Evolving Faces of SARS-CoV-2 with the Emergence of Diverse Variants
Abstract
Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in December 2019, scientists have tracked five variants of concern (VOC) of SARS-CoV-2. The variants such as B.1.1.7 and B.1.617.2 primarily originated independently from the United Kingdom and India, respectively, and subsequently became dominant across the globe. The adaptability of these variants depends on their relative survival fitness to the positive selection pressure acting on them. Antiviral drugs and vaccine usage might act as a selective environment, thus, facilitating the positive selection resulting in the rapid emergence of new variants with higher fitness and survival value. The recently emerged VOC, the omicron variant (B.1.1.529), was first reported from South African samples, and it has a large number of mutations some of which are concerning as per the preliminary evidence. Owing to the dynamism of mutations in the SARS-CoV-2 genome, we may expect many unexpected events as far as the emergence of variants, virulence, and transmissibility is concerned. However, as an evolutionary trade-off strategy, the virulence of SARS-CoV-2 might get reduced with an increase in the transmissibility to attain a wider host range. The intermingling of vaccinated and unvaccinated individuals provides the virus opportunity to amplify by infecting the unvaccinated individuals and causing breakthrough infections. Moreover, the prevalence of different variants of SARS-CoV-2 has been different in different geographic zones as far as the cases and causalities are concerned. Sustained viral surveillance and monitoring with region-wise variant-specific preventive strategies are required to prevent and contain the outbreak of emerging variants of SARS-CoV-2.
How to cite this article:
Sinha S, Bhattacharya S, Ray SD, Tilak R. Evolving Faces of SARS-CoV-2 with the Emergence of Diverse Variants. J Commun Dis. 2022;54(1):141-149.
DOI: https://doi.org/10.24321/0019.5138.202260
References
World Health Organization [Internet]. Tracking SARSCoV-2 variants; 2021 [cited 2021 Dec 9]. Available from: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
Sola M, Wain-Hobson S. Drift and conservatism in RNA virus evolution: are they adapting or merely changing? In: Domingo E, Webster R, Holland J, editors. Origin and evolution of viruses. UK: Academic Press; 1999. [Google Scholar]
GISAID [Internet]. Tracking of variants; 2022 [cited 2022 Feb 19]. Available from: https://www.gisaid.org/hcov19-variants/
Domingo E, Escarmis C, Menendez-Arias L, Holland JJ. Viral quasispecies and fitness variations. In: Domingo E, Webster R, Holland J, editors. Origin and evolution of viruses. UK: Academic Press; 1999. [Google Scholar]
Piszczatoski CR, Powell J. Emergency authorization of chloroquine and hydroxychloroquine for treatment of COVID-19. Ann Pharmacother. 2020;54(8):827-31. [PubMed] [Google Scholar]
World Health Organization [Internet]. COVID-19 vaccine tracker and landscape; 2021 [2021 Dec 9]. Available from: https://www.who.int/publications/m/item/draftlandscape-of-covid-19-candidate-vaccines
Centre of Disease Control and Prevention [Internet]. What you should know about the possibility of COVID-19 illness after vaccination; 2021 [cited 2021 Dec 9]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/vaccines/effectiveness/whymeasure-effectiveness/breakthrough-cases.html
Singh TU, Parida S, Lingaraju MC, Kesavan M, Kumar D, Singh RK. Drug repurposing approach to fight COVID-19. Pharmacol Rep. 2020;72(6):1479-508. [PubMed] [Google Scholar]
D’Arienzo M, Coniglio A. Assessment of the SARS-CoV-2 basic reproduction number, R0, based on the early phase of COVID-19 outbreak in Italy. Biosaf Health. 2020;2(2):57-9. [PubMed] [Google Scholar]
Petersen E, Koopmans M, Go U, Hamer DH, Petrosillo N, Castelli F, Storgaard M, Khalili SA, Simonsen L. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. Lancet Infect Dis. 2020;20(9):e238-e44. [PubMed] [Google Scholar]
Rodpothong P, Auewarakul P. Viral evolution and transmission effectiveness. World J Virol. 2012;1(5):131-4. [PubMed] [Google Scholar]
Lazarevic I, Pravica V, Miljanovic D, Cupic M. Immune evasion of SARS-CoV-2 emerging variants: what have we learnt so far? Viruses. 2021;13(7):1192. [PubMed] [Google Scholar]
Smith EC, Denison MR. Coronaviruses as DNA wannabes: a new model for the regulation of RNA virus replication fidelity. PLoS Pathog. 2013;9(12):e1003760. [PubMed] [Google Scholar]
World Health Organization [Internet]. Episode #45 - Delta variant; 2021 [cited 2021 Jul 14]. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/media-resources/science-in-5/episode-45---delta-variant
World Health Organization [Internet]. Episode #44 - Delta variant and vaccines; 2021 [cited 2021 Jul 14]. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/media-resources/science-in-5/episode-44---delta-variant-and-vaccines
Liu L, Wang P, Nair MS, Yu J, Rapp M, Wang Q, Luo Y, Chan J, Sahi V, Figueroa A, Guo XV, Cerutti G, Bimela J, Gorman J, Zhou T, Chen Z, Yuen KY, Kwong PD, Sodroski JG, Yin MT, Sheng Z, Huang Y, Shapiro L, Ho DD. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature. 2020;584(7821):450-6. [PubMed] [Google Scholar]
McCallum M, De Marco A, Lempp FA, Tortorici MA, Pinto D, Walls AC, Beltramello M, Chen A, Liu Z, Zatta F, Zepeda S, di Iulio J, Bowen JE, Montiel-Ruiz M, Zhou J, Rosen LE, Bianchi S, Guarino B, Fregni CS, Abdelnabi R, Foo SY, Rothlauf PW, Bloyet LM, Benigni F, Cameroni E, Neyts J, Riva A, Snell G, Telenti A, Whelan SP, Virgin HW, Corti D, Pizzuto MS, Veesler D. N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell. 2021;184(9):2332-47. [PubMed] [Google Scholar]
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 Apr;592(7852):116-21. [PubMed] [Google Scholar]
Lauring AS, Hodcroft EB. Genetic variants of SARS-CoV-2-what do they mean? JAMA. 2021;325(6):529-31.[PubMed] [Google Scholar]
Zhang L, Cui Z, Li Q, Wang B, Yu Y, Wu J, Nie J, Ding R, Wang H, Zhang Y, Liu S, Chen Z, He Y, Su X, Xu W, Huang W, Wang Y. Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Commun Biol. 2021;4(1):1196. [PubMed] [Google Scholar]
Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, Rakshit P, Singh S, Abraham P, Panda S; Nic Team. SARS-CoV-2 spike mutations, L452R, T478K, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Microorganisms. 2021;9(7):1542. [PubMed] [Google Scholar]
Baj A, Novazzi F, Pasciuta R, Genoni A, Ferrante FD, Valli M, Partenope M, Tripiciano R, Ciserchia A, Catanoso G, Focosi D, Maggi F. Breakthrough infections of E484KHarboring SARS-CoV-2 Delta variant, Lombardy, Italy. Emerg Infect Dis. 2021;27(12):3180-2. [PubMed] [Google Scholar]
Cai HY, Cai A. SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. J Vet Diagn Invest. 2021;33(5):939-42. [PubMed] [Google Scholar]
World Health Organization [Internet]. Classification of Omicron (B.1.1.529): SARS-CoV-2 variant of concerns; 2021 [cited 2021 Dec 3]. Available from: https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
Kannan SR, Spratt AN, Sharma K, Chand HS, Byrareddy SN, Singh K. Omicron SARS-CoV-2 variant: unique features and their impact on pre-existing antibodies. J Autoimmun. 2022;126:102779. [PubMed] [Google Scholar]
Centre of Disease Control and Prevention [Internet]. Science Brief: Omicron (B.1.1.529) variant; 2021 [cited 2022 Feb 20]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/scientific-brief-omicron-variant.html
Mohammadi M, Shayestehpour M, Mirzaei H. The impact of spike mutated variants of SARS-CoV2 [Alpha, Beta, Gamma, Delta, and Lambda] on the efficacy of subunit recombinant vaccines. Braz J Infect Dis. 2021;25(4):101606. [PubMed] [Google Scholar]
Meng B, Kemp SA, Papa G, Datir R, Ferreira IA, Marelli S, Harvey WT, Lytras S, Mohamed A, Gallo G, Thakur N, Collier DA, Mlcochova P; COVID-19 Genomics UK (COG-UK) Consortium 7; Duncan LM, Carabelli AM, Kenyon JC, Lever AM, Marco AD, Saliba C, Culap K, Cameroni E, Matheson NJ, Piccoli L, Corti D, James LC, Robertson DL, Bailey D, Gupta RK. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep. 2021;35(13):109292. [PubMed] [Google Scholar]
Barnes CO, Jette CA, Abernathy ME, Dam KM, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West Jr AP, Bjorkman PJ. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature. 2020 Dec;588(7839):682-7. [PubMed] [Google Scholar]
World Health Organization [Internet]. Coronavirus disease (COVID-19): vaccine access and allocation; 2020 [cited 2021 Jul 31]. Available from: https://www.who.int/news-room/q-a-detail/coronavirus-disease-(covid-19)-vaccine-access-and-allocation
Cella E, Benedetti F, Fabris S, Borsetti A, Pezzuto A, Ciotti M, Pascarella S, Ceccarelli G, Zella D, Ciccozzi M, Giovanetti M. SARS-CoV-2 lineages and sublineages circulating worldwide: a dynamic overview. Chemotherapy. 2021;66(1-2):3-7. [PubMed] [Google Scholar]
Tenthorey JL, Young C, Sodeinde A, Emerman M, Malik HS. Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races. Elife. 2020;9:e59988. [PubMed] [Google Scholar]
Guruprasad L. Human SARS CoV-2 spike protein mutations. Proteins. 2021;89(5):569-76. [PubMed] [Google Scholar]
SeyedAlinaghi S, Mehrtak M, MohsseniPour M, Mirzapur P, Barzegary A, Habibi P, Moradmand-Badie B, Afsahi
M, Karimi A, Heydari M, Mehraeen E, Dadras O, Sabatier JM, Voltarelli F. Genetic susceptibility of COVID-19: a systematic review of current evidence. Eur J Med Res. 2021;26(1):46. [PubMed] [Google Scholar]
Abdelzaher H, Saleh BM, Ismail HA, Hafiz M, Gabal MA, Mahmoud M, Hashish S, Gawad RM, Gharieb RY, Abdelnaser A. COVID-19 genetic and environmental risk factors: a look at the evidence. Front Pharmacol. 2020;11:579415. [PubMed] [Google Scholar]
Bhattacharya S, Basu P, Poddar S. Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic. J Prev Med Hyg. 2020 Jul 4;61(2):E130-E136. [PubMed] [Google Scholar]
Kyriakidis NC, López-Cortés A, González EV, Grimaldos AB, Prado EO. SARS-CoV-2 vaccines strategies: a comprehensive review of phase 3 candidates. NPJ Vaccines. 2021;6(1):28. [PubMed] [Google Scholar]
Singh J, Rahman SA, Ehtesham NZ, Hira S, Hasnain SE. SARS-CoV-2 variants of concern are emerging in India. Nat Med. 2021;27(7):1131-3. [PubMed] [Google Scholar]
Liu L, Wei Q, Lin Q, Fang J, Wang H, Kwok H, Tang H, Nishiura K, Peng J, Tan Z, Wu T, Cheung KW, Chan KH, Alvarez X, Qin C, Lackner A, Perlman S, Yuen KY, Chen Z. Anti-spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection. JCI Insight. 2019;4(4):e123158. [PubMed][Google Scholar]
Wang Q, Zhang L, Kuwahara K, Li L, Liu Z, Li T, Zhu H, Liu J, Xu Y, Xie J, Morioka H, Sakaguchi N, Qin C, Liu G. Correction: immunodominant SARS Coronavirus epitopes in humans elicited both enhancing and neutralizing effects on infection in non-human primates. ACS Infect Dis. 2020;6(5):1284-5. [PubMed] [Google Scholar]
Lee WS, Wheatley AK, Kent SJ, DeKosky BJ. Antibodydependent enhancement and SARS-CoV-2 vaccines and therapies. Nat Microbiol. 2020;5(10):1185-91. [PubMed] [Google Scholar]
Centre for Disease Control and Prevention [Internet]. COVID-19 vaccine breakthrough case investigation and reporting; 2021 [cited 2021 Aug 8]. Available from: https://www.cdc.gov/vaccines/covid-19/healthdepartments/breakthrough-cases.html
Levine-Tiefenbrun M, Yelin I, Katz R, Herzel E, Golan Z, Schreiber L, Wolf T, Nadler V, Ben-Tov A, Kuint J, Gazit S, Patalon T, Chodick G, Kishony R. Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine. Nat Med. 2021;27(5):790-2. [PubMed] [Google Scholar]
Gohil SK, Olenslager K, Quan KA, Dastur CK, Afsar N, Chang W, Huang SS. Asymptomatic and symptomatic COVID-19 infections among health care personnel before and after vaccination. JAMA Netw Open. 2021;4(7):e2115980. [PubMed] [Google Scholar]
Chatterjee R, Bhattacharya S, Tilak R. Is man the new prospective amplifying host? Evolving faces of SARSCoV dynamics and the epidemiological challenges. J Commun Dis. 2021;53(2):89-99. [Google Scholar]
He D, Zhao S, Lin Q, Zhuang Z, Cao P, Wang MH, Yang L. The relative transmissibility of asymptomatic COVID-19 infections among close contacts. Int J Infect Dis. 2020;94:145-7. [PubMed] [Google Scholar]
Huang Y, Yang C, Xu XF, Xu W, Liu SW. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin. 2020;41(9):1141-9. [PubMed] [Google Scholar]
Copyright (c) 2022 Open Access
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.