Difference between revisions of "Template:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Adding COVID-19 and other virus testing to your laboratory/What kind of space, equipment, and supplies will you need?"

From LIMSWiki
Jump to navigationJump to search
(November updates, though more still to be made.)
Line 42: Line 42:
{| class="wikitable" border="1" cellpadding="5" cellspacing="0" width="80%"
{| 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:white; padding-left:10px; padding-right:10px;" colspan="8"|'''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;"|Date EUA issued

Revision as of 21:18, 19 November 2020

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.[1][2][3][4][5][6][7] 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.[1][2][4][6]

When possible, separate rooms for sample preparation, PCR setup, and post-PCR activities, each with their own airflow control, are encouraged.[1][2][5][6][7] 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.[1][3][7] 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 PCR Applications Manual[2] provides a detailed breakdown of setting up the laboratory for PCR. Das et al.[6] and Dr. Jennifer Redig[4] provide additional valuable insight. The World Health Organization (WHO) also provides guidance for setting up molecular testing in the lab.[7]

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[8], as does opening the reaction chamber after reaction is completed.[9] 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."[10][11] Even more cutting-edge techniques to reduce contamination such as the CUT-LAMP technique of Bao et al.[12] or the dUTP/UDG system for COVID-19 RT-LAMP reactions of Kellner et al.[13] 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.[14][15]

3.2.2 Instruments and assays

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 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 posed five questions potential buyers should ask before making PCR purchases[16]:

  1. Do your current and long-term needs require basic PCR systems, qPCR systems, or digital PCR systems?
  2. What sample formats do you anticipate using?
  3. What throughput requirements do you have now and anticipate in the near future?
  4. What are you willing to sacrifice in regards to temperature ramp up and cool down times and accuracies?
  5. 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.[17]

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.[18] 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.[19] 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:

Table 1. CLIA-waived COVID-19-related in vitro diagnostic tests receiving U.S. FDA Emergency Use Authorizations (EUAs)
Date EUA issued Manufacturer Name of test or assay Required instrument Technology (method) Multi-analyte? RADx-funded? Additional comments
20 March 2020 Cepheid Xpert Xpress SARS-CoV-2 test GeneXpert Xpress System (Tablet and Hub Configurations) Molecular (RT-PCR) No No Has largely received positive review of sensitivity and specificity.[20][21][22]
23 March 2020 Mesa Biotech Inc. Accula SARS-CoV-2 test Accula Dock or Silaris Dock Molecular (RT-PCR) No Yes Has received only minor scrutiny[23], with no formal FDA complaints[24]
27 March 2020 Abbott Diagnostics Scarborough, Inc. ID NOW COVID-19 ID NOW Molecular (isothermal amplification) No No Targets "a unique region of the RNA-dependent RNA polymerase (RdRP) gene"[25]; as of November 2020, the sensitivity of the test is still under scrutiny[26][27][28][29] In October 2020, Abbott released additional study data showing overall sensitivity of 93.3% and specificity of 98.4%, emphasizing the ID NOW's best use with samples taken within seven days of symptom onset.[30]
08 May 2020 Quidel Corporation Sofia SARS Antigen FIA Sofia 2 Antigen No Yes With a comparatively lower specificity, best used as surveillance, repeat screening tool[31][32]
10 June 2020 Cue Health Inc. Cue COVID-19 Test Cartridge Cue Health Monitoring System Molecular (isothermal amplification) No No "Test primers amplify the nucleocapsid (N) region of the gene"[33]
02 July 2020 Becton, Dickinson and Company BD Veritor System for Rapid Detection of SARS-CoV-2 BD Veritor Plus Antigen No No With a comparatively lower specificity, best used as surveillance, repeat screening tool[31][32]
14 September 2020 Roche Molecular Systems, Inc. cobas SARS-CoV-2 & Influenza A/B Assay cobas Liat PCR System Molecular (RT-PCR) Yes No Everitt et al. offer some discussion and citations concerning research related to the cobas LIAT PCR system and its assays.[34]
24 September 2020 Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV test GeneXpert Xpress System (Tablet and Hub Configurations) Molecular (RT-PCR) Yes No Development of this multiplex assay for SARS-CoV-2, Flu A, Flu B, and RSV was announced in June.[35] After receiving its EUA in September, received advanced development support through the Department of Health and Human Services and the Department of Defense.[36]
02 October 2020 BioFire Diagnostics, LLC BioFire Respiratory 2.1 (RP2.1) Panel BioFire FilmArray Systems Molecular (RT-PCR) Yes No From the manufacturer: "The BioFire RP2.1 Panel (EUA) detects 22 respiratory pathogens, including SARS-CoV-2, to help clinicians quickly rule in and rule out common causes of respiratory illness in about 45 minutes."[37] Creager et al. reported their evaluation findings in the Journal of Clinical Virology, stating that the panel "has similar performance to high throughput assays used for the detection of COVID-19."[38]
N/A (Anticipated) Talis Biomedical Talis One Cartridge Talis One Instrument Molecular (RT-LAMP) No Yes Expectations are that it will receive an FDA EUA and be CLIA-waived[39], 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.[40] 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.[41] Yale's SalivaDirect is a more flexible test, validated for use with multiple instruments and reagents that are not proprietary to Yale.[42][43] 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."[44]

Reagent cost and usage for isothermal amplification methods such as LAMP are similar, though buffers and primers specific to the method are required.[8][14][45][46]

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.[13]

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[47] and the Xpert Xpress SARS-CoV-2 kit comes with disposable transfer pipettes.[47] 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.[48] 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."[48] The Association of Public Health Laboratories comes to a similar conclusion in regard to laboratory informatics solutions and public health laboratories' COVID-19 testing.[49]

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[48]:

  • 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.[50][51] 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.[52][53][54] 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.

Table 2. Major players operating in the global diagnostic PCR, isothermal amplification, and NGS market
Vendor Shop all products PCR machines Nucleic acid extraction
and purification machines 		Immunoassay analyzers
and assays 		PCR and qPCR assays PCR and qPCR enzymes
and master mixes 		DNA/RNA purification,
quantitation, and
amplification supplies 		LAMP assays Isothermal amplification
enzymes and
master mixes 		NGS supplies Supporting labware
and supplies 		Software
Abbott Abbott products ✓ - - ✓ ✓ - - - - ✓ ✓
Agilent Technologies Agilent products ✓ - - ✓ ✓ ✓ - - ✓ ✓ ✓
Becton, Dickinson and Company BD products ✓ - - ✓ - - - - - ✓ -
Bio-Rad Laboratories, Inc. Bio-Rad products ✓ - ✓ ✓ ✓ ✓ - - ✓ ✓ -
bioMérieux SA bioMérieux products - ✓ ✓ ✓ - - - - - ✓ ✓
Danaher Corporation and its companies Cepheid products,
Beckman Coulter products, and
Beckman Life Sciences products 		✓ - ✓ ✓ - ✓ - - - ✓ -
F. Hoffmann-La Roche AG Roche Diagnostics products ✓ ✓ - ✓ ✓ ✓ - - ✓ - ✓
Jena Bioscience GmbH Jena Bioscience products - - - ✓ ✓ ✓ ✓ ✓ ✓ - -
LGC Limited and its companies Lucigen products - - - ✓ ✓ ✓ - ✓ ✓ - -
Merck KGaA Sigma-Aldrich products and
Millipore Sigma products 		- - - ✓ ✓ ✓ - - ✓ ✓ -
New England BioLabs, Inc. NEB products - - - ✓ ✓ ✓ ✓ ✓ ✓ - -
Promega Promega products and catalog - ✓ - ✓ ✓ ✓ - - ✓ - -
QIAGEN N.V. QIAGEN products ✓ ✓ - ✓ ✓ ✓ - - ✓ - ✓
Siemens Healthcare GmbH Siemens Healthcare products - ✓ - ✓ - ✓ - - - - ✓
Thermo Fisher Scientific, Inc. Thermo Fisher products and
Fisher Scientific products 		✓ ✓ - ✓ ✓ ✓ - ✓ ✓ ✓ ✓

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:

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:

  1. ↑ 1.0 1.1 1.2 1.3 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. 
  2. ↑ 2.0 2.1 2.2 2.3 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. 
  3. ↑ 3.0 3.1 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. 
  4. ↑ 4.0 4.1 4.2 Redig, 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. 
  5. ↑ 5.0 5.1 "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. 
  6. ↑ 6.0 6.1 6.2 6.3 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. 
  7. ↑ 7.0 7.1 7.2 7.3 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. 
  8. ↑ 8.0 8.1 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. 
  9. ↑ 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. 
  10. ↑ 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. 
  11. ↑ 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. 
  12. ↑ 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. 
  13. ↑ 13.0 13.1 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. 
  14. ↑ 14.0 14.1 "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. 
  15. ↑ 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. 
  16. ↑ 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. 
  17. ↑ 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. 
  18. ↑ 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. 
  19. ↑ "Alethia". Meridian Bioscience. https://www.meridianbioscience.com/platform/molecular/alethia/. Retrieved 14 August 2020. 
  20. ↑ 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. 
  21. ↑ 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. 
  22. ↑ 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. 
  23. ↑ 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. 
  24. ↑ "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. 
  25. ↑ 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. 
  26. ↑ 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. 
  27. ↑ 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. 
  28. ↑ 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. 
  29. ↑ 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. 
  30. ↑ Taylor, N.P. (7 October 2020). "Abbott, on defense, details embattled rapid COVID-19 test results". MedTechDive. https://www.medtechdive.com/news/abbott-on-defense-id-now-coronavirus-test-postmarket-study/586579/. Retrieved 18 November 2020. 
  31. ↑ 31.0 31.1 Service, R.F. (2020). "Radical shift in COVID-19 testing needed to reopen schools and businesses, researchers say". Science. doi:10.1126/science.abe1546. 
  32. ↑ 32.0 32.1 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. 
  33. ↑ "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. 
  34. ↑ Everitt, M.L.; Tillery, A.; David, M.G. et al. (2020). "A critical review of point-of-care diagnostic technologies to combat viral pandemics". Analytica Chimica Acta In Press. doi:10.1016/j.aca.2020.10.009. PMC PMC7548029. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7548029. 
  35. ↑ 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. 
  36. ↑ Global Biodefense Staff (8 October 2020). "BARDA and JPEO-CBRND Back Cepheid’s Multiplex Test for Influenza, SARS-CoV2 and RSV". Global Biodefense. https://globalbiodefense.com/2020/10/08/barda-and-jpeo-cbrnd-back-cepheids-multiplex-test-for-flu-rsv-and-sars-cov2/. Retrieved 19 November 2020. 
  37. ↑ [https://www.biofiredx.com/covid-19/ "BioFire’s Respiratory Solutions with SARS-CoV-2"]. BioFire Diagnostics, LLC. https://www.biofiredx.com/covid-19/. Retrieved 19 November 2020. 
  38. ↑ Creager, H.M.; Cabrera, B.; Schnaubelt, A. et al. (2020). "Clinical evaluation of the BioFire Respiratory Panel 2.1 and detection of SARS-CoV-2". Journal of Clinical Virology 129: 104538. doi:10.1016/j.jcv.2020.104538. PMC PMC7336953. PMID 32650276. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336953. 
  39. ↑ "The Talis Advantage". Talis Biomedical. https://talis.bio/technology/. Retrieved 13 August 2020. 
  40. ↑ "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. 
  41. ↑ "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. 
  42. ↑ 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. 
  43. ↑ 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. 
  44. ↑ "PCR Master Mix (2X)". Thermo Fisher Scientific. https://www.thermofisher.com/order/catalog/product/K0171#/K0171. Retrieved 16 August 2020. 
  45. ↑ "Isothermal Reaction Guide". OptiGene Limited. http://www.optigene.co.uk/isothermal-reaction-guide/. Retrieved 16 August 2020. 
  46. ↑ 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 ..." 
  47. ↑ 47.0 47.1 "Accula Test" (PDF). Mesa Biotech, Inc. April 2020. https://www.fda.gov/media/136355/download. Retrieved 16 August 2020.  Cite error: Invalid <ref> tag; name "MBAccula20" defined multiple times with different content
  48. ↑ 48.0 48.1 48.2 Weemaes, M.; Martens, S.; Cuypers, L. et al. (2020). "Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center". JAMIA: ocaa081. doi:10.1093/jamia/ocaa081. PMC PMC7197526. PMID 32348469. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197526. 
  49. ↑ Association of Public Health Laboratories (2020). "LIMS (Laboratory Information Management System)" (PDF). Association of Public Health Laboratories. https://www.aphl.org/aboutAPHL/publications/Documents/INFO-2020-LIMS.pdf. Retrieved 18 August 2020. 
  50. ↑ 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. 
  51. ↑ Global Center for Health Innovation (30 April 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. 
  52. ↑ Glaser, J. (12 June 2020). "It’s Time for a New Kind of Electronic Health Record". Harvard Business Review. https://hbr.org/2020/06/its-time-for-a-new-kind-of-electronic-health-record. Retrieved 18 August 2020. 
  53. ↑ Limoli, C.; Papathomas, G. (7 July 2020). "Physicians deserve better software: Covid-19 has shown why medical records need to adapt". MedCity News. https://medcitynews.com/2020/07/physicians-deserve-better-software-covid-19-has-shown-why-medical-records-need-to-adapt/. Retrieved 18 August 2020. 
  54. ↑ Jason, C. (23 July 2020). "EHR Optimization, Health IT Projects Needed After COVID-19 Surge". EHR Intelligence. https://ehrintelligence.com/news/ehr-optimization-health-it-projects-needed-after-covid-19-surge. Retrieved 18 August 2020. 
Retrieved from "https://www.limswiki.org/index.php?title=Template:COVID-19_Testing,_Reporting,_and_Information_Management_in_the_Laboratory/Adding_COVID-19_and_other_virus_testing_to_your_laboratory/What_kind_of_space,_equipment,_and_supplies_will_you_need%3F&oldid=41066"