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• W4385514174 abstract "Journal of Medical VirologyVolume 95, Issue 8 e29002 LETTER TO THE EDITOR Deciphering the evolutionary mechanisms of SARS-CoV-2: Absence of ORF8 protein and its potential advantage in the emergence of viral lineages Lauro Velazquez-Salinas, Corresponding Author Lauro Velazquez-Salinas [email protected] Plum Island Animal Disease Center, Agricultural Research Service, USDA, Greenport, New York, USA Correspondence Lauro Velazquez-Salinas, Plum Island Animal Disease Center, Agricultural Research Service, USDA, Greenport, NY 11944, USA. Email: [email protected]Search for more papers by this author Lauro Velazquez-Salinas, Corresponding Author Lauro Velazquez-Salinas [email protected] Plum Island Animal Disease Center, Agricultural Research Service, USDA, Greenport, New York, USA Correspondence Lauro Velazquez-Salinas, Plum Island Animal Disease Center, Agricultural Research Service, USDA, Greenport, NY 11944, USA. Email: [email protected]Search for more papers by this author First published: 03 August 2023 https://doi.org/10.1002/jmv.29002Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat REFERENCES 1Maxmen A. One million coronavirus sequences: popular genome site hits mega milestone. Nature. 2021; 593: 21. 2Mavian C, Marini S, Prosperi M, Salemi M. Authors' reply to: Errors in tracing coronavirus SARS-CoV-2 transmission using a maximum likelihood tree. Comment on “A snapshot of SARS-CoV-2 genome availability up to April 2020 and its implications: Data analysis.” JMIR Public Health Surveill. 2020; 6:24661. 3Tegally H, Moir M, Everatt J, et al. Emergence of SARS-CoV-2 omicron lineages BA.4 and BA.5 in South Africa. Nature Med. 2022; 28: 1785-1790. 4O'Toole Á, Pybus OG, Abram ME, Kelly EJ, Rambaut A. Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. BMC Genomics. 2022; 23: 121. 5Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol. 2015; 32: 1342-1353. 6Murrell B, Weaver S, Smith MD, et al. Gene-wide identification of episodic selection. Mol Biol Evol. 2015; 32: 1365-1371. 7Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 2012; 8:e1002764. 8Khare S, Gurry C, Freitas L, et al. GISAID's role in pandemic response. China CDC Weekly. 2021; 3: 1049-1051. 9Weaver S, Shank SD, Spielman SJ, Li M, Muse SV, Kosakovsky Pond SL. Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Mol Biol Evol. 2018; 35: 773-777. 10Zhang Y, Zhang T, Fang Y, Liu J, Ye Q, Ding L. SARS-CoV-2 spike L452R mutation increases omicron variant fusogenicity and infectivity as well as host glycolysis. Signal Transduct Target Ther. 2022; 7: 76. 11Liu L, Iketani S, Guo Y, et al. Striking antibody evasion manifested by the omicron variant of SARS-CoV-2. Nature. 2022; 602: 676-681. 12Liu Y, Liu J, Plante KS, et al. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature. 2022; 602: 294-299. 13Oulas A, Zanti M, Tomazou M, et al. Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. PLoS One. 2021; 16:e0238665. 14Benvenuto D, Angeletti S, Giovanetti M, et al. Evolutionary analysis of SARS-CoV-2: how mutation of non-structural protein 6 (NSP6) could affect viral autophagy. J Infect. 2020; 81: e24-e27. 15Velazquez-Salinas L, Zarate S, Eberl S, Gladue DP, Novella I, Borca MV. Positive selection of ORF1ab, ORF3a, and ORF8 genes drives the early evolutionary trends of SARS-CoV-2 during the 2020 COVID-19 pandemic. Front Microbiol. 2020; 11:550674. 16Martin DP, Weaver S, Tegally H, et al. The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell. 2021; 184: 5189-5200. 17Velazquez-Salinas L. The complex evolutionary dynamics of SARS-CoV-2, a big challenge to control the pandemic of COVID-19. J Med Virol. 2022; 94: 5082-5085. 18Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol. 2015; 32: 820-832. 19Hachmann NP, Miller J, Collier AY, Barouch DH. Neutralization escape by SARS-CoV-2 omicron subvariant BA.4.6. N Engl J Med. 2022; 387: 1904-1906. 20Wang R, Chen J, Wei GW. Mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. J Phys Chem Lett. 2021; 12: 11850-11857. 21Colson P, Gautret P, Delerce J, et al. The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule. J Med Virol. 2023; 95(1):e28102. doi:10.1002/jmv.28102 22Hachim A, Kavian N, Cohen CA, et al. ORF8 and ORF3b antibodies are accurate serological markers of early and late SARS-CoV-2 infection. Nat Immunol. 2020; 21: 1293-1301. 23Kosakovsky Pond SL, Frost SDW. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 2005; 22: 1208-1222. 24Silvas JA, Vasquez DM, Park JG, et al. Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 human ACE2 transgenic mice. J Virol. 2021; 95:e0040221. 25Li JY, Liao CH, Wang Q, et al. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 2020; 286:198074. 26Moody R, Wilson KL, Boer JC, et al. Predicted B cell epitopes highlight the potential for COVID-19 to drive self-reactive immunity. Front Bioinform. 2021; 1:709533. Volume95, Issue8August 2023e29002 ReferencesRelatedInformation" @default.
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