Molecular Diagnosis of SARS-CoV-2: Assessing and Interpreting Nucleic Acid and Antigen Tests
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Abstract
In this review, we summarize the current status of nucleic acid and antigen testing required for diagnosing SARS-CoV-2 infection and COVID-19 disease. Nucleic acid amplification (NAAT) and antigen-detection (Ag) tests occupy a critically important frontline of defense against SARS-CoV-2 in clinical and public health settings. In early stages of this outbreak, we observed that identifying the causative agent of a new illness of unknown origin was greatly accelerated by characterizing the nucleic acid signature of the novel coronavirus. Results from nucleic acid sequencing led to the development of highly sensitive RT-PCR testing for use in clinical settings and to informing best practices for patient care, and in public health settings to the development of strategies for protecting populations. As the current COVID-19 pandemic has evolved, we have seen how NAAT performance has been used to guide and optimize specimen collection, inform patient triage decisions, reveal unexpected clinical symptoms, clarify risks of transmission within patient care facilities, and guide appropriate treatment strategies. For public health settings during the earliest stages of the pandemic, NAATs served as the only tool available for studying the epidemiology of this new disease by identifying infected individuals, studying transmission patterns, modeling population impacts, and enabling disease control organizations and governments to make challenging disease mitigation recommendations to protect the expanding breadth of populations at risk. With time, the nucleic acid signature has provided the information necessary to understand SARS-CoV-2 protein expression for further development of antigen-based point-of-care (POC) diagnostic tests. The advent of massive parallel sequencing (ie, next generation sequencing) has afforded the characterization of this novel pathogen, informed the sequences best adapted for RT-PCR assays, guided vaccine production, and is currently used for tracking and monitoring SARS-CoV-2 variants.
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References
Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270-3. doi: 10.1038/s41586-020-2012-7. PubMed PMID: 32015507; PMCID: PMC7095418.
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus I, Research T. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020;382(8):727-33. doi: 10.1056/NEJMoa2001017. PubMed PMID: 31978945; PMCID: PMC7092803.
Dabisch-Ruthe M, Vollmer T, Adams O, Knabbe C, Dreier J. Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis. 2012;12:163. doi: 10.1186/1471-2334-12-163. PubMed PMID: 22828244; PMCID: PMC3519643.
Coronaviridae Study Group of the International Committee on Taxonomy of V. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020;5(4):536-44. doi: 10.1038/s41564-020-0695-z. PubMed PMID: 32123347; PMCID: PMC7095448.
Bi S, Qin E, Xu Z, Li W, Wang J, Hu Y, Liu Y, Duan S, Hu J, Han Y, Xu J, Li Y, Yi Y, Zhou Y, Lin W, Xu H, Li R, Zhang Z, Sun H, Zhu J, Yu M, Fan B, Wu Q, Lin W, Tang L, Yang B, Li G, Peng W, Li W, Jiang T, Deng Y, Liu B, Shi J, Deng Y, Wei W, Liu H, Tong Z, Zhang F, Zhang Y, Wang C, Li Y, Ye J, Gan Y, Ji J, Li X, Tian X, Lu F, Tan G, Yang R, Liu B, Liu S, Li S, Wang J, Wang J, Cao W, Yu J, Dong X, Yang H. Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04). Genomics Proteomics Bioinformatics. 2003;1(3):180-92. doi: 10.1016/s1672-0229(03)01023-4. PubMed PMID: 15629030; PMCID: PMC5172409.
Hu D, Zhu C, Ai L, He T, Wang Y, Ye F, Yang L, Ding C, Zhu X, Lv R, Zhu J, Hassan B, Feng Y, Tan W, Wang C. Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats. Emerg Microbes Infect. 2018;7(1):154. doi: 10.1038/s41426-018-0155-5. PubMed PMID: 30209269; PMCID: PMC6135831.
Chan JF, Yuan S, Kok KH, To KK, Chu H, Yang J, Xing F, Liu J, Yip CC, Poon RW, Tsoi HW, Lo SK, Chan KH, Poon VK, Chan WM, Ip JD, Cai JP, Cheng VC, Chen H, Hui CK, Yuen KY. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020;395(10223):514-23. doi: 10.1016/S0140-6736(20)30154-9. PubMed PMID: 31986261; PMCID: PMC7159286.
Rothe C, Schunk M, Sothmann P, Bretzel G, Froeschl G, Wallrauch C, Zimmer T, Thiel V, Janke C, Guggemos W, Seilmaier M, Drosten C, Vollmar P, Zwirglmaier K, Zange S, Wolfel R, Hoelscher M. Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany. N Engl J Med. 2020;382(10):970-1. doi: 10.1056/NEJMc2001468. PubMed PMID: 32003551; PMCID: PMC7120970.
Buckley C, Kirkpatrick DD, Qin A, Hernandez JC. 25 Days That Changed the World: How COVID-19 Slipped China’s Grasp. The New York Times. 2020 December 30, 2020.
Zhou F, Yu T, Du R, Fan G, Liu Y, Liu Z, Xiang J, Wang Y, Song B, Gu X, Guan L, Wei Y, Li H, Wu X, Xu J, Tu S, Zhang Y, Chen H, Cao B. Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study. Lancet. 2020;395(10229):1054-62. doi: 10.1016/S0140-6736(20)30566-3. PubMed PMID: 32171076; PMCID: PMC7270627.
Wolfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Muller MA, Niemeyer D, Jones TC, Vollmar P, Rothe C, Hoelscher M, Bleicker T, Brunink S, Schneider J, Ehmann R, Zwirglmaier K, Drosten C, Wendtner C. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020;581(7809):465-9. doi: 10.1038/s41586-020-2196-x. PubMed PMID: 32235945.
He X, Lau EHY, Wu P, Deng X, Wang J, Hao X, Lau YC, Wong JY, Guan Y, Tan X, Mo X, Chen Y, Liao B, Chen W, Hu F, Zhang Q, Zhong M, Wu Y, Zhao L, Zhang F, Cowling BJ, Li F, Leung GM. Author Correction: Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat Med. 2020;26(9):1491-3. doi: 10.1038/s41591-020-1016-z. PubMed PMID: 32770170; PMCID: PMC7413015.
To KK, Tsang OT, Leung WS, Tam AR, Wu TC, Lung DC, Yip CC, Cai JP, Chan JM, Chik TS, Lau DP, Choi CY, Chen LL, Chan WM, Chan KH, Ip JD, Ng AC, Poon RW, Luo CT, Cheng VC, Chan JF, Hung IF, Chen Z, Chen H, Yuen KY. Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis. 2020;20(5):565-74. doi: 10.1016/S1473-3099(20)30196-1. PubMed PMID: 32213337; PMCID: PMC7158907.
He X, Lau EHY, Wu P, Deng X, Wang J, Hao X, Lau YC, Wong JY, Guan Y, Tan X, Mo X, Chen Y, Liao B, Chen W, Hu F, Zhang Q, Zhong M, Wu Y, Zhao L, Zhang F, Cowling BJ, Li F, Leung GM. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat Med. 2020;26(5):672-5. doi: 10.1038/s41591-020-0869-5. PubMed PMID: 32296168.
Shrestha NK, Marco Canosa F, Nowacki AS, Procop GW, Vogel S, Fraser TG, Erzurum SC, Terpeluk P, Gordon SM. Distribution of Transmission Potential During Nonsevere COVID-19 Illness. Clin Infect Dis. 2020;71(11):2927-32. doi: 10.1093/cid/ciaa886. PubMed PMID: 32594116; PMCID: PMC7337652.
Dong Y, Mo X, Hu Y, Qi X, Jiang F, Jiang Z, Tong S. Epidemiology of COVID-19 Among Children in China. Pediatrics. 2020;145(6). doi: 10.1542/peds.2020-0702. PubMed PMID: 32179660.
Kim GU, Kim MJ, Ra SH, Lee J, Bae S, Jung J, Kim SH. Clinical characteristics of asymptomatic and symptomatic patients with mild COVID-19. Clin Microbiol Infect. 2020;26(7):948 e1- e3. doi: 10.1016/j.cmi.2020.04.040. PubMed PMID: 32360780; PMCID: PMC7252018.
Kasper MR, Geibe JR, Sears CL, Riegodedios AJ, Luse T, Von Thun AM, McGinnis MB, Olson N, Houskamp D, Fenequito R, Burgess TH, Armstrong AW, DeLong G, Hawkins RJ, Gillingham BL. An Outbreak of Covid-19 on an Aircraft Carrier. N Engl J Med. 2020;383(25):2417-26. doi: 10.1056/NEJMoa2019375. PubMed PMID: 33176077; PMCID: PMC7675688.
Yamagishi T, Kamiya H, Kakimoto K, Suzuki M, Wakita T. Descriptive study of COVID-19 outbreak among passengers and crew on Diamond Princess cruise ship, Yokohama Port, Japan, 20 January to 9 February 2020. Euro Surveill. 2020;25(23). doi: 10.2807/1560-7917.ES.2020.25.23.2000272. PubMed PMID: 32553062; PMCID: PMC7403638.
Hilton J, Keeling MJ. Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices. PLoS Comput Biol. 2020;16(7):e1008031. doi: 10.1371/journal.pcbi.1008031. PubMed PMID: 32614817; PMCID: PMC7363110.
Kucharski AJ, Funk S, Eggo RM. The COVID-19 response illustrates that traditional academic reward structures and metrics do not reflect crucial contributions to modern science. PLoS Biol. 2020;18(10):e3000913. doi: 10.1371/journal.pbio.3000913. PubMed PMID: 33064730; PMCID: PMC7592912.
Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, Ren R, Leung KSM, Lau EHY, Wong JY, Xing X, Xiang N, Wu Y, Li C, Chen Q, Li D, Liu T, Zhao J, Liu M, Tu W, Chen C, Jin L, Yang R, Wang Q, Zhou S, Wang R, Liu H, Luo Y, Liu Y, Shao G, Li H, Tao Z, Yang Y, Deng Z, Liu B, Ma Z, Zhang Y, Shi G, Lam TTY, Wu JT, Gao GF, Cowling BJ, Yang B, Leung GM, Feng Z. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. N Engl J Med. 2020;382(13):1199-207. doi: 10.1056/NEJMoa2001316. PubMed PMID: 31995857; PMCID: PMC7121484.
Riou J, Althaus CL. Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Euro Surveill. 2020;25(4). doi: 10.2807/1560-7917.ES.2020.25.4.2000058. PubMed PMID: 32019669; PMCID: PMC7001239.
Lambert SB, Whiley DM, O’Neill NT, Andrews EC, Canavan FM, Bletchly C, Siebert DJ, Sloots TP, Nissen MD. Comparing nose-throat swabs and nasopharyngeal aspirates collected from children with symptoms for respiratory virus identification using real-time polymerase chain reaction. Pediatrics. 2008;122(3):e615-20. doi: 10.1542/peds.2008-0691. PubMed PMID: 18725388.
Irving SA, Vandermause MF, Shay DK, Belongia EA. Comparison of nasal and nasopharyngeal swabs for influenza detection in adults. Clin Med Res. 2012;10(4):215-8. doi: 10.3121/cmr.2012.1084. PubMed PMID: 22723469; PMCID: PMC3494547.
Frazee BW, Rodriguez-Hoces de la Guardia A, Alter H, Chen CG, Fuentes EL, Holzer AK, Lolas M, Mitra D, Vohra J, Dekker CL. Accuracy and Discomfort of Different Types of Intranasal Specimen Collection Methods for Molecular Influenza Testing in Emergency Department Patients. Ann Emerg Med. 2018;71(4):509-17 e1. doi: 10.1016/j.annemergmed.2017.09.010. PubMed PMID: 29174837.
Centers for Disease Control and Prevention. Specimen Collection: Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19) Atlanta, GA2020 [cited 2020 Novemmber 22, 2020]. Available from: https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html.
Mallett S, Allen AJ, Graziadio S, Taylor SA, Sakai NS, Green K, Suklan J, Hyde C, Shinkins B, Zhelev Z, Peters J, Turner PJ, Roberts NW, di Ruffano LF, Wolff R, Whiting P, Winter A, Bhatnagar G, Nicholson BD, Halligan S. At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR-based tests? A systematic review of individual participant data. BMC Med. 2020;18(1):346. doi: 10.1186/s12916-020-01810-8. PubMed PMID: 33143712; PMCID: PMC7609379.
Trypsteen W, Van Cleemput J, Snippenberg WV, Gerlo S, Vandekerckhove L. On the whereabouts of SARS-CoV-2 in the human body: A systematic review. PLoS Pathog. 2020;16(10):e1009037. doi: 10.1371/journal.ppat.1009037. PubMed PMID: 33125439; PMCID: PMC7679000.
Venkatakrishnan AJ, Puranik A, Anand A, Zemmour D, Yao X, Wu X, Chilaka R, Murakowski DK, Standish K, Raghunathan B, Wagner T, Garcia-Rivera E, Solomon H, Garg A, Barve R, Anyanwu-Ofili A, Khan N, Soundararajan V. Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors. Elife. 2020;9. doi: 10.7554/eLife.58040. PubMed PMID: 32463365; PMCID: PMC7371427.
Zipeto D, Palmeira JDF, Arganaraz GA, Arganaraz ER. ACE2/ADAM17/TMPRSS2 Interplay May Be the Main Risk Factor for COVID-19. Front Immunol. 2020;11:576745. doi: 10.3389/fimmu.2020.576745. PubMed PMID: 33117379; PMCID: PMC7575774.
Cox JL, Koepsell SA. 3D-Printing to Address COVID-19 Testing Supply Shortages. Lab Med. 2020;51(4):e45-e6. doi: 10.1093/labmed/lmaa031. PubMed PMID: 32386057; PMCID: PMC7239181.
Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. N Engl J Med. 2020;383(13):1283-6. doi: 10.1056/NEJMc2016359. PubMed PMID: 32857487; PMCID: PMC7484747.
Chen JH, Yip CC, Poon RW, Chan KH, Cheng VC, Hung IF, Chan JF, Yuen KY, To KK. Evaluating the use of posterior oropharyngeal saliva in a point-of-care assay for the detection of SARS-CoV-2. Emerg Microbes Infect. 2020;9(1):1356-9. doi: 10.1080/22221751.2020.1775133. PubMed PMID: 32459137; PMCID: PMC7448919.
Fernández-Pittol M, Hurtado JC, Moreno-García E, Rubio E, Navarro M, Valiente M, Peiró A, Capón A, Seijas N, Martínez MJ, Casals-Pascual C, Vila J. Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19. bioRxiv. 2020. doi: 10.1101/2020.06.25.172734.
Procop GW, Shrestha NK, Vogel S, Van Sickle K, Harrington S, Rhoads DD, Rubin BP, Terpeluk P. A Direct Comparison of Enhanced Saliva to Nasopharyngeal Swab for the Detection of SARS-CoV-2 in Symptomatic Patients. J Clin Microbiol. 2020;58(11). doi: 10.1128/JCM.01946-20. PubMed PMID: 32883744; PMCID: PMC7587117.
Pasomsub E, Watcharananan SP, Boonyawat K, Janchompoo P, Wongtabtim G, Suksuwan W, Sungkanuparph S, Phuphuakrat A. Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study. Clin Microbiol Infect. 2021;27(2):285 e1-e4. doi: 10.1016/j.cmi.2020.05.001. PubMed PMID: 32422408; PMCID: PMC7227531.
Kojima N, Turner F, Slepnev V, Bacelar A, Deming L, Kodeboyina S, Klausner JD. Self-Collected Oral Fluid and Nasal Swab Specimens Demonstrate Comparable Sensitivity to Clinician-Collected Nasopharyngeal Swab Specimens for the Detection of SARS-CoV-2. Clin Infect Dis. 2020. doi: 10.1093/cid/ciaa1589. PubMed PMID: 33075138; PMCID: PMC7665422.
Yokota I, Shane PY, Okada K, Unoki Y, Yang Y, Inao T, Sakamaki K, Iwasaki S, Hayasaka K, Sugita J, Nishida M, Fujisawa S, Teshima T. Mass screening of asymptomatic persons for SARS-CoV-2 using saliva. Clin Infect Dis. 2020. doi: 10.1093/cid/ciaa1388. PubMed PMID: 32976596; PMCID: PMC7543374.
Ambrosi C, Prezioso C, Checconi P, Scribano D, Sarshar M, Capannari M, Tomino C, Fini M, Garaci E, Palamara AT, De Chiara G, Limongi D. SARS-CoV-2: Comparative analysis of different RNA extraction methods. J Virol Methods. 2021;287:114008. doi: 10.1016/j.jviromet.2020.114008. PubMed PMID: 33160015; PMCID: PMC7640895.
Tremeaux P, Lhomme S, Abravanel F, Raymond S, Mengelle C, Mansuy JM, Izopet J. Evaluation of the Aptima transcription-mediated amplification assay (Hologic(R)) for detecting SARS-CoV-2 in clinical specimens. J Clin Virol. 2020;129:104541. doi: 10.1016/j.jcv.2020.104541. PubMed PMID: 32659713; PMCID: PMC7336924.
Centers for Disease Control and Prevention. CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. Atlanta, GA2020.
Procop GW, Brock JE, Reineks EZ, Shrestha NK, Demkowicz R, Cook E, Ababneh E, Harrington SM. A Comparison of Five SARS-CoV-2 Molecular Assays With Clinical Correlations. Am J Clin Pathol. 2021;155(1):69-78. doi: 10.1093/ajcp/aqaa181. PubMed PMID: 33015712; PMCID: PMC7665304.
Smyrlaki I, Ekman M, Lentini A, Rufino de Sousa N, Papanicolaou N, Vondracek M, Aarum J, Safari H, Muradrasoli S, Rothfuchs AG, Albert J, Hogberg B, Reinius B. Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR. Nat Commun. 2020;11(1):4812. doi: 10.1038/s41467-020-18611-5. PubMed PMID: 32968075; PMCID: PMC7511968.
United States Food and Drug Administration. Emergency Use Authorization (EUA) Summary Covid-19 RT-PCR Test (Laboratory Corporation of America). Lab Corp; December 9, 2020.
United States Food and Drug Administration. SARS-CoV-2 Reference Panel Comparative Data. Silver Spring, MD2020.
Afzal A. Molecular diagnostic technologies for COVID-19: Limitations and challenges. J Adv Res. 2020;26:149-59. doi: 10.1016/j.jare.2020.08.002. PubMed PMID: 32837738; PMCID: PMC7406419.
CLSI, editor. Developing and Managing a Medical Laboratory (Test) Utilization Management Program. 1st ed. Wayne, PA: The Clinical and Laboratory Standards Institute; 2017.
Magleby R, Westblade LF, Trzebucki A, Simon MS, Rajan M, Park J, Goyal P, Safford MM, Satlin MJ. Impact of SARS-CoV-2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients with Coronavirus Disease 2019. Clin Infect Dis. 2020. doi: 10.1093/cid/ciaa851. PubMed PMID: 32603425; PMCID: PMC7337625.
Rao SN, Manissero D, Steele VR, Pareja J. A Narrative Systematic Review of the Clinical Utility of Cycle Threshold Values in the Context of COVID-19. Infectious Diseases and Therapy. 2020;9(3):573-86. doi: 10.6084/m9.figshare.12668408.
Salvatore PP, Dawson P, Wadhwa A, Rabold EM, Buono S, Dietrich EA, Reses HE, Vuong J, Pawloski L, Dasu T, Bhattacharyya S, Pevzner E, Hall AJ, Tate JE, Kirking HL. Epidemiological Correlates of PCR Cycle Threshold Values in the Detection of SARS-CoV-2. Clin Infect Dis. 2020. doi: 10.1093/cid/ciaa1469. PubMed PMID: 32986120; PMCID: PMC7543310.
Jaafar R, Aherfi S, Wurtz N, Grimaldier C, Hoang VT, Colson P, Raoult D, La Scola B. Correlation between 3790 qPCR positives samples and positive cell cultures including 1941 SARS-CoV-2 isolates. Clin Infect Dis. 2020. doi: 10.1093/cid/ciaa1491. PubMed PMID: 32986798; PMCID: PMC7543373.
Rhee C, Kanjilal S, Baker M, Klompas M. Duration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity: When Is It Safe to Discontinue Isolation? Clin Infect Dis. 2021;72(8):1467-74. doi: 10.1093/cid/ciaa1249. PubMed PMID: 33029620; PMCID: PMC7499497.
Centers for Disease Control and Prevention. Coronavirus Disease 2019 (COVID-19): Overview of Testing for SARS-CoV-2 (COVID-19) Atlanta, GA2020 [December 7, 2020]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/hcp/testing-overview.html.
van Dorp L, Richard D, Tan CCS, Shaw LP, Acman M, Balloux F. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nat Commun. 2020;11(1):5986. doi: 10.1038/s41467-020-19818-2. PubMed PMID: 33239633; PMCID: PMC7688939.
Chowdhury J, Scarr S, Wardell J. How the novel coronavirus has evolved2020 12/12/2020. Available from: https://graphics.reuters.com/HEALTH-CORONAVIRUS/EVOLUTION/yxmpjqkdzvr/.
Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, Seattle Flu Study I, Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Muller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. Cryptic transmission of SARS-CoV-2 in Washington state. Science. 2020;370(6516):571-5. doi: 10.1126/science.abc0523. PubMed PMID: 32913002; PMCID: PMC7810035.
Team CC-R, Jorden MA, Rudman SL, Villarino E, Hoferka S, Patel MT, Bemis K, Simmons CR, Jespersen M, Iberg Johnson J, Mytty E, Arends KD, Henderson JJ, Mathes RW, Weng CX, Duchin J, Lenahan J, Close N, Bedford T, Boeckh M, Chu HY, Englund JA, Famulare M, Nickerson DA, Rieder MJ, Shendure J, Starita LM. Evidence for Limited Early Spread of COVID-19 Within the United States, January-February 2020. MMWR Morb Mortal Wkly Rep. 2020;69(22):680-4. doi: 10.15585/mmwr.mm6922e1. PubMed PMID: 32497028; PMCID: PMC7315848
Zhang L, Jackson CB, Mou H, Ojha A, Peng H, Quinlan BD, Rangarajan ES, Pan A, Vanderheiden A, Suthar MS, Li W, Izard T, Rader C, Farzan M, Choe H. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun. 2020;11(1):6013. doi: 10.1038/s41467-020-19808-4. PubMed PMID: 33243994; PMCID: PMC7693302.
Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH, 3rd, Leist SR, Schafer A, Nakajima N, Takahashi K, Lee RE, Mascenik TM, Graham R, Edwards CE, Tse LV, Okuda K, Markmann AJ, Bartelt L, de Silva A, Margolis DM, Boucher RC, Randell SH, Suzuki T, Gralinski LE, Kawaoka Y, Baric RS. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science. 2020;370(6523):1464-8. doi: 10.1126/science.abe8499. PubMed PMID: 33184236; PMCID: PMC7775736.
Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2021;592(7852):116-21. doi: 10.1038/s41586-020-2895-3. PubMed PMID: 33106671.
Al Khatib HA, Benslimane FM, Elbashir IE, Coyle PV, Al Maslamani MA, Al-Khal A, Al Thani AA, Yassine HM. Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities. Front Cell Infect Microbiol. 2020;10:575613. doi: 10.3389/fcimb.2020.575613. PubMed PMID: 33123498; PMCID: PMC7572854.
Bedford T, Hodcroft EB, Neher RA. Neher TBaRA, editor2021. [cited 2021]. Available from: https://nextstrain.org/blog/2021-01-06-updated-SARS-CoV-2-clade-naming.
Wang R, Hozumi Y, Yin C, Wei GW. Mutations on COVID-19 diagnostic targets. Genomics. 2020;112(6):5204-13. doi: 10.1016/j.ygeno.2020.09.028. PubMed PMID: 32966857; PMCID: PMC7502284.
Osorio NS, Correia-Neves M. Implication of SARS-CoV-2 evolution in the sensitivity of RT-qPCR diagnostic assays. Lancet Infect Dis. 2021;21(2):166-7. doi: 10.1016/S1473-3099(20)30435-7. PubMed PMID: 32473662; PMCID: PMC7255733.
Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020;18(1):179. doi: 10.1186/s12967-020-02344-6. PubMed PMID: 32321524; PMCID: PMC7174922.
Brown KA, Gubbay J, Hopkins J, Patel S, Buchan SA, Daneman N, Goneau LW. S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021. JAMA. 2021. doi: 10.1001/jama.2021.5607. PubMed PMID: 33830171.
Artesi M, Bontems S, Gobbels P, Franckh M, Maes P, Boreux R, Meex C, Melin P, Hayette MP, Bours V, Durkin K. A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay. J Clin Microbiol. 2020;58(10). doi: 10.1128/JCM.01598-20. PubMed PMID: 32690547; PMCID: PMC7512182.
Hasan MR, Sundararaju S, Manickam C, Mirza F, Al-Hail H, Lorenz S, Tang P. A Novel Point Mutation in the N Gene of SARS-CoV-2 May Affect the Detection of the Virus by Reverse Transcription-Quantitative PCR. J Clin Microbiol. 2021;59(4). doi: 10.1128/JCM.03278-20. PubMed PMID: 33472904.
United States Food and Drug Administration. SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests. Silver Spring, MD2021.
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, Sheffield C-GG, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell. 2020;182(4):812-27 e19. doi: 10.1016/j.cell.2020.06.043. PubMed PMID: 32697968; PMCID: PMC7332439.
Baric RS. Emergence of a Highly Fit SARS-CoV-2 Variant. N Engl J Med. 2020;383(27):2684-6. doi: 10.1056/NEJMcibr2032888. PubMed PMID: 33326716.
McAuley AJ, Kuiper MJ, Durr PA, Bruce MP, Barr J, Todd S, Au GG, Blasdell K, Tachedjian M, Lowther S, Marsh GA, Edwards S, Poole T, Layton R, Riddell SJ, Drew TW, Druce JD, Smith TRF, Broderick KE, Vasan SS. Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. NPJ Vaccines. 2020;5:96. doi: 10.1038/s41541-020-00246-8. PubMed PMID: 33083031; PMCID: PMC7546614.
Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, Schaefer-Babajew D, Cipolla M, Gaebler C, Lieberman JA, Oliveira TY, Yang Z, Abernathy ME, Huey-Tubman KE, Hurley A, Turroja M, West KA, Gordon K, Millard KG, Ramos V, Da Silva J, Xu J, Colbert RA, Patel R, Dizon J, Unson-O’Brien C, Shimeliovich I, Gazumyan A, Caskey M, Bjorkman PJ, Casellas R, Hatziioannou T, Bieniasz PD, Nussenzweig MC. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. bioRxiv. 2021. doi: 10.1101/2021.01.15.426911. PubMed PMID: 33501451; PMCID: PMC7836122.
Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE, Jr., Bloom JD. Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host Microbe. 2021;29(1):44-57 e9. doi: 10.1016/j.chom.2020.11.007. PubMed PMID: 33259788; PMCID: PMC7676316.
Centers for Disease Control and Prevention. COVID Data Tracker: Variant Proportions. Atlanta, GA2021. Available from: https://covid.cdc.gov/covid-data-tracker/#datatracker-home
Procop GW. On Antigen Testing for COVID-19. ASCP News [Internet]. 2020. Available from: https://www.ascp.org/content/news-archive/news-detail/2020/11/11/on-antigen-testing-for-covid-19.
Cohen JF, Bertille N, Cohen R, Chalumeau M. Rapid antigen detection test for group A streptococcus in children with pharyngitis. Cochrane Database Syst Rev. 2016;7:CD010502. doi: 10.1002/14651858.CD010502.pub2. PubMed PMID: 27374000; PMCID: PMC6457926.
Jang JW, Cho CH, Nam MH, Yoon SY, Lee CK, Lim CS, Kim WJ. Clinical performance evaluation of the Sofia RSV FIA rapid antigen test for diagnosis of respiratory syncytial virus infection. J Clin Microbiol. 2015;53(2):684-6. doi: 10.1128/JCM.03324-14. PubMed PMID: 25428155; PMCID: PMC4298519.
Centers for Disease Control and Prevention. Interim Guidance for Antigen Testing for SARS-CoV-2. Atlanta, GA2020. Available from: Centers for Disease Control and Prevention. Interim Guidance for Antigen Testing for SARS-CoV-2. Atlanta, GA2020
Boobalan J, Dinesha TR, Gomathi S, Elakkiya E, Pradeep A, Chitra D, Murugave KG, Balakrishnan P, Shantha S, Solomon SS, Kumarasamy N, Smith DM, Saravanan S. Pooled nucleic acid testing strategy for monitoring HIV-1 treatment in resource limited settings. J Clin Virol. 2019;117:56-60. doi: 10.1016/j.jcv.2019.05.012. PubMed PMID: 31212189.
Dinesha TR, Boobalan J, Sivamalar S, Subashini D, Solomon SS, Murugavel KG, Balakrishnan P, Smith DM, Saravanan S. Occult HBV infection in HIV-infected adults and evaluation of pooled NAT for HBV. J Viral Hepat. 2018;25(6):718-23. doi: 10.1111/jvh.12858. PubMed PMID: 29316078; PMCID: PMC5980682.
Rohde R. COVID-19 Pool Testing: Is It Time to Jump In? ASM News. 2020;2020(December 5, 22020). Epub July 20, 2020.
Procop GW, Tuohy M, Ramsey C, Rhoads DD, Rubin BP, Figler R. Asymptomatic Patient Testing After 10:1 Pooling Using the Xpert Xpress SARS-CoV-2 Assay. Am J Clin Pathol. 2021;155(4):522-6. doi: 10.1093/ajcp/aqaa273. PubMed PMID: 33399200; PMCID: PMC7929460.