SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays

References

• Centers for Disease Control and Prevention [homepage on the Internet]. COVID-19: SARS-CoV-2 variant classifications and definitions. Available from:https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html. Accessed August 6, 2021.
   Google Scholar
• U.S Food and Drug Administration [homepage on the Internet]. SARS-CoV-2 viral mutations: impact on COVID-19 tests 2021. Available from: https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests. Accessed August 6, 2021.
   Google Scholar
• Korber B, Fischer WM, Gnanakaran S, et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell. 2020;182(4):812–827.e19. doi:10.1016/j.cell.2020.06.04332697968
   PubMed Web of Science ®Google Scholar
• Paul P, France AM, Aoki Y, et al. Genomic surveillance for SARS-CoV-2 variants circulating in the United States, December 2020–May 2021. MMWR Morb Mortal Wkly Rep. 2021;70:846–850. doi:10.15585/mmwr.mm7023a334111060
   PubMed Web of Science ®Google Scholar
• Lind A, Barlinn R, Landaas ET, et al. Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory. J Clin Virol. 2021;141:104906. doi:10.1016/j.jcv.2021.10490634273860
   PubMed Web of Science ®Google Scholar
• TaqManTM SARS-CoV-2 mutation panel user guide (package insert). Publication number MAN0024768, 2021.
   Google Scholar
• Université de Genève and Hôpitaux Universitaires de Genève. Protocol for specific RT-PCRs for marker regions of the spike region indicative of the UK SARS-CoV-2 variant B.1.1.7 and the South African variant 501Y.V2 2021. Available from: https://www.hug.ch/sites/interhug/files/structures/laboratoire_de_virologie/protocol_amplification_voc_20201201_uk_geneva.pdf. Accessed October 14, 2021.
   Google Scholar
• Gulay K, Kolukirik M, Bayrakdar F, et al. 40 minutes RT-qPCR assay for screening spike N501Y and HV69-70del mutations 2021. Available from: https://www.biorxiv.org/content/10.1101/2021.01.26.428302v1.full.pdf. Accessed October 14, 2021.
   Google Scholar
• Vogels CBF AT, Breban M, Fauver JR, et al. Multiplexed RT-qPCR to screen for SARS-COV-2 B.1.1.7 variants: preliminary results 2021. Available from: https://virological.org/t/multiplexed-rt-qpcr-to-screen-for-sars-cov-2-b-1-1-7-variants-preliminary-results/588. Accessed October 14, 2021.
   Google Scholar
• Public Health England. SARS-CoV-2 lateral flow antigen tests: evaluation of VUI-202012/01 2020. [homepage on the internet]. Available from: https://www.gov.uk/government/publications/sars-cov-2-lateral-flow-antigen-tests-evaluation-of-vui-20201201/sars-cov-2-lateral-flow-antigen-tests-evaluation-of-vui-20201201. Accessed October 14, 2021.
   Google Scholar
• Hirotsu Y, Omata M. Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/ E484K/G769V mutations in Japan. PLoS Pathog. 2021;17(6):e1009619. doi:10.1371/journal.ppat.100961934097716
   PubMed Web of Science ®Google Scholar
• Zhao S, Ran J, Han L. Exploring the interaction between E484K and N501Y substitutions of SARS-CoV-2 in shaping the transmission advantage of COVID-19 in Brazil: a Modeling Study. Am J Trop Med Hyg. 2021;tpmd210412. doi:10.4269/ajtmh.21-041234583340
   PubMed Web of Science ®Google Scholar
• Barton MI, MacGowan SA, Kutuzov MA, Dushek O, Barton GJ, van der Merwe PA. Effects of common mutations in the SARS-CoV-2 spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Elife. 2021;10:e70658. PMID: 34435953. doi:10.7554/eLife.7065834435953
   PubMed Web of Science ®Google Scholar
• Hu J, Li C, Wang S, Li T, Zhang H. Genetic variants are identified to increase risk of COVID-19 related mortality from UK biobank data. medRxiv. 2020:20226761. PMID: 33200144. doi:10.1101/2020.11.05.20226761
   Google Scholar
• Pivonello R, Auriemma RS, Pivonello C, et al. Sex disparities in COVID-19 severity and outcome: are men weaker or women stronger? Neuroendocrinology. 2020:1–20. PMID: 33242856. doi:10.1159/000513346
   Web of Science ®Google Scholar
• Yanez ND, Weiss NS, Romand JA, Treggiari MM. COVID-19 mortality risk for older men and women. BMC Public Health. 2020;20(1):1742. PMID: 33213391. doi:10.1186/s12889-020-09826-833213391
   PubMed Web of Science ®Google Scholar
• Pinto BGG, Oliveira AER, Singh Y, et al. ACE2 expression is increased in the lungs of patients with comorbidities associated with severe COVID-19. J Infect Dis. 2020;222(4):556–563. doi:10.1093/infdis/jiaa33232526012
   PubMed Web of Science ®Google Scholar
• Isabel S, Graña-Miraglia L, Gutierrez JM, et al. Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Sci Rep. 2020;10(1):14031. PMID: 32820179. doi:10.1038/s41598-020-70827z32820179
   PubMed Web of Science ®Google Scholar
• Hodcroft EB, Zuber M, Nadeau S, et al. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. 2021;595(7869):707–712. doi:10.1038/s41586-021-03677-y34098568
   PubMed Web of Science ®Google Scholar
• Edmunds WJ, Jewell NP, Diaz-Ordaz K, Keogh RH. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Davies NG, Jarvis CI; CMMID COVID-19 Working Group. Nature. 2021;593(7858):270–274. PMID: 33723411. doi:10.1038/s41586-021-03426-133723411
   PubMed Web of Science ®Google Scholar
• Winger A, Thomas C. The spike of concern—the novel variants of SARS-CoV-2. Viruses. 2021;13(6):1002. doi:10.3390/v1306100234071984
   PubMed Web of Science ®Google Scholar
• Centers for disease control and prevention [homepage on the internet]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variantproportions.html:VariantProportions. Accessed October 14, 2021.
   Google Scholar
• Peng K, Wang Q, Yin Y, et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over alpha variant. mSystems. 2021:e0070221. PMID: 34609171. doi:10.1128/mSystems.00702-2134609171
   PubMed Web of Science ®Google Scholar
• Li B, Deng A, Li K, et al. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. medRxiv. 2021. doi:10.1101/2021.07.07.21260122
   Google Scholar
• Latif AA, Julia L, Mulle LJ, et al. And the center for viral systems biology. “B.1.1.7 lineage report.” outbreak.info. Available from: https://outbreak.info/situation-reports?pango=B.1.1.7&loc=GBR&loc=USA&loc=USA_US-CA&selected=GBR). Accessed October 14, 2021.
   Google Scholar
• Sheikh A, McMenamin J, Taylor B, et al. SARS-CoV-2 delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. Lancet. 2021;397(10293):2461–2462. doi:10.1016/S0140-6736(21)01358-134139198
   PubMed Web of Science ®Google Scholar
• Davies NG, Klepac P, Liu Y, et al; CMMID COVID-19 working group. Age-dependent effects in the transmission and control of COVID-19 epidemics. Nat Med. 2020;26(8):1205–1211. doi:10.1038/s41591-020-0962-932546824
   PubMed Web of Science ®Google Scholar
• Goldstein E, Lipsitch M, Cevik M. On the effect of age on the transmission of SARS-CoV-2 in households, schools, and the community. J Infect Dis. 2021;223(3):362–369. doi:10.1093/infdis/jiaa69133119738
   PubMed Web of Science ®Google Scholar
• Fishman DN, Tuite AR. Age-specific changes in virulence associated with SARS-C0V-2 variants of concern. medRxiv. 2021;09:25.21264097. doi:10.1101/2021.09.25.21264097
   Google Scholar
• Mwenda M, Saasa N, Sinyange N, et al. Detection of B.1.351 SARS-CoV-2 variant strain - Zambia, December 2020. MMWR Morb Mortal Wkly Rep. 2021;70(8):280–282. doi:10.15585/mmwr.mm7008e233630820
   PubMed Web of Science ®Google Scholar
• Fujino T, Nomoto H, Kutsuna S, et al. Novel SARS-CoV-2 variant identified in travelers from Brazil to Japan. Emerg Infect Dis. 2021. doi:10.3201/eid2704.210138
   Web of Science ®Google Scholar
• Ho D, Wang P, Liu L, et al. Increased resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 to antibody neutralization. Res Sq. 2021:rs.3.rs–155394. PMID: 33532763. doi:10.21203/rs.3.rs-155394/v1
   Google Scholar
• Wang P, Casner RG, Nair MS, et al. Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. bioRxiv. 2021:433466. PMID: 33688656. doi:10.1101/2021.03.01.433466
   Google Scholar
• Deng X, Garcia-Knight MA, Khalid MM, et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell. 2021;184(13):3426–3437.e8. PMID: 33991487. doi:10.1016/j.cell.2021.04.02533991487
   PubMed Web of Science ®Google Scholar
• Maxmen A. Why US coronavirus tracking can’t keep up with concerning variants. Nature. 2021;592(7854):336–337. doi:10.1038/d41586-021-00908-033828280
   PubMed Web of Science ®Google Scholar
• Washington NL, Gangavarapu K, Zeller M, et al. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Cell. 2021;184(10):2587–2594.e7. doi:10.1016/j.cell.2021.03.05233861950
   PubMed Web of Science ®Google Scholar