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As mentioned in the previous chapter, the benefits of antigen testing For COVID-19 and other viral infections are 1. specimen collection can typically be done with a simple nasal swab rather than a more invasive [[nasopharyngeal swab]], 2. testing is more rapid and convenient, and 3. it takes some pressure off the PCR supply chain. However, antigen testing only tests what's there, rather than amplifying the amount, resulting in generally lower sensitivities.<ref name="ServiceRadical2020">{{cite journal |title=Radical shift in COVID-19 testing needed to reopen schools and businesses, researchers say |journal=Science |author=Service, R.F. |year=2020 |doi=10.1126/science.abe1546}}</ref><ref name="GuglielmiTheExp20">{{cite journal |title=The explosion of new coronavirus tests that could help to end the pandemic |journal=Nature |author=Guglielmi, G. |volume=583 |pages=506–09 |year=2020 |doi=10.1038/d41586-020-02140-8}}</ref> As such, the real utility of antigen testing, despite its lower sensitivity, appears to be surveillance situations where a large group of individuals who are at risk can be screened at regularly scheduled intervals of two to four days. If your lab is able to support this sort of testing, then this type of testing may be an option. As of September 2021, thirty-four FDA EUAs for antigen tests have been issues; 28 of those 34 include allowances for CLIA-waived testing, and 10 were authorized for home use.<ref name="FDAInVitroAntigen21">{{cite web |url=https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-antigen-diagnostic-tests-sars-cov-2 |title=In Vitro Diagnostics EUAs - Antigen Diagnostic Tests for SARS-CoV-2 |publisher=U.S. Food and Drug Administration |date=07 September 2021 |accessdate=07 September 2021}}</ref> Review [https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-antigen-diagnostic-tests-sars-cov-2 the FDA list] to further examine your options.
Early on in the pandemic, while PCR was getting most of the attention, reverse transcription loop-mediated isothermal amplification (RT-LAMP), an isothermal [[Nucleic acid test|nucleic acid amplification]] technique that allows for RNA amplification, was also quietly being discussed<ref name="LambRapid20">{{cite journal |title=Rapid Detection of Novel Coronavirus (COVID-19) by Reverse Transcription-Loop-Mediated Isothermal Amplification |journal=medRxiv |author=Lamb, L.E.; Barolone, S.N.; Ward, E. et al. |year=2020 |doi=10.1101/2020.02.19.20025155}}</ref><ref name="Schmid-BurgkLAMP20">{{cite journal |title=LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding |journal=bioRxiv |author=Schmid-Burgk, J.L.; Li, D.; Feldman, D. et al. |year=2020 |url=https://www.biorxiv.org/content/10.1101/2020.04.06.025635v2.article-info |doi=10.1101/2020.04.06.025635}}</ref>, and it has since gained more attention.<ref name="YuRapid20">{{cite journal |title=Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform |journal=Clinical Chemistry |author=Yu, L.; Wu, S.; Hao, X. et al. |volume=66 |issue=7 |pages=975–77 |year=2020 |doi=10.1093/clinchem/hvaa102 |pmid=32315390 |pmc=PMC7188121}}</ref><ref name="ParkDevelop20">{{cite journal |title=Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) |journal=Journal of Molecular Diagnostics |author=Park, G.-S.; Ku, K.; Baek, S.-H. et al. |volume=22 |issue=6 |pages=729–35 |year=2020 |doi=10.1016/j.jmoldx.2020.03.006 |pmid=32276051 |pmc=PMC7144851}}</ref><ref name="KellnerARapid20">{{cite journal |title=A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing |journal=bioRxiv |author=Kellner, M.J.; Ross, J.J.; Schnabl, J. et al. |year=2020 |doi=10.1101/2020.06.23.166397}}</ref><ref name="ThiAColor20">{{cite journal |title=A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples |journal=Science Translational Medicine |author=Thi, V.L.D.; Herbst, K.; Boerner, K. et al. |at=eabc7075 |year=2020 |doi=10.1126/scitranslmed.abc7075 |pmid=32719001}}</ref><ref name="EsbinOver20">{{cite journal |title=Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection |journal=RNA |author=Esbin, M.N.; Whitney, O.N.; Chong, S. et al. |volume=26 |issue=7 |pages=771–83 |year=2020 |doi=10.1261/rna.076232.120 |pmid=32358057 |pmc=PMC7297120}}</ref><ref name="HaleOxford20">{{cite web |url=https://www.fiercebiotech.com/medtech/oxford-researchers-develop-portable-covid-19-test-costing-less-than-25 |title=Oxford researchers develop portable COVID-19 test costing less than $25 |author=Hale, C. |work=Fierce Biotech |date=09 July 2020 |accessdate=07 August 2020}}</ref> In July 2020, the University of Oxford was in the process of getting a rapid, affordable, clinically-validated RT-LAMP test approved for the European market. Oxford also notes that "[a]n advantage of using LAMP technology is that it uses different reagents to most laboratory-based PCR tests."<ref name="HaleOxford20" /> Thi ''et al.'' have tested a two-color RT-LAMP assay with an N gene primer set and diagnostic validation using LAMP-sequencing, concluding that the pairing of the two "could offer scalable testing that would be difficult to achieve with conventional qRT-PCR based tests."<ref name="ThiAColor20" /> And California-based Color Genomics set up their own proprietary RT-LAMP system in the summer of 2020, capable of handling up to 10,000 tests per day.<ref name="SheridanThisCal20">{{cite web |url=https://www.statnews.com/2020/08/06/better-simpler-faster-covid-19-test/ |title=This California company has a better version of a simpler, faster Covid-19 test |author=Sheridan, K. |work=STAT |date=06 August 2020 |accessdate=08 August 2020}}</ref>


The CDC emphasizes that molecular testing remains the "gold standard" for detecting SARS-CoV-2 in a sample, and it "may be necessary to confirm an antigen test result with a laboratory-based NAAT, especially if the result of the antigen test is inconsistent with the clinical context." However, some molecular tests designed for point-of-care testing may not be sufficiently designed for confirmatory testing; consult the instructions for use for any confirmatory test.<ref name="CDCInterim21">{{cite web |url=https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html |title=Interim Guidance for Antigen Testing for SARS-CoV-2 |author=Centers for Disease Control and Prevention |publisher=Centers for Disease Control and Prevention |date=09 September 2021 |accessdate=18 September 2021}}</ref> The CDC [https://www.cdc.gov/coronavirus/2019-ncov/lab/resources/antigen-tests-guidelines.html#anchor_1631295114633 makes available] two antigen testing algorithms for determining when confirmatory testing is actually recommended.<ref name="CDCInterim21" />
In most cases, LAMP-based testing is much simpler than PCR, lacking the requirement of specialized instruments. Despite LAMP generally being thought of as less sensitive than PCR<ref name="SheridanThisCal20" /><ref name="GuglielmiTheExp20">{{cite journal |title=The explosion of new coronavirus tests that could help to end the pandemic |journal=Nature |author=Guglielmi, G. |volume=583 |pages=506–09 |year=2020 |doi=10.1038/d41586-020-02140-8}}</ref><ref name="HeidtSaliva20">{{cite web |url=https://www.the-scientist.com/news-opinion/saliva-tests-how-they-work-and-what-they-bring-to-covid-19-67720 |title=Saliva Tests: How They Work and What They Bring to COVID-19 |author=Heidt, A. |work=The Scientist |date=09 July 2020 |accessdate=08 August 2020}}</ref>, the explosion of research into RT-LAMP methods for testing for the presence of SARS-CoV-2 continues to indicate that "under optimized conditions," RT-LAMP methods may actually be able to rival the sensitivity and specificity of many RT-PCR COVID-19 tests.<ref name="EsbinOver20" /> Esbin ''et al.'' add<ref name="EsbinOver20" />:
 
<blockquote>These methods allow for faster amplification, less specialized equipment, and easy readout. LAMP methods also benefit from the ability to multiplex targets in a single reaction and can be combined with other isothermal methods, like &#91;[[recombinase polymerase amplification]]&#93; in the RAMP technique, to increase test accuracy even more. These techniques may be particularly useful for rapid, point-of-care diagnoses or for remote clinical testing without the need for laboratory equipment.</blockquote>
 
CRISPR methods are also being used in conjunction with RT-LAMP.<ref name="GuglielmiTheExp20" /><ref name="EsbinOver20" /><ref name="BroughtonCRISPR20">{{cite journal |title=CRISPR–Cas12-based detection of SARS-CoV-2 |journal=Nature Biotechnology |author=Broughton, J.P.; Deng, X.; Yu, G. et al. |volume=38 |pages=870–74 |year=2020 |doi=10.1038/s41587-020-0513-4 |pmid=32300245}}</ref> RT-LAMP creates complementary double-stranded DNA (cDNA) from specimen RNA and then copies (amplifies) it. Then CRISPR methods are used to detect a predefined coronavirus sequence (from a cleaved molecular marker) in the resulting amplified specimen. Though as of September 2021 approved assays using CRISPR-based detection of SARS-CoV-2 are limited to a handful of companies<ref name="FDAInVitroEUAs21" /><ref name="GuglielmiTheExp20" /><ref name="GDHCRISPR20">{{cite web |url=https://www.medicaldevice-network.com/comment/crispr-biotechnology-disrupt-covid-19-testing-market/ |title=CRISPR biotechnology set to disrupt Covid-19 testing market |author=GlobalData Healthcare |work=Verdict Medical Devices |date=14 July 2020}}</ref>, the technology has some promise as an alternative testing method. CRISPR has the additional advantage of being readily coupled with lateral flow assay technology to be deployed in the point-of-care (POC) setting<ref name="EsbinOver20" /><ref name="GDHCRISPR20" />, though it's worth noting the currently EUAed RT-LAMP-based CRISPR kits are only approved for high-complexity CLIA labs. (The current molecular diagnostic test kits running CRISPR technology are Sherlock BioSciences' Sherlock CRISPR SARS-CoV-2 Kit and Mammoth Biosciences' SARS-CoV-2 DETECTR Reagent Kit, both high-complexity.<ref name="FDAInVitroEUAs21">{{cite web |url=https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-molecular-diagnostic-tests-sars-cov-2 |title=In Vitro Diagnostics EUAs - Molecular Diagnostic Tests for SARS-CoV-2 |publisher=U.S. Food and Drug Administration |date=07 September 2021 |accessdate=07 September 2021}}</ref>)


==References==
==References==
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{{Reflist|colwidth=30em}}

Revision as of 19:21, 3 February 2022

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[1][2], and it has since gained more attention.[3][4][5][6][7][8] In July 2020, the University of Oxford was 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."[8] 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."[6] And California-based Color Genomics set up their own proprietary RT-LAMP system in the summer of 2020, capable of handling up to 10,000 tests per day.[9]

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[9][10][11], the explosion of research into RT-LAMP methods for testing for the presence of SARS-CoV-2 continues to indicate that "under optimized conditions," RT-LAMP methods may actually be able to rival the sensitivity and specificity of many RT-PCR COVID-19 tests.[7] Esbin et al. add[7]:

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.[10][7][12] 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 September 2021 approved assays using CRISPR-based detection of SARS-CoV-2 are limited to a handful of companies[13][10][14], the technology has some promise as an alternative testing method. CRISPR has the additional advantage of being readily coupled with lateral flow assay technology to be deployed in the point-of-care (POC) setting[7][14], though it's worth noting the currently EUAed RT-LAMP-based CRISPR kits are only approved for high-complexity CLIA labs. (The current molecular diagnostic test kits running CRISPR technology are Sherlock BioSciences' Sherlock CRISPR SARS-CoV-2 Kit and Mammoth Biosciences' SARS-CoV-2 DETECTR Reagent Kit, both high-complexity.[13])

References

  1. ↑ 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. 
  2. ↑ 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. 
  3. ↑ 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. 
  4. ↑ 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. 
  5. ↑ 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. 
  6. ↑ 6.0 6.1 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. 
  7. ↑ 7.0 7.1 7.2 7.3 7.4 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. 
  8. ↑ 8.0 8.1 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. 
  9. ↑ 9.0 9.1 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. 
  10. ↑ 10.0 10.1 10.2 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. 
  11. ↑ 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. 
  12. ↑ 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. 
  13. ↑ 13.0 13.1 "In Vitro Diagnostics EUAs - Molecular Diagnostic Tests for SARS-CoV-2". U.S. Food and Drug Administration. 7 September 2021. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas-molecular-diagnostic-tests-sars-cov-2. Retrieved 07 September 2021. 
  14. ↑ 14.0 14.1 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/. 
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