using saliva-based molecular testing that skips RNA extraction.[28][29]
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[30][31], and the first saliva-based COVID-19 test, produced by Spectrum Solutions in cooperation with RUCDR Infinite Biologics Laboratory[32] and Vault Health[33], 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.[34][35] 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.[29] While sensitivity and specificity may be slightly less comparable to other PCR options[36], 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."[37] 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.[37][38][39]
The downside of pooled testing comes with the issues of dillution, 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.[37][38][39]Finally, at least in the U.S., an Food and Drug Administration (FDA) emergency use authorization (EUA) for a validated pooled testing method is required.[37] (Validation of pooled methods may differ in other countries.[38]) The U.S. Centers for Disease Control and Prevention (CDC) has published 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.[3][5] 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 great. However, as of August 2020, only two vendors have EUAs for antigen diagnostic tests: Quidel Corporation and Becton, Dickinson and Company.[40] With six U.S. states already contracted to purchase hundreds of thousands of the two companies' test kits[6][8], 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 amplification technique that allows for RNA amplification, was also quietly being discussed[41][42], and it has since gained more attention.[43][44][45][46][47][48] 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."[48] 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."[46] And California-based Color Genomics have set up their own proprietary RT-LAMP system, capable of handling up to 10,000 tests per day.[49]
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[49][5][50], 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 test.[47] Esbin et al. add[47]:
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 [recombinase polymerase amplification] 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.
CRISPR methods are also being used in conjunction with RT-LAMP.[5][47][51] 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[5][52], the technology has some promise as an alternative testing method. It has the additional advantage of being readily couples with lateral flow assay technology to be deployed in the point-of-care (POC) setting.[47][52]
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.[53] Addressing POC testing, the WHO recommends that such assays[53][54]:
- 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.[54][55][55][56][57] 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."[58] 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.[59] 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[40], 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[47][57][60]:
- a method of DNA nanoswitch detection of virus particles;
- a dual biomarker-based fingerstick 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 addtional use of an artificial intelligence (AI) application to better scrutenize 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 thinking that have some kind of chance at playing a greater role in the clinical laboratory or 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 into 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.[61][62][63][64][65][66][67] 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.[61][62][64][66]
Where possible, separate rooms for sample preparation, PCR setup, and post-PCR activities, each with their own airflow control, are encouraged.[61][62][65][66][67] 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.[61][63][67] Of course, always maintaining unidirectional workflow—regardless of number of rooms—is also criticial to minimizing contamination. For example, technicians shouldn't be transporting amplified materials into the DNA extraction area.
Although dated, Roche Diagnostics' 2006 PCR Applications Manual[62] provides a detailed breakdown of setting up the laboratory for PCR. Das et al.[66] and Dr. Jennifer Redig[64] provide additional valuable insight. The World Health Organization (WHO) also provides guidance for setting up molecular testing in the lab.[67]
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[68], as does opening the reaction chamber after reaction is completed.[69] 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."[70][71] Even more cutting-edge techniques to reduce contamination such as the CUT-LAMP technique of Bao et al.[72] or the dUTP/UDG system for COVID-19 RT-LAMP reactions of Kellner et al.[45] 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.[73][74]
3.2.2 Instruments and assays
High and moderate CLIA testing
Thermal cyclers are the standard instruments for PCR testing. Today, real-time or quantitative (qPCR) systems largely fill this niche. However, digital and droplet digital PCR systems are emerging, and they have the benefit of producing even more rapid, precise, sensitive, accurate, and reproducable 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[75]:
- 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.[76]
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 FDA website. However, sorting through the extra details can be tedious. The Center for Systems Biology at Harvard has been maintaining a 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.[46] 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.[77] 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 an 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:
|
3.2.3 Reagents
High and moderate 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. 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.[91] 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.[92] Yale's SalivaDirect is a more flexible test, validated for use with multiple instruments and reagents that are not proprietary to Yale.[34][35] Pay close attention to what comes with the assay, typically by reviewing the instructions for use (IFU; found on the FDA site).
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."[93]
Reagent cost and usage for isothermal amplification methods such as LAMP are similar, though buffers and primers specific to the method are required.[68][73][94][95]
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.
3.2.4 Consumables
High and moderate 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.[45]
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 withs swabs[96] and the Xpert Xpress SARS-CoV-2 kit comes with disposable transfer pipettes.[96] Refer to the IFU for the waived test kit to determine what additional consumbales you'll require.
3.2.5 Software and services
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.[97][98]
3.2.6 Major vendors
Major players operating in the global PCR market are Bio-Rad Laboratories, Inc., QIAGEN N.V., F. Hoffmann-La Roche AG, Thermo Fisher Scientific, Inc. Becton, Dickinson and Company, Abbott, Siemens Healthcare GmbH (Siemens AG), bioMérieux SA, Danaher Corporation, and Agilent Technologies. Merck KGaA, Promega
https://www.thermofisher.com/search/browse/category/us/en/602552/PCR+Machines+%28Thermal+Cyclers%29+%26+Accessories https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis.html https://blog.biomeme.com/how-do-you-test-for-covid-19 https://www.fishersci.com/us/en/browse/90217014/thermal-cyclers https://www.biocompare.com/PCR-Real-Time-PCR/6482-PCR-Equipment/ https://www.biocompare.com/PCR-Real-Time-PCR/6731-PCR-Consumables/ https://www.sigmaaldrich.com/labware/labware-products.html?TablePage=9577275
3.3 What other considerations should be made?
3.3.1 Regulatory compliance
3.3.2 Reporting
3.3.3 Billing, Medicare, and Medicaid
References
- ↑ "Antigen". MedlinePlus. U.S. National Library of Medicine. https://medlineplus.gov/ency/article/002224.htm. Retrieved 07 August 2020.
- ↑ Anderson, K. (6 August 2020). "5 Investigates: Concerns about current use of rapid antigen tests for COVID-19". WCVB 5 ABC. https://www.wcvb.com/article/5-investigates-concerns-about-current-use-of-rapid-antigen-tests-for-covid-19/33538332. Retrieved 07 August 2020.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 Service, R.F. (2020). "Radical shift in COVID-19 testing needed to reopen schools and businesses, researchers say". Science. doi:10.1126/science.abe1546.
- ↑ 4.0 4.1 Kremer, R. (7 August 2020). "UW System Orders 350,000 COVID-19 Tests". Urban Milwaukee. https://urbanmilwaukee.com/2020/08/07/uw-system-orders-350000-covid-19-tests/. Retrieved 07 August 2020.
- ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 Guglielmi, G. (2020). "The explosion of new coronavirus tests that could help to end the pandemic". Nature 583: 506–09. doi:10.1038/d41586-020-02140-8.
- ↑ 6.0 6.1 6.2 6.3 Clark, C. (6 August 2020). "COVID Antigen Tests: Coming to Case Counts Near You?". MedPage Today. https://www.medpagetoday.com/infectiousdisease/covid19/87930. Retrieved 07 August 2020.
- ↑ 7.0 7.1 7.2 Courage, K.H. (31 July 2020). "Should we be testing fewer people to stop the spread of Covid-19?". Vox. https://www.vox.com/2020/7/31/21336212/covid-19-test-results-delays. Retrieved 05 August 2020.
- ↑ 8.0 8.1 8.2 Mervosh, S.; Fernandez, M. (4 August 2020). "‘It’s Like Having No Testing’: Coronavirus Test Results Are Still Delayed". The New York Times. https://www.nytimes.com/2020/08/04/us/virus-testing-delays.html. Retrieved 05 August 2020.
- ↑ Kenneth Research (23 June 2020). "Polymerase Chain Reaction Market Sector Analysis Report, Regional Outlook & Competitive Share & Forecast - 2023". MarketWatch. https://www.marketwatch.com/press-release/polymerase-chain-reaction-market-sector-analysis-report-regional-outlook-competitive-share-forecast---2023-2020-06-23. Retrieved 06 August 2020.
- ↑ Dove, A. (2018). "PCR: Thirty-five years and counting". Science 360 (6389): 670–672. doi:10.1126/science.360.6389.673-c.
- ↑ Wong, G.; Wong, I. Chan, K. et al. (2015). "A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings". PLoS One 10 (7): e0131701. doi:10.1371/journal.pone.0131701.
- ↑ Kuznetsov, S.; Doonan, C.; Wilson, N. et al. (2015). "DIYbio Things: Open Source Biology Tools as Platforms for Hybrid Knowledge Production and Scientific Participation". Proceedings of the 33rd Annual ACM Conference on Human Factors in Computing Systems: 4065–68. doi:10.1145/2702123.2702235.
- ↑ Norton, D. (11 May 2016). "Phila. med tech startup working on multimillion dollar government contract". Philadelphia Business Journal. https://www.bizjournals.com/philadelphia/news/2016/05/11/government-contract-biomeme-hiring-med-tech.html. Retrieved 06 August 2020.
- ↑ An, J.; Jiang, Y.; Shi, B. et al. (2020). "Low-Cost Battery-Powered and User-Friendly Real-Time Quantitative PCR System for the Detection of Multigene". Micromachines 11: 435. doi:10.3390/mi11040435.
- ↑ Herper, M.; Branswell, H. (10 March 2020). "Shortage of crucial chemicals creates new obstacle to U.S. coronavirus testing". STAT. https://www.statnews.com/2020/03/10/shortage-crucial-chemicals-us-coronavirus-testing/. Retrieved 10 April 2020.
- ↑ Hale, C. (18 March 2020). "Qiagen aims to more than quadruple its COVID-19 reagent production in 6 weeks". Fierce Biotech. https://www.fiercebiotech.com/medtech/qiagen-aims-to-more-than-quadruple-its-covid-19-reagent-production-6-weeks. Retrieved 10 April 2020.
- ↑ Mehta, A. (3 April 2020). "Mystery surrounds UK claim of Covid-19 test reagent ‘shortage’". Chemistry World. https://www.chemistryworld.com/mystery-surrounds-uk-claim-of-covid-19-test-reagent-shortage/4011457.article. Retrieved 10 April 2020.
- ↑ Roche, B. (8 April 2020). "Irish scientists develop reagent in effort to ease Covid-19 testing delays". The Irish Times. https://www.irishtimes.com/news/science/irish-scientists-develop-reagent-in-effort-to-ease-covid-19-testing-delays-1.4223897. Retrieved 10 April 2020.
- ↑ Padma, T.V. (13 May 2020). "Efforts to combat Covid-19 in India hit by imported reagent shortages". Chemistry World. https://www.chemistryworld.com/news/efforts-to-combat-covid-19-in-india-hit-by-imported-reagent-shortages/4011718.article#/. Retrieved 19 May 2020.
- ↑ David, E.; Farber, S.E. (20 June 2020). "Survey shows resources for COVID-19 diagnostic testing still limited months later". ABC News. https://abcnews.go.com/Health/survey-shows-resources-covid-19-diagnostic-testing-limited/story?id=71341885. Retrieved 08 July 2020.
- ↑ Johnson, K. (2 July 2020). "NC Labs Facing Shortages In COVID-19 Testing Chemicals". Patch. https://patch.com/north-carolina/charlotte/nc-labs-facing-shortages-covid-19-testing-chemicals. Retrieved 08 July 2020.
- ↑ Alcoba-Florez, J.; González-Montelongo, R.; Íñigo-Campos, A.; García-Martínezde Artola, D.; Gil-Campesino, H.;
The Microbiology Technical Support Team; Ciuffreda, L.; Valenzuela-Fernández, A.; Flores, C. (2020). "Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples". International Journal of Infectious Diseases 97: 66–68. doi:10.1016/j.ijid.2020.05.099. - ↑ Shapiro, M. (29 July 2020). "Streamlined diagnostic approach to COVID-19 can avoid potential testing logjam". Research News @ Vanderbilt. https://news.vanderbilt.edu/2020/07/29/streamlined-diagnostic-approach-to-covid-19-can-avoid-potential-testing-logjam/. Retrieved 06 August 2020.
- ↑ Adams, N.M.; Leelawong, M.; Benton, A. et al. (2020). "COVID‐19 diagnostics for resource‐limited settings: Evaluation of “unextracted” qRT‐PCR". Journal of Medical Virology. doi:10.1002/jmv.26328.
- ↑ Mehar, P. (27 July 2020). "Improving the speed of gold-standard COVID-19 diagnostic test". Tech Explorist. https://www.techexplorist.com/improving-speed-gold-standard-covid-19-diagnostic-test/34069/. Retrieved 06 August 2020.
- ↑ Wee, S.K.; Sivalingam, S.P.; Yap, E.P.H. (2020). "Rapid Direct Nucleic Acid Amplification Test without RNA Extraction for SARS-CoV-2 Using a Portable PCR Thermocycler". Genes 11 (6): 664. doi:10.3390/genes11060664.
- ↑ Council for Scientific and Industrial Research (30 July 2020). "Faster, local COVID-19 test kits could be ready by year-end". Engineering News. Creamer Media. https://www.engineeringnews.co.za/article/faster-local-covid-19-test-kits-could-be-ready-by-year-end-2020-07-30/. Retrieved 07 August 2020.
- ↑ Ranoa, D.R.E.; Holland, R.L.; Alnaji, F.G. et al. (2020). "Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction". bioRxiv. doi:10.1101/2020.06.18.159434.
- ↑ 29.0 29.1 Thomas, L. (6 August 2020). "Fast, cheap and easy COVID-19 test from Yale". News Medical - Life Sciences. https://www.news-medical.net/news/20200806/Fast-cheap-and-easy-COVID-19-test-from-Yale.aspx. Retrieved 16 August 2020.
- ↑ Xu, R.; Cui, B.; Duan, X. et al. (2020). "Saliva: Potential diagnostic value and transmission of 2019-nCoV". International Journal of Oral Science 12: 11. doi:10.1038/s41368-020-0080-z.
- ↑ Greenwood, M. (24 April 2020). "Saliva samples preferable to deep nasal swabs for testing COVID-19". YaleNews. https://news.yale.edu/2020/04/24/saliva-samples-preferable-deep-nasal-swabs-testing-covid-19. Retrieved 01 May 2020.
- ↑ "First saliva collection device FDA EUA authorized for COVID-19 testing". Spectrum Solutions. 2020. https://spectrumsolution.com/fda-authorized-covid-19-updates/. Retrieved 16 August 2020.
- ↑ Vault Health (14 April 2020). "Vault Health Launches First-of-its-Kind Saliva-based FDA EUA Approved Test for COVID-19". PR Newswire. https://www.prnewswire.com/news-releases/vault-health-launches-first-of-its-kind-saliva-based-fda-eua-approved-test-for-covid-19-301039633.html. Retrieved 01 May 2020.
- ↑ 34.0 34.1 Gallagher, G.M. (15 August 2020). "FDA Grants Emergency COVID-19 Authorization to Yale's Open Source Method of Saliva Testing". ContagionLive. https://www.contagionlive.com/news/fda-grants-emergency-covid19-authorization-yale-open-source-method-saliva-testing. Retrieved 16 August 2020.
- ↑ 35.0 35.1 Zillgitt, J. (15 August 2020). "FDA approves COVID-19 saliva test developed at Yale in partnership with the NBA, NBPA". USA Today. https://www.usatoday.com/story/sports/nba/2020/08/15/fda-approves-covid-19-saliva-test-developed-yale-nba-nbpa-aid/5590452002/. Retrieved 16 August 2020.
- ↑ Weissleder, R.; Lee, H.; Ko, J. et al. (15 August 2020). "COVID-19 Diagnostics in Context". Harvard Center for Systems Biology. https://csb.mgh.harvard.edu/covid. Retrieved 16 August 2020.
- ↑ 37.0 37.1 37.2 37.3 Rohde, R. (20 July 2020). "COVID-19 Pool Testing: Is It Time to Jump In?". American Society for Microbiology. https://asm.org/Articles/2020/July/COVID-19-Pool-Testing-Is-It-Time-to-Jump-In. Retrieved 06 August 2020.
- ↑ 38.0 38.1 38.2 Masha, M.; Chau, S. (4 August 2020). "Pooled virus tests help stretched health services". Asia Times. https://asiatimes.com/2020/08/pooled-virus-tests-help-stretched-health-services/. Retrieved 06 August 2020.
- ↑ 39.0 39.1 Citroner, G. (3 August 2020). "How Pooled Testing Can Help Us Fight Spread of COVID-19". Healthline. https://www.healthline.com/health-news/how-pooled-testing-can-help-us-fight-spread-of-covid-19. Retrieved 06 August 2020.
- ↑ 40.0 40.1 "In Vitro Diagnostics EUAs". U.S. Food and Drug Administration. 11 August 2020. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas. Retrieved 12 August 2020.
- ↑ Lamb, L.E.; Barolone, S.N.; Ward, E. et al. (2020). "Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification". medRxiv. doi:10.1101/2020.02.19.20025155.
- ↑ Schmid-Burgk, J.L.; Li, D.; Feldman, D. et al. (2020). "LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding". bioRxiv. doi:10.1101/2020.04.06.025635. https://www.biorxiv.org/content/10.1101/2020.04.06.025635v2.article-info.
- ↑ Yu, L.; Wu, S.; Hao, X. et al. (2020). "Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform". Clinical Chemistry 66 (7): 975–77. doi:10.1093/clinchem/hvaa102. PMC PMC7188121. PMID 32315390. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188121.
- ↑ Park, G.-S.; Ku, K.; Baek, S.-H. et al. (2020). "Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)". Journal of Molecular Diagnostics 22 (6): 729–35. doi:10.1016/j.jmoldx.2020.03.006. PMC PMC7144851. PMID 32276051. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144851.
- ↑ 45.0 45.1 45.2 Kellner, M.J.; Ross, J.J.; Schnabl, J. et al. (2020). "A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing". bioRxiv. doi:10.1101/2020.06.23.166397.
- ↑ 46.0 46.1 46.2 Thi, V.L.D.; Herbst, K.; Boerner, K. et al. (2020). "A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples". Science Translational Medicine: eabc7075. doi:10.1126/scitranslmed.abc7075. PMID 32719001.
- ↑ 47.0 47.1 47.2 47.3 47.4 47.5 Esbin, M.N.; Whitney, O.N.; Chong, S. et al. (2020). "Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection". RNA 26 (7): 771–83. doi:10.1261/rna.076232.120. PMC PMC7297120. PMID 32358057. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297120.
- ↑ 48.0 48.1 Hale, C. (9 July 2020). "Oxford researchers develop portable COVID-19 test costing less than $25". Fierce Biotech. https://www.fiercebiotech.com/medtech/oxford-researchers-develop-portable-covid-19-test-costing-less-than-25. Retrieved 07 August 2020.
- ↑ 49.0 49.1 Sheridan, K. (6 August 2020). "This California company has a better version of a simpler, faster Covid-19 test". STAT. https://www.statnews.com/2020/08/06/better-simpler-faster-covid-19-test/. Retrieved 08 August 2020.
- ↑ Heidt, A. (9 July 2020). "Saliva Tests: How They Work and What They Bring to COVID-19". The Scientist. https://www.the-scientist.com/news-opinion/saliva-tests-how-they-work-and-what-they-bring-to-covid-19-67720. Retrieved 08 August 2020.
- ↑ Broughton, J.P.; Deng, X.; Yu, G. et al. (2020). "CRISPR–Cas12-based detection of SARS-CoV-2". Nature Biotechnology 38: 870–74. doi:10.1038/s41587-020-0513-4. PMID 32300245.
- ↑ 52.0 52.1 GlobalData Healthcare (14 July 2020). "CRISPR biotechnology set to disrupt Covid-19 testing market". Verdict Medical Devices. https://www.medicaldevice-network.com/comment/crispr-biotechnology-disrupt-covid-19-testing-market/.
- ↑ 53.0 53.1 World Health Organization (5 August 2020). "COVID-19 Target product profiles for priority diagnostics to support response to the COVID-19 pandemic v.0.1". World Health Organization. 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. Retrieved 12 August 2020.
- ↑ 54.0 54.1 Peplow, M. (10 August 2020). "Rapid COVID-19 testing breaks free from the lab". Chemical & Engineering News. https://cen.acs.org/analytical-chemistry/diagnostics/Rapid-COVID-19-testing-breaks/98/web/2020/08. Retrieved 12 August 2020.
- ↑ 55.0 55.1 Krieger, L.M. (10 August 2020). "Coronavirus: How to test everyone, all the time". The Mercury News. https://www.mercurynews.com/2020/08/10/coronavirus-how-to-test-everyone-all-the-time/. Retrieved 12 August 2020.
- ↑ Brown, D. (10 August 2020). "Point-of-care testing could be ‘biggest advance’ in COVID-19 fight". McKnight's. https://www.mcknights.com/news/point-of-care-testing-could-be-biggest-advance-in-covid-19-fight/. Retrieved 12 August 2020.
- ↑ 57.0 57.1 Wisson, J. (28 July 2020). "COVID-19 and effective cohorting: Rapid point of care triage testing". Health Europa. https://www.healtheuropa.eu/covid-19-and-effective-cohorting-rapid-point-of-care-triage-testing/101696/. Retrieved 12 August 2020.
- ↑ Tromberg, B.J.; Schwetz, T.A.; Pérez-Stable, E.J. et al. (2020). "Rapid Scaling Up of Covid-19 Diagnostic Testing in the United States — The NIH RADx Initiative". New England Journal of Medicine. doi:10.1056/NEJMsr2022263.
- ↑ National Institutes of Health (31 July 2020). "NIH delivering new COVID-19 testing technologies to meet U.S. demand". News Releases. National Institutes of Health. https://www.nih.gov/news-events/news-releases/nih-delivering-new-covid-19-testing-technologies-meet-us-demand. Retrieved 12 August 2020.
- ↑ Leichman, A.K. (27 July 2020). "10 ways Israeli scientists are improving corona testing". Isael21c. https://www.israel21c.org/how-israeli-scientists-are-improving-corona-testing/. Retrieved 11 August 2020.
- ↑ 61.0 61.1 61.2 61.3 Mifflin, T.E. (2003). "Chapter 1: Setting Up a PCR Laboratory". In Dieffenbach, C.; Dveksler, G. (PDF). PCR Primer (2nd ed.). Cold Spring Harbor Laboratory Press. pp. 5–14. ISBN 9780879696542. http://www.biosupplynet.com/pdf/01_pcr_primer_p.5_14.pdf. Retrieved 13 August 2020.
- ↑ 62.0 62.1 62.2 62.3 Degen, H.-J.; Deufel, A.; Eisel, D. et al., ed. (2006). "Chapter 2: General Guidelines" (PDF). PCR Applications Manual (3rd ed.). Roche Diagnostics GmbH. pp. 19–38. https://www.gene-quantification.de/ras-pcr-application-manual-3rd-ed.pdf. Retrieved 13 August 2020.
- ↑ 63.0 63.1 Ahmed, S. (2014). "Chapter 12: Setting-up a PCR Lab" (PDF). Manual of PCR. Genetics Resource Centre. http://grcpk.com/wp-content/uploads/2014/10/12.-Setting-up-PCR-Lab.pdf. Retrieved 13 August 2020.
- ↑ 64.0 64.1 64.2 Refig, J. (1 August 2014). "The Devil is in the Details: How to Setup a PCR Laboratory". BiteSizeBio. https://bitesizebio.com/19880/the-devil-is-in-the-details-how-to-setup-a-pcr-laboratory/. Retrieved 13 August 2020.
- ↑ 65.0 65.1 "The basics of PCR: Detecting viruses and bacteria red-handed" (PDF). BioChek BV. May 2018. https://www.biochek.com/wp-content/uploads/2018/05/BioChek-E-book-The-basics-of-PCR.pdf. Retrieved 13 August 2020.
- ↑ 66.0 66.1 66.2 66.3 Das, P.K.; Ganguly, S.B.; Mandal, B. (2018). "Mitigating PCR /Amplicon Contamination in a High Risk High Burden Mycobacterial Reference Laboratory in a Resource Limited Setting". Mycobacterial Diseases 8 (2): 261. doi:10.4172/2161-1068.1000261.
- ↑ 67.0 67.1 67.2 67.3 World Health Organization (31 January 2018). "Dos and Don'ts for molecular testing". World Health Organization. https://www.who.int/malaria/areas/diagnosis/molecular-testing-dos-donts/en/. Retrieved 14 August 2020.
- ↑ 68.0 68.1 Diego, J. G.-B.; Fernández-Soto, P.; Crego-Vicente, B. et al. (2019). "Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: Towards a ready-to-use test". Scientific Reports 9: 14744. doi:10.1038/s41598-019-51342-2. PMC PMC6791938. PMID 31611563. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791938.
- ↑ Martzy, R.; Kolm, C.; Krska, R. et al. (2019). "Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis". Analytical and Bioanalytical Chemistry 411: 1695–1702. doi:10.1007/s00216-018-1553-1. PMC PMC6453865. PMID 30617408. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453865.
- ↑ Zanoli, L.M.; Spoto, G. (2013). "Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices". Biosensors 3 (1): 18–43. doi:10.3390/bios3010018. PMC PMC4263587. PMID 25587397. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263587.
- ↑ Roskos, K.; Hickerson, A.I.; Lu, H.-W. et al. (2013). "Simple System for Isothermal DNA Amplification Coupled to Lateral Flow Detection". PLoS One 8 (7): e69355. doi:10.1371/journal.pone.0069355. PMC PMC3724848. PMID 23922706. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724848.
- ↑ Bao, Y.; Jiang, Y.; Xiong, E. et al. (2020). "CUT-LAMP: Contamination-Free Loop-Mediated Isothermal Amplification Based on the CRISPR/Cas9 Cleavage". ACS Sensors 5 (4): 1082–91. doi:10.1021/acssensors.0c00034. PMID 32242409.
- ↑ 73.0 73.1 "Loop-mediated Isothermal Amplification (LAMP)". New England BioLabs. 17 June 2014. https://www.neb.com/protocols/2014/06/17/loop-mediated-isothermal-amplification-lamp. Retrieved 14 August 2020.
- ↑ Fernández-Soto, P.; Mvoulouga, P.O.; Akue, J.P. et al. (2014). "Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of Loa loa". PLoS One 9 (4): e94664. doi:10.1371/journal.pone.0094664. PMC PMC3983228. PMID 24722638. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983228.
- ↑ Kerkhof, J. (13 June 2018). "PCR Equipment Survey Results". Lab Manager. https://www.labmanager.com/surveys/what-to-look-for-in-a-pcr-system-2154. Retrieved 14 August 2020.
- ↑ Lab Manager (7 April 2020). "Results from the Lab Manager Life Science Technology Survey". Lab Manager. https://www.labmanager.com/surveys/results-from-the-lab-manager-life-science-technology-survey-22257. Retrieved 14 August 2020.
- ↑ "Alethia". Meridian Bioscience. https://www.meridianbioscience.com/platform/molecular/alethia/. Retrieved 14 August 2020.
- ↑ Moran, A.; Beavis, K.G.; Matushek, S.M. et al. (2020). "Detection of SARS-CoV-2 by Use of the Cepheid Xpert Xpress SARS-CoV-2 and Roche cobas SARS-CoV-2 Assays". Journal of Clinical Microbiology 58 (8): e00772-20. doi:10.1128/JCM.01072-20. PMC PMC7383516. PMID 32303565. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383516.
- ↑ Loeffelholz, M.J.; Alland, D.; Butler-Wu, S.M. et al. (2020). "Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2 Test". Journal of Clinical Microbiology 58 (8): e00926-20. doi:10.1128/JCM.00926-20. PMC PMC7383535. PMID 32366669. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383535.
- ↑ Goldenberger, D.; Leusinger, K.; Sogaard, K.K. et al. (2020). "Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay". Journal of Virological Methods 284: 113925. doi:10.1016/j.jviromet.2020.113925. PMC PMC7351036. PMID 32659240. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351036.
- ↑ Cepheid (9 June 2020). "Cepheid Announces Development of Four-in-One Combination Test for SARS-CoV-2, Flu A, Flu B and RSV". PR Newswire. 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. Retrieved 13 August 2020.
- ↑ Hogan, C.A.; Garamani, N.; Lee, A.S. et al. (2020). "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 of Clinical Microbiology 58 (8): e01072-20. doi:10.1128/JCM.01072-20. PMC PMC7383558. PMID 32461285. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383558.
- ↑ "MAUDE - Manufacturer and User Facility Device Experience". U.S. Food and Drug Administration. https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfMAUDE/TextSearch.cfm. Retrieved 13 August 2020.
- ↑ Ravi, N.; Cortade, D.L.; Ng, E. et al. (2020). "Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscape". Biosensors and Bioelectronics 165: 112454. doi:10.1016/j.bios.2020.112454. PMC PMC7368663. PMID 32729549. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368663.
- ↑ Devine, C. (3 July 2020). "Coronavirus test used by White House has questionable accuracy". CNN Politics. https://www.cnn.com/2020/07/03/politics/coronavirus-white-house-test-abbott/index.html. Retrieved 08 July 2020.
- ↑ Perrone, M. (14 May 2020). "FDA probes accuracy issue with Abbott’s rapid virus test". Associated Press. https://apnews.com/c8ab010e8e02dfe7beb34a5e5df11279. Retrieved 19 May 2020.
- ↑ Basu, A.; Zinger, T.; Inglima, K. et al. (2020). "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 of Clinical Microbiology 58 (8): e01136-20. doi:10.1128/JCM.01136-20. PMC PMC7383552. PMID 32471894. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383552.
- ↑ Mitchell, S.L.; St. George, K. (2020). "Evaluation of the COVID19 ID NOW EUA assay". Journal of Clinical Virology 128: 104429. doi:10.1016/j.jcv.2020.104429. PMC PMC7227587. PMID 32425657. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227587.
- ↑ "Cue COVID-19 Test Instructions for Use" (PDF). Cue Health, Inc. June 2020. https://www.cuehealth.com/s/IN9100003-1_10_IFU-Cue-COVID-19-Test-Cartridge-Pack-Professional.pdf. Retrieved 13 August 2020.
- ↑ "The Talis Advantage". Talis Biomedical. https://talis.bio/technology/. Retrieved 13 August 2020.
- ↑ "SARS-CoV-2 Test Kit (Real-time PCR) Instructions for Use" (PDF). Xiamen Zeesan Biotech. July 2020. https://www.fda.gov/media/140717/download. Retrieved 14 August 2020.
- ↑ "Biomeme SARS-CoV-2 Real-Time RT-PCR Test Instructions for Use" (PDF). Biomeme, Inc. 2020. https://www.fda.gov/media/141052/download. Retrieved 14 August 2020.
- ↑ "PCR Master Mix (2X)". Thermo Fisher Scientific. https://www.thermofisher.com/order/catalog/product/K0171#/K0171. Retrieved 16 August 2020.
- ↑ "Isothermal Reaction Guide". OptiGene Limited. http://www.optigene.co.uk/isothermal-reaction-guide/. Retrieved 16 August 2020.
- ↑ Kashir, J.; Yaqinuddin, A. (2020). "Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19". Medical Hypotheses 141: 109786. doi:10.1016/j.mehy.2020.109786. PMC PMC7182526. PMID 32361529. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182526. "Reagent-wise, the costs would be similar to that of real time RT-PCR ..."
- ↑ 96.0 96.1 "Accula Test" (PDF). Mesa Biotech, Inc. April 2020. https://www.fda.gov/media/136355/download. Retrieved 16 August 2020.
Cite error: Invalid
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tag; name "MBAccula20" defined multiple times with different content - ↑ Kun, L.; Coatrieux, G.; Quantin, C. et al. (2008). "Improving outcomes with interoperable EHRs and secure global health information infrastructure". Studies in Health Technology and Informatics 137: 68–79. PMID 18560070.
- ↑ Global Center for Health Innovation (1 November 2024). "Improving Patient Care through Interoperability" (PDF). Global Center for Health Innovation. http://s3.amazonaws.com/rdcms-himss/files/production/public/Improving-Patient-Carethrough-Interoperability.pdf. Retrieved 16 August 2020.