Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24(6):490–502.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo PCY, Lau SKP, Lam CSF, Lau CCY, Tsang AKL, Lau JHN, et al. Discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol. 2012;86(7):3995–4008.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cui J, Li F, Shi Z-L. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17(3):181–92.
Article
CAS
PubMed
Google Scholar
Lin C-M, Saif LJ, Marthaler D, Wang Q. Evolution, antigenicity and pathogenicity of global porcine epidemic diarrhea virus strains. Virus Res. 2016;226:20–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou P, Fan H, Lan T, Yang X-L, Shi W-F, Zhang W, et al. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature. 2018;556(7700):255–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
MacLachlan NJ, Dubovi EJ. Coronaviridae. In: Maclachlan NJ, Dubovi EJ, editors. Fenner’s veterinary virology. Elsevier; 2017. p. 435–61.
Google Scholar
Chen B, Tian E-K, He B, Tian L, Han R, Wang S, et al. Overview of lethal human coronaviruses. Sig Transduct Target Ther. 2020;5(1):89.
Article
CAS
Google Scholar
van der Hoek L. Human coronaviruses: what do they cause? Antivir Ther (Lond). 2007;12(4 Pt B):651–8.
Google Scholar
Chan-Yeung M, Xu R-H. SARS: epidemiology. Respirology. 2003;8(s1):S9-14.
Article
PubMed
PubMed Central
Google Scholar
Memish ZA, Perlman S, Van Kerkhove MD, Zumla A. Middle East respiratory syndrome. Lancet. 2020;395(10229):1063–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
ArcGIS. . COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU). Johns Hopkins University; 2020.
Google Scholar
Lim Y, Ng Y, Tam J, Liu D. Human coronaviruses: a review of virus–host interactions. Diseases. 2016;4(4):26.
Article
PubMed Central
CAS
Google Scholar
Touma M. COVID-19: molecular diagnostics overview. J Mol Med. 2020;98(7):947–54.
Article
CAS
PubMed
Google Scholar
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
European Centre for Disease Prevention and Control. MERS-CoV worldwide overview. ECDC; 2021.
Google Scholar
Mehand MS, Al-Shorbaji F, Millett P, Murgue B. The WHO R&D Blueprint: 2018 review of emerging infectious diseases requiring urgent research and development efforts. Antivir Res. 2018;159:63–7.
Article
CAS
PubMed
Google Scholar
Alshukairi AN, Zheng J, Zhao J, Nehdi A, Baharoon SA, Layqah L, et al. High prevalence of MERS-CoV infection in camel workers in Saudi Arabia. MBio. 2018;9(5):e01985-e2018.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li X, Song Y, Wong G, Cui J. Bat origin of a new human coronavirus: there and back again. Sci China Life Sci. 2020;63(3):461–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Frieman M, Baric R. Mechanisms of severe acute respiratory syndrome pathogenesis and innate immunomodulation. MMBR. 2008;72(4):672–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tao Y, Shi M, Chommanard C, Queen K, Zhang J, Markotter W, et al. Surveillance of bat coronaviruses in Kenya identifies relatives of human coronaviruses NL63 and 229E and their recombination history. J Virol. 2017;91(5):e01953-e2016.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pfefferle S, Oppong S, Drexler JF, Gloza-Rausch F, Ipsen A, Seebens A, et al. Distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus 229E in bats. Ghana Emerg Infect Dis. 2009;15(9):1377–84.
Article
PubMed
Google Scholar
Vijaykrishna D, Smith GJD, Zhang JX, Peiris JSM, Chen H, Guan Y. Evolutionary insights into the ecology of coronaviruses. J Virol. 2007;81(8):4012–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Adney DR, Bielefeldt-Ohmann H, Hartwig AE, Bowen RA. Infection, replication, and transmission of middle east respiratory syndrome coronavirus in alpacas. Emerg Infect Dis J. 2016;22(6):1031–7.
Article
CAS
Google Scholar
Munster VJ, Adney DR, van Doremalen N, Brown VR, Miazgowicz KL, Milne-Price S, et al. Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis). Sci Rep. 2016;6(1):21878.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mohd HA, Al-Tawfiq JA, Memish ZA. Middle east respiratory syndrome coronavirus (MERS-CoV) origin and animal reservoir. Virol J. 2016;13(1):87.
Article
PubMed
PubMed Central
CAS
Google Scholar
Alraddadi BM, Watson JT, Almarashi A, Abedi GR, Turkistani A, Sadran M, et al. Risk factors for primary middle east respiratory syndrome coronavirus illness in humans, Saudi Arabia. Emerg Infect Dis. 2016;22(1):49–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Farag E, Sikkema RS, Mohamedani AA, de Bruin E, Munnink BBO, Chandler F, et al. MERS-CoV in camels but not camel handlers, Sudan, 2015 and 2017. Emerg Infect Dis J. 2019;25(12):2333–5.
Article
CAS
Google Scholar
Reusken C, Ababneh M, Raj V, Meyer B, Eljarah A, Abutarbush S, et al. Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013. Eurosurveillance. 2013;18(50):20662.
Article
CAS
PubMed
Google Scholar
Ralph R, Lew J, Zeng T, Francis M, Xue B, Roux M, et al. 2019-nCoV (Wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness. J Infect Dev Ctries. 2020;14(1):3–17.
Article
CAS
PubMed
Google Scholar
Banerjee A, Kulcsar K, Misra V, Frieman M, Mossman K. Bats and coronaviruses. Viruses. 2019;11(1):41.
Article
PubMed Central
CAS
Google Scholar
Menachery VD, Yount BL Jr, Debbink K, Agnihothram S, Gralinski LE, Plante JA, et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med. 2015;21:1508–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antivir Res. 2020;176:104742.
Article
CAS
PubMed
Google Scholar
Zhou H, Chen X, Hu T, Li J, Song H, Liu Y, et al. A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19. bioRxiv. 2020. https://doi.org/10.1101/2020.03.02.974139.
Article
PubMed
PubMed Central
Google Scholar
Zhang Y-Z, Holmes EC. A genomic perspective on the origin and emergence of SARS-CoV-2. Cell. 2020;181(2):223–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Day T, Gandon S, Lion S, Otto SP. On the evolutionary epidemiology of SARS-CoV-2. Curr Biol. 2020;30(15):R849–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020;26:1–3.
Article
CAS
Google Scholar
Wong MC, Cregeen SJJ, Ajami NJ, Petrosino JF. Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019. bioRxiv. 2020. https://doi.org/10.1101/2020.02.07.939207.
Article
PubMed
PubMed Central
Google Scholar
Wacharapluesadee S, Tan CW, Maneeorn P, Duengkae P, Zhu F, Joyjinda Y, et al. Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nat Commun. 2021;12(1):972.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lam TT-Y, Jia N, Zhang Y-W, Shum MH-H, Jiang J-F, Zhu H-C, et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature. 2020;583(7815):282–5.
Article
CAS
PubMed
Google Scholar
Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou J-J, et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature. 2020;583(7815):286–9.
Article
CAS
PubMed
Google Scholar
Wrobel AG, Benton DJ, Xu P, Borg A, Roustan C, Martin SR, et al. Structure and binding properties of Pangolin-CoV Spike glycoprotein inform the evolution of SARS-CoV-2. Nat Commun. 2020;12:837.
Article
CAS
Google Scholar
Lehmann D, Halbwax ML, Makaga L, Whytock R, Ndindiwe Malata L, Bombenda Mouele W, et al. Pangolins and bats living together in underground burrows in Lopé National Park, Gabon. Afr J Ecol. 2020;58(3):540–2.
Article
Google Scholar
Liu P, Jiang J-Z, Wan X-F, Hua Y, Li L, Zhou J, et al. Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? PLoS Pathog. 2020;16(5):e1008421.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao X, Ding Y, Du J, Fan Y. 2020 update on human coronaviruses: one health, one world. Med Nov Technol Devices. 2020;8:100043.
Article
PubMed
PubMed Central
Google Scholar
Zhao J, Cui W, Tian B. The potential intermediate hosts for SARS-CoV-2. Front Microbiol. 2020;11:580137. https://doi.org/10.3389/fmicb.2020.580137/full.
Article
PubMed
PubMed Central
Google Scholar
Novaes Rocha V. Viral replication of SARS-CoV-2 could be self-limitative—the role of the renin-angiotensin system on COVID-19 pathophysiology. Med Hypotheses. 2020;145:110330.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krieg AM. The role of CpG motifs in innate immunity. Curr Opin Immunol. 2000;12(1):35–43.
Article
CAS
PubMed
Google Scholar
Alnazawi M, Altaher A, Kandeel M. Comparative genomic analysis MERS CoV isolated from humans and camels with special reference to virus encoded helicase. Biol Pharm Bull. 2017;40(8):1289–98.
Article
CAS
PubMed
Google Scholar
Lin X-D, Wang W, Hao Z-Y, Wang Z-X, Guo W-P, Guan X-Q, et al. Extensive diversity of coronaviruses in bats from China. Virology. 2017;507:1–10.
Article
CAS
PubMed
Google Scholar
Yang X-L, Hu B, Wang B, Wang M-N, Zhang Q, Zhang W, et al. Isolation and characterization of a novel bat coronavirus closely related to the direct progenitor of severe acute respiratory syndrome coronavirus. J Virol. 2016;90(6):3253–6.
Article
CAS
PubMed Central
Google Scholar
Ge X-Y, Li J-L, Yang X-L, Chmura AA, Zhu G, Epstein JH, et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503(7477):535–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Becker DJ, Albery GF, Sjodin AR, Poisot T, Dallas TA, Eskew EA, et al. Predicting wildlife hosts of betacoronaviruses for SARS-CoV-2 sampling prioritization. Ecology. 2020. https://doi.org/10.1101/2020.05.22.111344.
Article
Google Scholar
Corman VM, Eckerle I, Memish ZA, Liljander AM, Dijkman R, Jonsdottir H, et al. Link of a ubiquitous human coronavirus to dromedary camels. PNAS. 2016;113(35):9864–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Crossley BM, Mock RE, Callison SA, Hietala SK. Identification and characterization of a novel alpaca respiratory coronavirus most closely related to the human coronavirus 229E. Viruses. 2012;4(12):3689–700.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perveen N, Muzaffar SB, Al-Deeb MA. Exploring human–animal host interactions and emergence of COVID-19: evolutionary and ecological dynamics. Saudi J Biol Sci. 2021;28(2):1417–25.
Article
CAS
PubMed
Google Scholar
Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. PNAS. 2020;117(26):15193–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Banerjee A, Doxey AC, Mossman K, Irving AT. Unraveling the zoonotic origin and transmission of SARS-CoV-2. Trends Ecol Evol. 2020;36:180–4.
Article
PubMed
PubMed Central
Google Scholar
Sabir JSM, Lam TT-Y, Ahmed MMM, Li L, Shen Y, Abo-Aba SEM, et al. Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia. Science. 2016;351(6268):81–4.
Article
CAS
PubMed
Google Scholar
Corman VM, Muth D, Niemeyer D, Drosten C. Hosts and sources of endemic human coronaviruses. Adv Virus Res. 2018;100:163–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rest JS, Mindell DP. SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. Infect Genet Evol. 2003;3(3):219–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolles M, Donaldson E, Baric R. SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission. Curr Opin Virol. 2011;1(6):624–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lorusso A, Desario C, Mari V, Campolo M, Lorusso E, Elia G, et al. Molecular characterization of a canine respiratory coronavirus strain detected in Italy. Virus Res. 2009;141(1):96–100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alekseev KP, Vlasova AN, Jung K, Hasoksuz M, Zhang X, Halpin R, et al. Bovine-like coronaviruses isolated from four species of captive wild ruminants are homologous to bovine coronaviruses, based on complete genomic sequences. J Virol. 2008;82(24):12422–31.
Article
CAS
PubMed
Google Scholar
Chan JF-W, To KK-W, Tse H, Jin D-Y, Yuen K-Y. Interspecies transmission and emergence of novel viruses: lessons from bats and birds. Trends Microbiol. 2013;21(10):544–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo PCY, Huang Y, Lau SKP, Yuen K-Y. Coronavirus genomics and bioinformatics analysis. Viruses. 2010;2(8):1804–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vijgen L, Lemey P, Keyaerts E, Van Ranst M, St-Jean JR, Jacomy H, et al. Genetic variability of human respiratory coronavirus OC43. J Virol. 2005;79(5):3223–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sánchez CM, Gebauer F, Suñé C, Mendez A, Dopazo J, Enjuanes L. Genetic evolution and tropism of transmissible gastroenteritis coronaviruses. Virology. 1992;190(1):92–105.
Article
PubMed
Google Scholar
Baric RS, Fu K, Schaad MC, Stohlman SA. Establishing a genetic recombination map for murine coronavirus strain A59 complementation groups. Virology. 1990;177(2):646–56.
Article
CAS
PubMed
Google Scholar
Banerjee A, Doxey AC, Tremblay BJ-M, Mansfield MJ, Subudhi S, Hirota JA, et al. Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. J Gen Virol. 2020;101(12):1251–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLoS Genet. 2008;4(12):e1000304.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tang X, Wu C, Li X, Song Y, Yao X, Wu X, et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 2020;7(6):1012–23.
Article
PubMed
PubMed Central
Google Scholar
van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol. 2020;83:104351.
Article
PubMed
PubMed Central
CAS
Google Scholar
Simmonds P. Rampant C→U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: causes and consequences for their short- and long-term evolutionary trajectories. mSphere. 2020;5(3):e00408-e420.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mavian C, Marini S, Manes C, Capua I, Prosperi M, Salemi M. Regaining perspective on SARS-CoV-2 molecular tracing and its implications. medRxiv. 2020. https://doi.org/10.1101/2020.03.16.20034470.
Article
Google Scholar
Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data. Infect Dis. 2021. https://doi.org/10.1101/2020.12.30.20249034.
Article
Google Scholar
Kemp SA, Harvey WT, Lytras S, Consortium TC-19 GU (COG-U), Carabelli AM, Robertson DL, et al. Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion H69/V70. bioRxiv. 2021. https://doi.org/10.1101/2020.12.14.422555.
Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday J, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B117 in England. Science. 2021;372(6538):eabg3055.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bush RM. Predicting adaptive evolution. Nat Rev Genet. 2001;2(5):387–92.
Article
CAS
PubMed
Google Scholar
Gallaher WR. A palindromic RNA sequence as a common breakpoint contributor to copy-choice recombination in SARS-COV-2. Arch Virol. 2020;165:1–8.
Article
CAS
Google Scholar
Tortorici MA, Veesler D. Structural insights into coronavirus entry, Chapter chapter 4. In: Rey FA, editor. Advances in virus research. Complementary strategies to understand virus structure and function, vol. 105. Academic Press; 2019. p. 93–116.
Chapter
Google Scholar
Chibo D, Birch C. Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains. J Gen Virol. 2006;87(5):1203–8.
Article
CAS
PubMed
Google Scholar
Ren L, Zhang Y, Li J, Xiao Y, Zhang J, Wang Y, et al. Genetic drift of human coronavirus OC43 spike gene during adaptive evolution. Sci Rep. 2015;5(1):11451.
Article
PubMed
PubMed Central
Google Scholar
Kiyuka PK, Agoti CN, Munywoki PK, Njeru R, Bett A, Otieno JR, et al. Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya. J Infect Dis. 2018;217(11):1728–39.
Article
CAS
PubMed
Google Scholar
Dominguez SR, Sims GE, Wentworth DE, Halpin RA, Robinson CC, Town CD, et al. Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination. J Gen Virol. 2012;93(11):2387–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pyrc K, Dijkman R, Deng L, Jebbink MF, Ross HA, Berkhout B, et al. Mosaic structure of human coronavirus NL63, one thousand years of evolution. J Mol Biol. 2006;364(5):964–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Li X, Liu W, Gan M, Zhang L, Wang J, et al. Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018. Emerg Microbes Infect. 2020;9(1):246–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rambaut A, Loman N, Pybus O, Barclay W, Barrett J, Carabelli A, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological. 2020. https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563/1.
McCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, et al. Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. bioRxiv. 2020. https://doi.org/10.1101/2020.11.19.389916.
Article
PubMed
PubMed Central
Google Scholar
Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020;9:e61312.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kemp SA, Collier DA, Datir R, Ferreira I, Gayed S, Jahun A, et al. Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. medRxiv. 2020. https://doi.org/10.1101/2020.12.05.20241927.
Article
PubMed
PubMed Central
Google Scholar
GISAID. hCoV-19 analysis update. 2021. https://www.gisaid.org/hcov-19-analysis-update/.
Mercatelli D, Giorgi FM. Geographic and genomic distribution of SARS-CoV-2 mutations. Front Microbiol. 2020;11:1800. https://doi.org/10.3389/fmicb.2020.01800/full.
Article
PubMed
PubMed Central
Google Scholar
Guan Q, Sadykov M, Mfarrej S, Hala S, Naeem R, Nugmanova R, et al. A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic. Int J Infect Dis. 2020;100:216–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ceraolo C, Giorgi FM. Genomic variance of the 2019-nCoV coronavirus. J Med Virol. 2020;92(5):522–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
GISAID. Global phylogeny updated by NextStrain. GISAID; 2021.
Google Scholar
Alam ASMRU, Islam OK, Hasan MS, Islam MR, Mahmud S, AlEmran HM, et al. Evolving infection paradox of SARS-CoV-2: fitness costs virulence? Infect Dis. 2021. https://doi.org/10.1101/2021.02.21.21252137.
Article
Google Scholar
European Centre for Disease Prevention and Control. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom. ECDC; 2020.
Google Scholar
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Epidemiology. 2020. https://doi.org/10.1101/2020.12.21.20248640.
Article
Google Scholar
Centers for Disease Control and Prevention. Emerging SARS-CoV-2 variants. COVID-19. 2021. https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html.
Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data—from vision to reality. Euro Surveill. 2017;22(13):30494.
Article
PubMed
PubMed Central
Google Scholar
Zhang L, Jackson CB, Mou H, Ojha A, Peng H, Quinlan BD, et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun. 2020;11(1):6013.
Article
CAS
PubMed
PubMed Central
Google Scholar
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, 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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lauring AS, Hodcroft EB. Genetic variants of SARS-CoV-2—what do they mean? JAMA. 2021;325:529–31.
Article
CAS
PubMed
Google Scholar
Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2020;325:1–6.
Google Scholar
Hou YJ, Chiba S, Halfmann P, Ehre C, Kuroda M, Dinnon KH, et al. SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Science. 2020;370(6523):1464–8.
CAS
PubMed
PubMed Central
Google Scholar
Mansbach RA, Chakraborty S, Nguyen K, Montefiori DC, Korber B, Gnanakaran S. The SARS-CoV-2 spike variant D614G favors an open conformational state. bioRxiv. 2020. https://doi.org/10.1101/2020.07.26.219741.
Article
PubMed
PubMed Central
Google Scholar
Butowt R, Bilinska K, Von Bartheld CS. Chemosensory dysfunction in COVID-19: integration of genetic and epidemiological data points to D614G spike protein variant as a contributing factor. ACS Chem Neurosci. 2020;11(20):3180–4.
Article
CAS
PubMed
Google Scholar
Eaaswarkhanth M, Madhoun AA, Al-Mulla F. Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Int J Infect Dis. 2020;96:459–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Omotoso OE. Contributory role of SARS-CoV-2 genomic variations and life expectancy in COVID-19 transmission and low fatality rate in Africa. Egypt J Med Hum Genet. 2020;21(1):72.
Article
Google Scholar
Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, Wang Y, et al. Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell. 2020;183(3):739-751.e8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weissman D, Alameh M-G, de Silva T, Collini P, Hornsby H, Brown R, et al. D614G spike mutation increases SARS CoV-2 susceptibility to neutralization. medRxiv. 2020. https://doi.org/10.1101/2020.07.22.20159905.
Article
Google Scholar
Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int J Clin Pract. 2020;74(8):e13525.
Article
CAS
PubMed
Google Scholar
Lorenzo-Redondo R, Nam HH, Roberts SC, Simons LM, Jennings LJ, Qi C, et al. A unique clade of SARS-CoV-2 viruses is associated with lower viral loads in patient upper airways. medRxiv. 2020. https://doi.org/10.1101/2020.05.19.20107144.
Article
PubMed
PubMed Central
Google Scholar
Nguyen TT, Pham TN, Van TD, Nguyen TT, Nguyen DTN, Le HNM, et al. Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. PLoS ONE. 2020;15(11):e0242537.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koyama T, Platt D, Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organ. 2020;98(7):495–504.
Article
PubMed
PubMed Central
Google Scholar
Min JS, Kim G-W, Kwon S, Jin Y-H. A cell-based reporter assay for screening inhibitors of MERS coronavirus RNA-dependent RNA polymerase activity. JCM. 2020;9(8):2399.
Article
CAS
PubMed Central
Google Scholar
Wang Y, Anirudhan V, Du R, Cui Q, Rong L. RNA-dependent RNA polymerase of SARS-CoV-2 as a therapeutic target. J Med Virol. 2021;93(1):300–10.
Article
CAS
PubMed
Google Scholar
Kirchdoerfer RN, Ward AB. Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nat Commun. 2019;10(1):2342.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020;18:179.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ilmjärv S, Abdul F, Acosta-Gutiérrez S, Estarellas C, Galdadas I, Casimir M, et al. Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein. medRxiv. 2020. https://doi.org/10.1101/2020.08.23.20180281.
Article
Google Scholar
Tomaszewski T, DeVries RS, Dong M, Bhatia G, Norsworthy MD, Zheng X, et al. New pathways of mutational change in SARS-CoV-2 proteomes involve regions of intrinsic disorder important for virus replication and release. Evol Bioinform Online. 2020;16:1176934320965149.
Article
PubMed
PubMed Central
Google Scholar
Velazquez-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.
Article
PubMed
PubMed Central
Google Scholar
Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, et al. Patterns of within-host genetic diversity in SARS-CoV-2. bioRxiv. 2020. https://doi.org/10.1101/2020.12.23.424229.
Article
Google Scholar
Cárdenas-Conejo Y, Liñan-Rico A, García-Rodríguez DA, Centeno-Leija S, Serrano-Posada H. An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human-pathogenic coronavirus (SARS-CoV-2). J Med Virol. 2020;92(6):688–92.
Article
PubMed
CAS
Google Scholar
Xia H, Cao Z, Xie X, Zhang X, Chen JY-C, Wang H, et al. Evasion of Type I Interferon by SARS-CoV-2. Cell Rep. 2020;33(1):108234.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cottam EM, Whelband MC, Wileman T. Coronavirus NSP6 restricts autophagosome expansion. Autophagy. 2014;10(8):1426–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benvenuto D, Angeletti S, Giovanetti M, Bianchi M, Pascarella S, Cauda R, et al. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy. J Infect. 2020;81(1):e24–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang R, Hozumi Y, Yin C, Wei G-W. Decoding asymptomatic COVID-19 infection and transmission. arXiv200701344. 2020. hp://arxivorg/abs/2007.01344.
Dudas G, Rambaut A. MERS-CoV recombination: implications about the reservoir and potential for adaptation. Virus Evol. 2016. https://doi.org/10.1093/ve/vev023.
Article
PubMed
PubMed Central
Google Scholar
Wu S, Tian C, Liu P, Guo D, Zheng W, Huang X, et al. Effects of SARS-CoV-2 mutations on protein structures and intraviral protein–protein interactions. J Med Virol. 2020;93(4):2132–40. https://doi.org/10.1002/jmv.26597.
Article
CAS
PubMed
Google Scholar
Issa E, Merhi G, Panossian B, Salloum T, Tokajian S. SARS-CoV-2 and ORF3a: nonsynonymous mutations, functional domains, and viral pathogenesis. mSystems. 2020;5(3):e00266-e320.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ren Y, Shu T, Wu D, Mu J, Wang C, Huang M, et al. The ORF3a protein of SARS-CoV-2 induces apoptosis in cells. Cell Mol Immunol. 2020;17:1–3.
Article
CAS
Google Scholar
Chaw S-M, Tai J-H, Chen S-L, Hsieh C-H, Chang S-Y, Yeh S-H, et al. The origin and underlying driving forces of the SARS-CoV-2 outbreak. J Biomed Sci. 2020;27(1):73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Zhang J, Chen Y, Luo B, Yuan Y, Huang F, et al. The ORF8 protein of SARS-CoV-2 mediates immune evasion through potently downregulating MHC-I. bioRxiv. 2020. https://doi.org/10.1101/2020.05.24.111823.
Article
PubMed
PubMed Central
Google Scholar
Flower TG, Buffalo CZ, Hooy RM, Allaire M, Ren X, Hurley JH. Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein. PNAS. 2021;118(2):e2021785118.
Article
CAS
PubMed
Google Scholar
The Chinese SARS Molecular Epidemiology Consortium. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science. 2004;303(5664):1666–9.
Article
CAS
Google Scholar
Forni D, Cagliani R, Clerici M, Sironi M. Molecular evolution of human coronavirus genomes. Trends Microbiol. 2017;25(1):35–48.
Article
CAS
PubMed
Google Scholar
Lau SKP, Feng Y, Chen H, Luk HKH, Yang W-H, Li KSM, et al. Severe acute respiratory syndrome (SARS) coronavirus ORF8 Protein Is acquired from SARS-related coronavirus from greater horseshoe bats through recombination. J Virol. 2015;89(20):10532–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
He R, Leeson A, Ballantine M, Andonov A, Baker L, Dobie F, et al. Characterization of protein–protein interactions between the nucleocapsid protein and membrane protein of the SARS coronavirus. Virus Res. 2004;105(2):121–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Masters PS. The molecular biology of coronaviruses. In: Luisa BG, editor. Advances in virus research. Elsevier; 2006. p. 193–292.
Google Scholar
Siu YL, Teoh KT, Lo J, Chan CM, Kien F, Escriou N, et al. The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles. J Virol. 2008;82(22):11318–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J-Y, Liao C-H, Wang Q, Tan Y-J, Luo R, Qiu Y, et al. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 2020;286:198074.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mu J, Xu J, Zhang L, Shu T, Wu D, Huang M, et al. SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells. Sci China Life Sci. 2020;63(9):1–4.
Article
CAS
Google Scholar
GISAID. Clade and lineage nomenclature aids in genomic epidemiology studies of active hCoV-19 viruses. Clade and lineage nomenclature, March 2, 2021. 2021.
Bartolini B, Rueca M, Gruber CEM, Messina F, Giombini E, Ippolito G, et al. The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy. medRxiv. 2020. https://doi.org/10.1101/2020.11.28.20237016.
Article
Google Scholar
Zhang B, Hu Y, Chen L, Yau T, Tong Y, Hu J, et al. Mining of epitopes on spike protein of SARS-CoV-2 from COVID-19 patients. Cell Res. 2020;30(8):702–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
To KK-W, Hung IF-N, Ip JD, Chu AW-H, Chan W-M, Tam AR, et al. Coronavirus disease 2019 (COVID-19) re-infection by a phylogenetically distinct severe acute respiratory syndrome coronavirus 2 strain confirmed by whole genome sequencing. Clin Infect Dis. 2020. https://doi.org/10.1093/cid/ciaa1275ciaa1275.
Article
PubMed
PubMed Central
Google Scholar
Hodcroft EB, Zuber M, Nadeau S, Crawford KHD, Bloom JD, Veesler D, et al. Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020. medRxiv. 2020. https://doi.org/10.1101/2020.10.25.20219063.
Article
PubMed
PubMed Central
Google Scholar
Wong AHM, Tomlinson ACA, Zhou D, Satkunarajah M, Chen K, Sharon C, et al. Receptor-binding loops in alphacoronavirus adaptation and evolution. Nat Commun. 2017;8(1):1735.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kim Y, Cheon S, Min C-K, Sohn KM, Kang YJ, Cha Y-J, et al. Spread of mutant middle east respiratory syndrome coronavirus with reduced affinity to human CD26 during the South Korean Outbreak. MBio. 2016;7(2):e00019.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li W, Zhang C, Sui J, Kuhn JH, Moore MJ, Luo S, et al. Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J. 2005;24(8):1634–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, et al. 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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piccoli L, Park Y-J, Tortorici MA, Czudnochowski N, Walls AC, Beltramello M, et al. Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology. Cell. 2020;183(4):1024-1042.e21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu A, Wang L, Zhou H-Y, Ji C-Y, Xia SZ, Cao Y, et al. One year of SARS-CoV-2 evolution. Cell Host Microbe. 2021;29:503–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen J, Wang R, Wang M, Wei G-W. Mutations strengthened SARS-CoV-2 infectivity. J Mol Biol. 2020;432(19):5212–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tu H, Avenarius MR, Kubatko L, Hunt M, Pan X, Ru P, et al. Distinct patterns of emergence of SARS-CoV-2 spike variants including N501Y in clinical samples in Columbus Ohio. Genomics. 2021. https://doi.org/10.1101/2021.01.12.426407.
Article
PubMed
PubMed Central
Google Scholar
Wan Y, Shang J, Graham R, Baric RS, Li F. Receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of SARS coronavirus. J Virol. 2020;94(7):e00127-e220.
Article
PubMed
PubMed Central
Google Scholar
Santos JC, Passos GA. The high infectivity of SARS-CoV-2 B.1.1.7 is associated with increased interaction force between Spike-ACE2 caused by the viral N501Y mutation. bioRxiv. 2021. https://doi.org/10.1101/2020.12.29.424708.
Article
PubMed
PubMed Central
Google Scholar
Grabowski F, Preibisch G, Kochańczyk M, Lipniacki T. SARS-CoV-2 variant under investigation 202012/01 has more than twofold replicative advantage. Epidemiology. 2021. https://doi.org/10.1101/2020.12.28.20248906.
Article
Google Scholar
Oluniyi P. Detection of SARS-CoV-2 P681H spike protein variant in Nigeria. Virological. 2020]. https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567.
McCallum M, Marco AD, Lempp F, Tortorici MA, Pinto D, Walls AC, et al. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Immunology. 2021. https://doi.org/10.1101/2021.01.14.426475.
Article
Google Scholar
Bascos NAD, Mirano-Bascos D, Saloma CP. Structural analysis of spike protein mutations in an emergent SARS-CoV-2 variant from the Philippines. Biophysics. 2021. https://doi.org/10.1101/2021.03.06.434059.
Article
Google Scholar
Xia S, Lan Q, Su S, Wang X, Xu W, Liu Z, et al. The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin. Signal Transduct Target Ther. 2020;5(1):1–3.
Article
CAS
Google Scholar
Hoffmann M, Kleine-Weber H, Pöhlmann S. A multibasic cleavage site in the spike protein of SARS-CoV-2 is essential for infection of human lung cells. Mol Cell. 2020;78(4):779-784.e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peacock TP, Goldhill DH, Zhou J, Baillon L, Frise R, Swann OC, et al. The furin cleavage site of SARS-CoV-2 spike protein is a key determinant for transmission due to enhanced replication in airway cells. bioRxiv. 2020. https://doi.org/10.1101/2020.09.30.318311.
Article
Google Scholar
Yarmarkovich M, Warrington JM, Farrel A, Maris JM. Identification of SARS-CoV-2 vaccine epitopes predicted to induce long-term population-scale immunity. CR Med. 2020;1(3):100036.
Google Scholar
Zinzula L. Lost in deletion: the enigmatic ORF8 protein of SARS-CoV-2. Biochem Biophys Res Commun. 2020;538:116–24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Horby P, Huntley C, Davies N, Edmunds J, Ferguson N, Medley G, et al. NERVTAG paper on COVID-19 variant of concern B.1.1.7: paper from the New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) on new coronavirus (COVID-19) variant B.1.1.7. New and Emerging Respiratory Virus Threats Advisory Group; 2021.
Public Health England. PHE statement on variant of concern and new variant under investigation. Gov.UK; 2021. https://www.gov.uk/government/news/phe-statement-on-variant-of-concern-and-new-variant-under-investigation.
Wise J. Covid-19: The E484K mutation and the risks it poses. BMJ. 2021;372:n359.
Article
PubMed
Google Scholar
Collier DA, Marco AD, Ferreira IATM, Meng B, Datir R, Walls AC, et al. SARS-CoV-2 B.1.1.7 escape from mRNA vaccine-elicited neutralizing antibodies. medRxiv. 2021. https://doi.org/10.1101/2021.01.19.21249840.
Article
PubMed
PubMed Central
Google Scholar
Lim H, Baek A, Kim J, Kim MS, Liu J, Nam K-Y, et al. Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method. Sci Rep. 2020;10(1):16862.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luan J, Lu Y, Jin X, Zhang L. Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection. Biochem Biophys Res Commun. 2020;526(1):165–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nelson G, Buzko O, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant. bioRxiv. 2021. https://doi.org/10.1101/2021.01.13.426558.
Article
PubMed
PubMed Central
Google Scholar
Cheng MH, Krieger JM, Kaynak B, Arditi M, Bahar I. Impact of South African 501V2 variant on SARS-CoV-2 spike infectivity and neutralization: a structure-based computational assessment. bioRxiv. 2021. https://doi.org/10.1101/2021.01.10.426143.
Article
PubMed
PubMed Central
Google Scholar
Liu Z, VanBlargan LA, Bloyet L-M, Rothlauf PW, Chen RE, Stumpf S, et al. Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. bioRxiv. 2021. https://doi.org/10.1101/2020.11.06.372037.
Article
PubMed
PubMed Central
Google Scholar
Gaebler C, Wang Z, Lorenzi JCC, Muecksch F, Finkin S, Tokuyama M, et al. Evolution of antibody immunity to SARS-CoV-2. Nature. 2021;591:639–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andreano E, Piccini G, Licastro D, Casalino L, Johnson NV, Paciello I, et al. SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. bioRxiv. 2020. https://doi.org/10.1101/2020.12.28.424451.
Article
PubMed
PubMed Central
Google Scholar
Barnes CO, Jette CA, Abernathy ME, Dam KM-A, Esswein SR, Gristick HB, et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature. 2020;588(7839):682–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baum A, Fulton BO, Wloga E, Copin R, Pascal KE, Russo V, et al. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science. 2020;369(6506):1014–8.
Article
CAS
PubMed
Google Scholar
Public Health England. Variants: distribution of cases data. Gov.UK; 2021. https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data.
Gröhs Ferrareze PA, Franceschi VB, de Menezes MA, Caldana GD, Zimerman RA, Thompson CE. E484K as an innovative phylogenetic event for viral evolution: genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Evol Biol. 2021. https://doi.org/10.1101/2021.01.27.426895.
Article
Google Scholar
West AP, Barnes CO, Yang Z, Bjorkman PJ. SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape. Bioinformatics. 2021. https://doi.org/10.1101/2021.02.14.431043.
Article
PubMed
PubMed Central
Google Scholar
Sabino EC, Buss LF, Carvalho MPS, Prete CA, Crispim MAE, Fraiji NA, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet. 2021;397(10273):452–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fratev F. The N501Y and K417N mutations in the spike protein of SARS-CoV-2 alter the interactions with both hACE2 and human derived antibody: a free energy of perturbation study. Mol Biol. 2020. https://doi.org/10.1101/2020.12.23.424283.
Article
Google Scholar
Villoutreix BO, Calvez V, Marcelin A-G, Khatib A-M. In silico investigation of the new UK (B117) and South African (501YV2) SARS-CoV-2 variants with a focus at the ACE2–spike RBD interface. IJMS. 2021;22(4):1695.
Article
CAS
PubMed
PubMed Central
Google Scholar
National Institute of Infectious Diseases. Brief report: new variant strain of SARS-CoV-2 identified in travelers from Brazil. National Institute of Infectious Diseases; 2021. p. 1.
Google Scholar
European Centre for Disease Prevention and Control. Risk related to the spread of new SARS-CoV-2 variants of concern in the EU/EEA—first update. ECDC; 2021.
Google Scholar
Toovey OTR, Harvey KN, Bird PW, Tang JW-TW-T. Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK. J Infect. 2021;82:e23–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voloch CM, da Silva FR, de Almeida LGP, Cardoso CC, Brustolini OJ, Gerber AL, et al. Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil. Genet Genomic Med. 2020. https://doi.org/10.1101/2020.12.23.20248598.
Article
Google Scholar
Vasques Nonaka CK, Miranda Franco M, Gräf T, Almeida Mendes AV, Santana de Aguiar R, Giovanetti M, et al. Genomic evidence of a Sars-Cov-2 reinfection case with E484K spike mutation in Brazil. Life Sci. 2021;27:1522–4.
Google Scholar
Faria NR, Morales Claro I, Candido D, Moyses Franco LA, Andrade PS, Coletti TM, et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings—SARS-CoV-2 coronavirus/nCoV-2019 genomic epidemiology. Virological. 2021. https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586.
Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, et al. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol. 2021;19(5):e3001236.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, et al. Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Mol Biol. 2021. https://doi.org/10.1101/2021.04.22.440932.
Article
Google Scholar
Motozono C, Toyoda M, Zahradnik J, Ikeda T, Saito A, Tan TS, et al. An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity. Microbiology. 2021. https://doi.org/10.1101/2021.04.02.438288.
Article
Google Scholar
Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, et al. The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell. 2020;182(5):1284-1294.e9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Di Giacomo S, Mercatelli D, Rakhimov A, Giorgi FM. Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. J Med Virol. 2021;93(9):5638–43.
Article
PubMed
CAS
Google Scholar
Wall EC, Wu M, Harvey R, Kelly G, Warchal S, Sawyer C, et al. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination. Lancet. 2021;397(10292):2331–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mlcochova P, Kemp S, Dhar MS, Papa G, Meng B, Mishra S, et al. SARS-CoV-2 B.1.617.2 Delta variant emergence, replication and sensitivity to neutralising antibodies. Microbiology. 2021. https://doi.org/10.1101/2021.05.08.443253.
Article
Google Scholar
Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021.
Peacock TP, Sheppard CM, Brown JC, Goonawardane N, Zhou J, Whiteley M, et al. The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin. Microbiology. 2021. https://doi.org/10.1101/2021.05.28.446163.
Article
PubMed
PubMed Central
Google Scholar
Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England. Gov.UK; 2021.
Thomson EC, Rosen LE, Shepherd JG, Spreafico R, Filipe AS, Wojcechowskyj JA, et al. Circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. Cell. 2021;184:1171–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edara VV, Floyd K, Lai L, Gardner M, Hudson W, Piantadosi A, et al. Infection and mRNA-1273 vaccine antibodies neutralize SARS-CoV-2 UK variant. medRxiv. 2021. https://doi.org/10.1101/2021.02.02.21250799.
Article
PubMed
PubMed Central
Google Scholar
Muik A, Wallisch A-K, Sänger B, Swanson KA, Mühl J, Chen W, et al. Neutralization of SARS-CoV-2 lineage B117 pseudovirus by BNT162b2 vaccine—elicited human sera. Science. 2021;371:1152–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Liu J, Xia H, Zhang X, Fontes-Garfias CR, Swanson KA, et al. Neutralizing activity of BNT162b2-elicited serum—preliminary report. N Engl J Med. 2021;384:1466–8.
Article
PubMed
Google Scholar
Wu K, Werner AP, Moliva JI, Koch M, Choi A, Stewart-Jones GBE, et al. mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. bioRxiv. 2021. https://doi.org/10.1101/2021.01.25.427948.
Article
PubMed
PubMed Central
Google Scholar
Choi A, Koch M, Wu K, Dixon G, Oestreicher J, Legault H, et al. Serum neutralizing activity of mRNA-1273 against SARS-CoV-2 variants. Microbiology. 2021. https://doi.org/10.1101/2021.06.28.449914.
Article
PubMed
PubMed Central
Google Scholar
Moderna. Moderna COVID-19 vaccine retains neutralizing activity against emerging variants first identified in the U.K. and the Republic of South Africa. Moderna; 2021. https://investors.modernatx.com/news-releases/news-release-details/moderna-covid-19-vaccine-retains-neutralizing-activity-against.
BioNTech. Pfizer and BioNTech publish results of study showing COVID-19 vaccine elicits antibodies that neutralize pseudovirus bearing the SARS-CoV-2 U.K. strain spike protein in cell culture. BioNTech. 2021. https://investors.biontech.de/news-releases/news-release-details/pfizer-and-biontech-publish-results-study-showing-covid-19.
Xie X, Liu Y, Liu J, Zhang X, Zou J, Fontes-Garfias CR, et al. Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat Med. 2021;27:1–2.
Article
CAS
Google Scholar
Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. bioRxiv. 2021. https://doi.org/10.1101/2021.01.15.426911.
Article
PubMed
PubMed Central
Google Scholar
Lopez Bernal J, Andrews N, Gower C, Gallagher E, Simmons R, Thelwall S, et al. Effectiveness of covid-19 vaccines against the B16172 (Delta) variant. N Engl J Med. 2021. https://doi.org/10.1056/NEJMoa2108891.
Article
PubMed
PubMed Central
Google Scholar
Hodcroft EB, Domman DB, Snyder DJ, Oguntuyo K, Van Diest M, Densmore KH, et al. Emergence in late 2020 of multiple lineages of SARS-CoV-2 spike protein variants affecting amino acid position 677. Infect Dis. 2021. https://doi.org/10.1101/2021.02.12.21251658.
Article
Google Scholar
Kim J-S, Jang J-H, Kim J-M, Chung Y-S, Yoo C-K, Han M-G. Genome-wide identification and characterization of point mutations in the SARS-CoV-2 genome. Osong Public Health Res Perspect. 2020;11(3):101–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sarkar R, Mitra S, Chandra P, Saha P, Banerjee A, Dutta S, et al. Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations. Arch Virol. 2021;166(3):801–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xia S, Zhu Y, Liu M, Lan Q, Xu W, Wu Y, et al. Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein. Cell Mol Immunol. 2020;17(7):765–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Forni D, Filippi G, Cagliani R, De Gioia L, Pozzoli U, Al-Daghri N, et al. The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses. Sci Rep. 2015;5(1):14480.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mejdani M, Haddadi K, Pham C, Mahadevan R. SARS-CoV-2 receptor binding mutations and antibody mediated immunity. Bioinformatics. 2021. https://doi.org/10.1101/2021.01.25.427846.
Article
Google Scholar
Singh A, Steinkellner G, Köchl K, Gruber K, Gruber CC. Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Res Square. 2020;11:4320.
Google Scholar
Tea F, Stella AO, Aggarwal A, Darley DR, Pilli D, Vitale D, et al. SARS-CoV-2 neutralizing antibodies; longevity, breadth, and evasion by emerging viral variants. Infect Dis. 2020. https://doi.org/10.1101/2020.12.19.20248567.
Article
Google Scholar
Wang D, Mai J, Zhou W, Yu W, Zhan Y, Wang N, et al. Immunoinformatic analysis of T- and B-cell epitopes for SARS-CoV-2 vaccine design. Vaccines. 2020;3(8):355.
Article
CAS
Google Scholar
Bugembe DL, Phan MVT, Ssewanyana I, Semanda P, Nansumba H, Dhaala B, et al. A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic. Infect Dis. 2021. https://doi.org/10.1101/2021.02.08.21251393.
Article
Google Scholar
Dudas G, Hong SL, Potter B, Calvignac-Spencer S, Niatou-Singa FS, Tombolomako TB, et al. Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe. Epidemiology. 2021. https://doi.org/10.1101/2021.05.04.21256637.
Article
Google Scholar
Tandel D, Gupta D, Sah V, Harinivas Harshan K. N440K variant of SARS-CoV-2 has higher infectious fitness. Microbiology. 2021. https://doi.org/10.1101/2021.04.30.441434.
Article
Google Scholar
Hirotsu Y, Omata M. Detection of R1 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.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCallum M, Bassi J, Marco AD, Chen A, Walls AC, Iulio JD, et al. SARS-CoV-2 immune evasion by variant B.1.427/B.1.429. Immunology. 2021. https://doi.org/10.1101/2021.03.31.437925.
Article
Google Scholar
World Health Organization. Tracking SARS-CoV-2 variants. WHO; 2021.
Google Scholar
Romero PE, Dávila-Barclay A, Salvatierra G, González L, Cuicapuza D, Solis L, et al. The emergence of SARS-CoV-2 variant lambda (C.37) in South America. Epidemiology. 2021. https://doi.org/10.1101/2021.06.26.21259487.
Article
Google Scholar
Audi A, AlIbrahim M, Kaddoura M, Hijazi G, Yassine HM, Zaraket H. Seasonality of respiratory viral infections: will COVID-19 follow suit? Front Public Health. 2020. https://doi.org/10.3389/fpubh.2020.567184/full.
Article
PubMed
PubMed Central
Google Scholar
Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science. 2020;368(6493):860–8.
Article
CAS
PubMed
Google Scholar
Kanzawa M, Spindler H, Anglemyer A, Rutherford GW. Will coronavirus disease 2019 become seasonal? J Infect Dis. 2020;222(5):719–21.
Article
CAS
PubMed
Google Scholar
Monto AS, DeJonge PM, Callear AP, Bazzi LA, Capriola SB, Malosh RE, et al. Coronavirus occurrence and transmission over 8 years in the HIVE cohort of households in Michigan. J Infect Dis. 2020;222(1):9–16.
Article
PubMed
PubMed Central
CAS
Google Scholar
Price RHM, Graham C, Ramalingam S. Association between viral seasonality and meteorological factors. Sci Rep. 2019;9(1):929.
Article
PubMed
PubMed Central
CAS
Google Scholar
Polozov IV, Bezrukov L, Gawrisch K, Zimmerberg J. Progressive ordering with decreasing temperature of the phospholipids of influenza virus. Nat Chem Biol. 2008;4(4):248–55.
Article
CAS
PubMed
Google Scholar
Paynter S. Humidity and respiratory virus transmission in tropical and temperate settings. Epidemiol Infect. 2015;143(6):1110–8.
Article
CAS
PubMed
Google Scholar
Harper GJ. Airborne micro-organisms: survival tests with four viruses. J Hyg (Lond). 1961;59(4):479–86.
CAS
Google Scholar
Shephard RJ, Shek PN. Cold exposure and immune function. Can J Physiol Pharmacol. 1998;76(9):828–36.
Article
CAS
PubMed
Google Scholar
Eccles R. An explanation for the seasonality of acute upper respiratory tract viral infections. Acta Otolaryngol. 2002;122(2):183–91.
Article
CAS
PubMed
Google Scholar
Kudo E, Song E, Yockey LJ, Rakib T, Wong PW, Homer RJ, et al. Low ambient humidity impairs barrier function and innate resistance against influenza infection. Proc Natl Acad Sci USA. 2019;116(22):10905–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sajadi MM, Habibzadeh P, Vintzileos A, Shokouhi S, Miralles-Wilhelm F, Amoroso A. Temperature and latitude analysis to predict potential spread and seasonality for COVID-19. SSRN J. 2020. https://www.ssrn.com/abstract=3550308.
Bukhari Q, Jameel Y. Will coronavirus pandemic diminish by summer? Social Science Research Network; 2020. Report No.: ID 3556998. https://papers.ssrn.com/abstract=3556998.
Wang J, Tang K, Feng K, Lv W. High temperature and high humidity reduce the transmission of COVID-19. SSRN J. 2020; https://www.ssrn.com/abstract=3551767.
Chen B, Liang H, Yuan X, Hu Y, Xu M, Zhao Y, et al. Predicting the local COVID-19 outbreak around the world with meteorological conditions: a model-based qualitative study. BMJ Open. 2020;10(11):e041397.
Article
PubMed
Google Scholar
Sharma A, Preece B, Swann H, Fan X, McKenney RJ, Ori-McKenney KM, et al. Structural stability of SARS-CoV-2 virus like particles degrades with temperature. Biochem Biophys Res Commun. 2021;1(534):343–6.
Article
CAS
Google Scholar
Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20(5):533–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petersen E, Koopmans M, Go U, Hamer DH, Petrosillo N, Castelli F, et al. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. Lancet Infect Dis. 2020;20(9):e238–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanche S, Lin YT, Xu C, Romero-Severson E, Hengartner N, Ke R. High contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis. 2020;26(7):1470–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Poirier C, Luo W, Majumder MS, Liu D, Mandl KD, Mooring TA, et al. The role of environmental factors on transmission rates of the COVID-19 outbreak: an initial assessment in two spatial scales. Sci Rep. 2020;10(1):17002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edridge AWD, Kaczorowska J, Hoste ACR, Bakker M, Klein M, Loens K, et al. Seasonal coronavirus protective immunity is short-lasting. Nat Med. 2020;26(11):1691–3.
Article
CAS
PubMed
Google Scholar
Aldridge RW, Lewer D, Beale S, Johnson AM, Zambon M, Hayward AC, et al. Seasonality and immunity to laboratory-confirmed seasonal coronaviruses (HCoV-NL63, HCoV-OC43, and HCoV-229E): results from the Flu Watch cohort study. Wellcome Open Res. 2020;5:52.
Article
PubMed
PubMed Central
Google Scholar
Galanti M, Shaman J. Direct observation of repeated infections with endemic coronaviruses. J Infect Dis. 2020;223:409–15.
Article
CAS
Google Scholar
Callow KA, Parry HF, Sergeant M, Tyrrell DAJ. The time course of the immune response to experimental coronavirus infection of man. Epidemiol Infect. 1990;105(2):435–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Galipeau Y, Greig M, Liu G, Driedger M, Langlois M-A. Humoral responses and serological assays in SARS-CoV-2 infections. Front Immunol. 2020;11:610688. https://doi.org/10.3389/fimmu.2020.610688/full#B23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Long Q-X, Tang X-J, Shi Q-L, Li Q, Deng H-J, Yuan J, et al. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nat Med. 2020;26(8):1200–4.
Article
CAS
PubMed
Google Scholar
Ibarrondo FJ, Fulcher JA, Goodman-Meza D, Elliott J, Hofmann C, Hausner MA, et al. Rapid decay of anti-SARS-CoV-2 antibodies in persons with mild covid-19. N Engl J Med. 2020;383(11):1085–7.
Article
PubMed
Google Scholar
Seow J, Graham C, Merrick B, Acors S, Pickering S, Steel KJA, et al. Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans. Nat Microbiol. 2020;5(12):1598–607.
Article
CAS
PubMed
PubMed Central
Google Scholar
Choe PG, Kang CK, Suh HJ, Jung J, Song K-H, Bang JH, et al. Waning antibody responses in asymptomatic and symptomatic SARS-CoV-2 infection. Emerg Infect Dis. 2021;27(1):327–9.
Article
CAS
PubMed Central
Google Scholar
Shaman J, Galanti M. Will SARS-CoV-2 become endemic? Science. 2020;370(6516):527–9.
Article
CAS
PubMed
Google Scholar
Chan K-H, Chan JF-W, Tse H, Chen H, Lau CC-Y, Cai J-P, et al. Cross-reactive antibodies in convalescent SARS patients’ sera against the emerging novel human coronavirus EMC (2012) by both immunofluorescent and neutralizing antibody tests. J Infect. 2013;67(2):130–40.
Article
PubMed
PubMed Central
Google Scholar
Patrick DM, Petric M, Skowronski DM, Guasparini R, Booth TF, Krajden M, et al. An outbreak of human coronavirus OC43 infection and serological cross-reactivity with SARS coronavirus. Can J Infect Dis Med Microbiol. 2006;17(6):330–6.
Article
PubMed
PubMed Central
Google Scholar
Kellam P, Barclay W. The dynamics of humoral immune responses following SARS-CoV-2 infection and the potential for reinfection. J Gen Virol. 2020;101(8):791–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, et al. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell. 2020;181(7):1489-1501.e15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mateus J, Grifoni A, Tarke A, Sidney J, Ramirez SI, Dan JM, et al. Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science. 2020;370(6512):89–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Le Bert N, Tan AT, Kunasegaran K, Tham CYL, Hafezi M, Chia A, et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020;584(7821):457–62.
Article
PubMed
CAS
Google Scholar
Braun J, Loyal L, Frentsch M, Wendisch D, Georg P, Kurth F, et al. SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature. 2020;587(7833):270–4.
Article
CAS
PubMed
Google Scholar
Gao Q, Bao L, Mao H, Wang L, Xu K, Yang M, et al. Development of an inactivated vaccine candidate for SARS-CoV-2. Science. 2020;369(6499):77–81.
Article
CAS
PubMed
Google Scholar
Duan K, Liu B, Li C, Zhang H, Yu T, Qu J, et al. Effectiveness of convalescent plasma therapy in severe COVID-19 patients. PNAS. 2020;117(17):9490–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wardeh M, Baylis M, Blagrove MSC. Predicting mammalian hosts in which novel coronaviruses can be generated. Nat Commun. 2021;12(1):780.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. Evol Biol. 2021. https://doi.org/10.1101/2021.02.03.429646.
Article
Google Scholar
Nikolai LA, Meyer CG, Kremsner PG, Velavan TP. Asymptomatic SARS coronavirus 2 infection: invisible yet invincible. Int J Infect Dis. 2020;100:112–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gandhi M, Yokoe DS, Havlir DV. Asymptomatic transmission, the achilles’ heel of current strategies to control covid-19. N Engl J Med. 2020;382(22):2158–60.
Article
CAS
PubMed
Google Scholar
Ye Z-W, Yuan S, Yuen K-S, Fung S-Y, Chan C-P, Jin D-Y. Zoonotic origins of human coronaviruses. Int J Biol Sci. 2020;16(10):1686–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vijgen L, Keyaerts E, Moës E, Thoelen I, Wollants E, Lemey P, et al. Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. JVI. 2005;79(3):1595–604.
Article
CAS
Google Scholar
St. Jean JR, Jacomy H, Desforges M, Vabret A, Freymuth F, Talbot PJ. Human respiratory coronavirus OC43: genetic stability and neuroinvasion. J Virol. 2004;78(16):8824–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bakkers MJG, Lang Y, Feitsma LJ, Hulswit RJG, de Poot SAH, van Vliet ALW, et al. Betacoronavirus adaptation to humans involved progressive loss of hemagglutinin-esterase lectin activity. Cell Host Microbe. 2017;21(3):356–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo PCY, Lau SKP, Chu C, Chan K, Tsoi H, Huang Y, et al. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005;79(2):884–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu B, Zeng L-P, Yang X-L, Ge X-Y, Zhang W, Li B, et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 2017;13(11):e1006698.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in Southern China. Science. 2003;302(5643):276–8.
Article
CAS
PubMed
Google Scholar
Corman VM, Ithete NL, Richards LR, Schoeman MC, Preiser W, Drosten C, et al. Rooting the phylogenetic tree of middle East respiratory syndrome coronavirus by characterization of a conspecific virus from an African bat. J Virol. 2014;88(19):11297–303.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang T, Wu Q, Zhang Z. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr Biol. 2020;30(7):1346-1351.e2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee J-S, Kim SY, Kim TS, Hong KH, Ryoo N-H, Lee J, et al. Evidence of severe acute respiratory syndrome coronavirus 2 reinfection after recovery from mild coronavirus disease 2019. Clin Infect Dis. 2020. https://doi.org/10.1093/cid/ciaa1421.
Article
PubMed
PubMed Central
Google Scholar
Leao JC, Gusmao TPL, Zarzar AM, Filho JCL, de Faria ABS, Silva IHM, et al. Coronaviridae—old friends, new enemy! Oral Dis. 2021. https://doi.org/10.1111/odi.13447.
Article
PubMed
Google Scholar
Pavlović-Lažetić GM, Mitić NS, Tomović AM, Pavlović MD, Beljanski MV. SARS-CoV genome polymorphism: a bioinformatics study. Genomics Proteomics Bioinf. 2005;3(1):18–35.
Article
Google Scholar
Naeem A, Hamed M, Alghoribi M, Aljabr W, Alsaran H, Enani M, et al. Molecular evolution and structural mapping of N-terminal domain in spike gene of middle east respiratory syndrome coronavirus (MERS-CoV). Viruses. 2020;12(5):502.
Article
CAS
PubMed Central
Google Scholar
Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, et al. Spread, circulation, and evolution of the middle east respiratory syndrome coronavirus. MBio. 2014;5(1):e01062-e1113.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lau S, Wong A, Lau T, Woo P. Molecular evolution of MERS coronavirus: dromedaries as a recent intermediate host or long-time animal reservoir? IJMS. 2017;18(10):2138.
Article
PubMed Central
CAS
Google Scholar
Forni D, Cagliani R, Mozzi A, Pozzoli U, Al-Daghri N, Clerici M, et al. Extensive positive selection drives the evolution of nonstructural proteins in lineage c betacoronaviruses. J Virol. 2016;90(7):3627–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
AlBalwi MA, Khan A, AlDrees M, Gk U, Manie B, Arabi Y, et al. Evolving sequence mutations in the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). J Infect Public Health. 2020;13(10):1544–50.
Article
PubMed
PubMed Central
Google Scholar
Hurdiss DL, Drulyte I, Lang Y, Shamorkina TM, Pronker MF, van Kuppeveld FJM, et al. Cryo-EM structure of coronavirus-HKU1 haemagglutinin esterase reveals architectural changes arising from prolonged circulation in humans. Nat Commun. 2020;11(1):4646.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shirato K, Kawase M, Watanabe O, Hirokawa C, Matsuyama S, Nishimura H, et al. Differences in neutralizing antigenicity between laboratory and clinical isolates of HCoV-229E isolated in Japan in 2004–2008 depend on the S1 region sequence of the spike protein. J Gen Virol. 2012;93(9):1908–17.
Article
CAS
PubMed
Google Scholar
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382(8):727–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boni MF, Lemey P, Jiang X, Lam TT-Y, Perry BW, Castoe TA, et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol. 2020;5(11):1408–17.
Article
CAS
PubMed
Google Scholar
Wu Z, Yang L, Ren X, Zhang J, Yang F, Zhang S, et al. ORF8-related genetic evidence for Chinese horseshoe bats as the source of human severe acute respiratory syndrome coronavirus. J Infect Dis. 2016;213(4):579–83.
Article
CAS
PubMed
Google Scholar
Centers for Disease Control and Prevention. Update: outbreak of severe acute respiratory syndrome—Worldwide, 2003. CDC; 2003. https://www.cdc.gov/mmwr/preview/mmwrhtml/mm5212a1.htm.
Drosten C, Günther S, Preiser W, van der Werf S, Brodt H-R, Becker S, et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003;348(20):1967–76.
Article
CAS
PubMed
Google Scholar
Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus ADME, Fouchier RAM. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367(19):1814–20.
Article
CAS
PubMed
Google Scholar
Ithete NL, Stoffberg S, Corman VM, Cottontail VM, Richards LR, Schoeman MC, et al. Close relative of human middle east respiratory syndrome coronavirus in Bat, South Africa. Emerg Infect Dis. 2013;19(10):1697–9.
Article
PubMed
PubMed Central
Google Scholar
Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH, et al. Middle east respiratory syndrome coronavirus in Bats, Saudi Arabia. Emerg Infect Dis J. 2013;19(11):1819–23.
Article
CAS
Google Scholar
Anthony SJ, Gilardi K, Menachery VD, Goldstein T, Ssebide B, Mbabazi R, et al. Further evidence for bats as the evolutionary source of middle east respiratory syndrome coronavirus. MBio. 2017;8(2):e00373-e417.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lau SKP, Zhang L, Luk HKH, Xiong L, Peng X, Li KSM, et al. Receptor usage of a novel bat lineage C betacoronavirus reveals evolution of middle east respiratory syndrome-related coronavirus spike proteins for human dipeptidyl peptidase 4 binding. J Infect Dis. 2018;218(2):197–207.
Article
CAS
PubMed
Google Scholar
Annan A, Baldwin HJ, Corman VM, Klose SM, Owusu M, Nkrumah EE, et al. Human betacoronavirus 2c EMC/2012-related viruses in Bats, Ghana and Europe. Emerg Infect Dis. 2013;19(3):456–9.
Article
PubMed
PubMed Central
Google Scholar
Moreno A, Lelli D, de Sabato L, Zaccaria G, Boni A, Sozzi E, et al. Detection and full genome characterization of two beta CoV viruses related to Middle East respiratory syndrome from bats in Italy. Virol J. 2017;14(1):239.
Article
PubMed
PubMed Central