A comparative overview of SARS‑CoV‑2 and its variants of concern (original) (raw)

Abstract

ID-19, which evolved from the SARS-CoV wild-type virus. Several novel variations developed during the COVID-19 pandemic, some of which are known as Variants of Concern (VOC). VOCs are classified as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) by WHO [1]. These five SARS-CoV-2 VOCs have a substantial level of pathogenicity and transmissibility. New SARS-CoV-2 variants widely recognized as variations of interest (VOI) have been determined based on their transmissibility, severity of sickness, diagnostic escape, and immunological escape. In December 2019, the severe acute respiratory syndrome 2 (SARS-CoV-2) coronavirus outbreak began in Wuhan, China, and quickly spread to practically every corner of the globe, killing millions of people. SARS-CoV-2 produced numerous variants, five of which have been identified as variants of concern (VOC) by the World Health Organization (WHO) (Alpha, Beta, Gamma, Delta, and Omicron). We conducted a comparative epidemiological analysis of SARS-CoV-2 and its VOC in this paper. We compared the effects of vari-SUMMARY ous spike (S) protein mutations in SARS-CoV-2 and its VOC on transmissibility, illness severity, hospitalization risk, fatality rate, immunological evasion, and vaccine efficacy in this review. We also looked into the clinical characteristics of patients infected with SARS-CoV-2 and its VOC.

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References (100)

  1. Aleem A, Samad AB, Slenker AK. Emerging variants of SARS-CoV-2 and novel therapeutics against corona- virus (COVID-19). InStatPearls [Internet]. StatPearls Publishing: 2022.
  2. Zhang L, Jackson CB, Mou H, et al. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun. 2020; 11 (1), 1-9.
  3. Wu L, Zhou L, Mo M, et al. SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2. Signal Trans- duct Target Ther. 2022; 7 (1), 1-3.
  4. Lai C-C, Shih T-P, Ko W-C, Tang H-J, Hsueh P-R. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COV- ID-19): The epidemic and the challenges. Int J Antimi- crob Agents. 2020; 55 (3), 105924.
  5. Wang MY, Zhao R, Gao LJ, Gao X-F, Wang DP, Cao JM. SARS-CoV-2: structure, biology, and struc- ture-based therapeutics development. Front Cell Infect Microbiol. 2020; 724.
  6. Khailany RA, Safdar M, Ozaslan M. Genomic char- acterization of a novel SARS-CoV-2. Gene reports. 2020; 19, 100682.
  7. Xie Y, Karki CB, Du D, et al. Spike proteins of SARS- CoV and SARS-CoV-2 utilize different mechanisms to bind with human ACE2. Front Mol Biosci. 2020; 392.
  8. Xia S, Liu M, Wang C, et al. Inhibition of SARS- CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res. 2020; 30 (4), 343-355.
  9. Lan J, Ge J, Yu J, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 re- ceptor. Nature. 2020; 581 (7807), 215-220.
  10. Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020; 181 (2), 281-292. e6.
  11. Johnson BA, Xie X, Kalveram B, et al. Furin cleav- age site is key to SARS-CoV-2 pathogenesis. BioRxiv. 2020.
  12. Laha S, Chakraborty J, Das S, Manna SK, Biswas S, Chatterjee R. Characterizations of SARS-CoV-2 muta- tional profile, spike protein stability and viral transmis- sion. Infect Genet Evol. 2020; 85, 104445.
  13. Gram MA, Nielsen J, Schelde AB, et al. Vaccine ef- fectiveness against SARS-CoV-2 infection, hospitaliza- tion, and death when combining a first dose ChAdOx1 vaccine with a subsequent mRNA vaccine in Denmark: A nationwide population-based cohort study. PLoS Med. 2021; 18 (12), e1003874.
  14. Chadeau-Hyam M, Wang H, Eales O, et al. SARS- CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random commu- nity surveys. Lancet Respir Med. 2022; 10 (4), 355-366.
  15. Chemaitelly H, Yassine HM, Benslimane FM, et al. mRNA-1273 COVID-19 vaccine effectiveness against the B. 1.1. 7 and B. 1.351 variants and severe COVID-19 disease in Qatar. Nat Med. 2021; 27 (9), 1614-1621.
  16. Walter EB, Talaat KR, Sabharwal C, et al. Evalua- tion of the BNT162b2 COVID-19 vaccine in children 5 to 11 years of age. N Engl J Med. 2022; 386 (1), 35-46.
  17. Pilishvili T, Gierke R, Fleming-Dutra KE, et al. Ef- fectiveness of mRNA Covid-19 vaccine among US health care personnel. N Engl J Med. 2021; 385 (25), e90.
  18. Barda N, Dagan N, Cohen C, et al. Effectiveness of a third dose of the BNT162b2 mRNA COVID-19 vac- cine for preventing severe outcomes in Israel: an obser- vational study. The Lancet. 2021; 398 (10316), 2093-2100.
  19. Saciuk Y, Kertes J, Shamir Stein N, Ekka Zohar A. Effectiveness of a third dose of BNT162b2 mRNA vac- cine. J Infect Dis. 2022; 225 (1), 30-33.
  20. Mohammadi M, Shayestehpour M, Mirzaei H. The impact of spike mutated variants of SARS-CoV2 [Al- pha, Beta, Gamma, Delta, and Lambda] on the efficacy of subunit recombinant vaccines. Braz J Infect Dis. 2021;
  21. Yang T-J, Yu P-Y, Chang Y-C, et al. Effect of SARS- CoV-2 B. 1.1. 7 mutations on spike protein structure and function. Nat Struct Mol Biol. 2021; 28 (9), 731-739.
  22. Liu Y, Liu J, Plante KS, et al. The N501Y spike sub- stitution enhances SARS-CoV-2 infection and transmis- sion. Nature. 2022; 602 (7896), 294-299.
  23. Fiorentini S, Messali S, Zani A, et al. First detection of SARS-CoV-2 spike protein N501 mutation in Italy in August, 2020. Lancet Infect. Dis. 2021; 21 (6), e147.
  24. 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.
  25. Challen R, Brooks-Pollock E, Read JM, Dyson L, Tsaneva-Atanasova K, Danon L. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. Brit Med J. 2021; 372, n579.
  26. Bernal JL, Andrews N, Gower C, et al. Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) vari- ant. N Engl J Med. 2021; 385, 585-594.
  27. Mahase E. Covid-19: Novavax vaccine efficacy is 86% against UK variant and 60% against South African variant. Brit Med J. 2021; 372, n296.
  28. Funk T, Pharris A, Spiteri G, et al. Characteristics of SARS-CoV-2 variants of concern B. 1.1. 7, B. 1.351 or P. 1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021; 26 (16), 2100348.
  29. Arena F, Pollini S, Rossolini GM, Margaglione M. Summary of the available molecular methods for detec- tion of SARS-CoV-2 during the ongoing pandemic. In J Mol Sci. 2021; 22 (3), 1298.
  30. Choi JY, Smith DM. SARS-CoV-2 variants of con- cern. Yonsei Med J. 2021; 62 (11), 961-968
  31. Singer SR, Angulo FJ, Swerdlow DL, et al. Effec- tiveness of BNT162b2 mRNA COVID-19 vaccine against SARS-CoV-2 variant Beta (B. 1.351) among per- sons identified through contact tracing in Israel: A pro- spective cohort study. EClinicalMedicine. 2021; 42, 101190.
  32. Davies NG, Abbott S, Barnard RC, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B. 1.1. 7 in England. Science. 2021; 372 (6538), eabg3055.
  33. Naveca F, Nascimento V, Souza V, et al. Phyloge- netic relationship of SARS-CoV-2 sequences from Ama- zonas with emerging Brazilian variants harboring mu- tations E484K and N501Y in the Spike protein. Virologi- cal Org. 2021; 1, 1-8.
  34. Naveca F, Costa CD, Nascimento V, Souza V, et al. Three SARS-CoV-2 reinfection cases by the new Variant of Concern (VOC) P.1/501Y.V3. Res Sq. 2021..
  35. Sabino EC, Buss LF, Carvalho MP, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprev- alence. The Lancet. 2021; 397 (10273), 452-455.
  36. Charmet T, Schaeffer L, Grant R, et al. Impact of original, B. 1.1. 7, and B. 1.351/P. 1 SARS-CoV-2 line- ages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-con- trol study in France. The Lancet Regional Health-Europe. 2021; 8, 100171.
  37. Tatsi E-B, Filippatos F, Michos A. SARS-CoV-2 var- iants and effectiveness of vaccines: a review of current evidence. Epidemiol Infect. 2021; 1-24.
  38. Zhang L, Jackson CB, Mou H, et al. The D614G mu- tation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. BioRxiv. 2020.
  39. Christie A, Brooks JT, Hicks LA, et al. Guidance for implementing COVID-19 prevention strategies in the context of varying community transmission levels and vaccination coverage. Morb Mort Wkly Rep. 2021; 70 (30), 1044.
  40. Chen J, Wang R, Wang M, Wei G-W. Mutations strengthened SARS-CoV-2 infectivity. J Mol Biol. 2020; 432 (19), 5212-5226.
  41. McCallum M, Walls AC, Sprouse KR, et al. Molecular basis of immune evasion by the Delta and Kappa SARS- CoV-2 variants. Science. 2021; 374 (6575), 1621-1626.
  42. Bruxvoort KJ, Sy LS, Qian L, et al. Effectiveness of mRNA-1273 against delta, mu, and other emerging variants of SARS-CoV-2: test negative case-control study. Brit Med J. 2021; 375.
  43. Deb P, Molla M, Ahmed M, Saif-Ur-Rahman K, Das MC, Das D. A review of epidemiology, clinical features and disease course, transmission dynamics, and neu- tralization efficacy of SARS-CoV-2 variants. Egypt J Bronchol. 2021; 15 (1), 1-14.
  44. Ella R, Reddy S, Blackwelder W, et al. Efficacy, safe- ty, and lot-to-lot immunogenicity of an inactivated SARS-CoV-2 vaccine (BBV152): interim results of a ran- domised, double-blind, controlled, phase 3 trial. The Lancet. 2021; 398 (10317), 2173-2184.
  45. Kim S, Nguyen TT, Taitt AS, et al. SARS-CoV-2 Omicron mutation is faster than the chase: multiple mutations on spike/ACE2 Interaction Residues. Im- mune Netw. 2021; 21 (6).
  46. Pulliam JR, van Schalkwyk C, Govender N, et al. Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa. MedRxiv. 2021.
  47. Chen J, Wang R, Gilby NB, Wei GW. Omicron vari- ant (B.1.1.529): infectivity, vaccine breakthrough, and an- tibody resistance. J Chem Inf Model. 2022; 62 (2), 412-422.
  48. Muik A, Lui BG, Wallisch A-K, et al. Neutralization of SARS-CoV-2 Omicron by BNT162b2 mRNA vaccine- elicited human sera. Science. 2022; eabn7591.
  49. Collie S, Champion J, Moultrie H, Bekker L-G, Gray G. Effectiveness of BNT162b2 vaccine against omicron variant in South Africa. N Engl J Med. 2022; 386 (5), 494-496.
  50. Hansen CH, Schelde AB, Moustsen-Helms IR, et al. Vaccine effectiveness against SARS-CoV-2 infection with the Omicron or Delta variants following a two- dose or booster BNT162b2 or mRNA-1273 vaccination series: A Danish cohort study. medRxiv. 2021.
  51. Evans JP, Zeng C, Qu P, et al. Neutralization of SARS- CoV-2 Omicron sub-lineages BA.1, BA.1.1, and BA.2. Cell Host Microbe. 2022. doi: 10.1016/j.chom.2022.04.014.
  52. Cucinotta D, Vanelli M. WHO declares COVID-19 a pandemic. Acta Bio Medica: Atenei Parmensis. 2020; 91 (1), 157.
  53. Zhu N, Zhang D, Wang W, et al. A novel coronavi- rus from patients with pneumonia in China, 2019. N Engl J Med. 2020; 382 (8), 727-733.
  54. Sharma A, Tiwari S, Deb MK, Marty JL. Severe acute respiratory syndrome coronavirus-2 (SARS- CoV-2): a global pandemic and treatment strategies. Int J Antimicrob Agents. 2020; 56 (2), 106054.
  55. Meyerowitz EA, Richterman A, Gandhi RT, Sax PE. Transmission of SARS-CoV-2: a review of viral, host, and environmental factors. Ann Intern Med. 2021; 174 (1), 69-79.
  56. Wang W, Xu Y, Gao R, et al. Detection of SARS- CoV-2 in different types of clinical specimens. JAMA. 2020; 323 (18), 1843-1844.
  57. Santarpia JL, Herrera VL, Rivera DN, et al. The in- fectious nature of patient-generated SARS-CoV-2 aero- sol. MedRxiv. 2020.
  58. Peiris JSM, Chu C-M, Cheng VC-C, et al. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospec- tive study. The Lancet. 2003; 361 (9371), 1767-1772.
  59. Shi J, Wen Z, Zhong G, et al. Susceptibility of fer- rets, cats, dogs, and other domesticated animals to SARS-coronavirus 2. Science. 2020; 368 (6494), 1016- 1020.
  60. Kotlyar AM, Grechukhina O, Chen A, et al. Vertical transmission of coronavirus disease 2019: a systematic review and meta-analysis. Am J Obstet Gynecol. 2021; 224 (1), 35-53. e3.
  61. Butt AA, Dargham SR, Chemaitelly H, et al. The global transmission of new coronavirus variants. Envi- ronmental research. JAMA Intern. Med. 2022; 182 (2), 197-205.
  62. Curran J, Dol J, Boulos L, et al. Transmission char- acteristics of SARS-CoV-2 variants of concern Rapid Scoping Review. medRxiv. 2021.
  63. Buchan SA, Tibebu S, Daneman N, et al. Increased household secondary attacks rates with variant of con- cern severe acute respiratory syndrome coronavirus 2 index cases. Clin Infect Dis. 2022; 74 (4), 703-706.
  64. Tegally H, Wilkinson E, Giovanetti M, et al. Detec- tion of a SARS-CoV-2 variant of concern in South Afri- ca. Nature. 2021; 592 (7854), 438-443.
  65. Maslo C, Friedland R, Toubkin M, Laubscher A, Akaloo T, Kama B. Characteristics and outcomes of hospitalized patients in South Africa during the COV- ID-19 Omicron wave compared with previous waves. JAMA. 2022; 327 (6), 583-584.
  66. Zhao Y, Huang J, Zhang L, Chen S, Gao J, Jiao H. The global transmission of new coronavirus variants. Environ Res. 2022; 206: 112240.
  67. Coutinho RM, Marquitti FMD, Ferreira LS, et al. Model-based estimation of transmissibility and reinfec- tion of SARS-CoV-2 P. 1 variant. Commun. Med. 2021; 1 (1), 1-8.
  68. Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of the P. 1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021; 372 (6544), 815-821.
  69. da Silva JF, Esteves RJ, Siza C, et al. Cluster of SARS-CoV-2 Gamma Variant Infections, Parintins, Bra- zil, March 2021. Emerg Infect Dis. 2022; 28 (1), 262.
  70. Pan A, Liu L, Wang C, et al. Association of public health interventions with the epidemiology of the COVID-19 outbreak in Wuhan, China. JAMA. 2020; 323 (19), 1915-1923.
  71. Inglesby TV. Public health measures and the repro- duction number of SARS-CoV-2. JAMA. 2020; 323 (21), 2186-2187.
  72. Liu Y, Gayle AA, Wilder-Smith A, Rocklöv J. The reproductive number of COVID-19 is higher compared to SARS coronavirus. J Travel Med. 2020; 27 (2), taaa021.
  73. Campbell F, Archer B, Laurenson-Schafer H, et al. Increased transmissibility and global spread of SARS- CoV-2 variants of concern as at June 2021. Eurosurveil- lance. 2021; 26 (24), 2100509.
  74. Salzberger B, Buder F, Lampl B, et al. Epidemiology of SARS-CoV-2. Infection. 2021; 49 (2), 233-239.
  75. Yang L, Dai J, Zhao J, Wang Y, Deng P, Wang J. Esti- mation of incubation period and serial interval of COV- ID-19: analysis of 178 cases and 131 transmission chains in Hubei province, China Epidemiol Infect. 2020; 148.
  76. Dhouib W, Maatoug J, Ayouni I, et al. The incubation period during the pandemic of COVID-19: a systematic review and meta-analysis. Syst Rev. 2021; 10 (1), 1-14.
  77. Li Q, Guan X, Wu P, et al. Early transmission dy- namics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl J Med. 2020; 382 (13), 1199-1207. doi: 10.1056/NEJMoa2001316.
  78. Varia M, Wilson S, Sarwal S, et al. Investigation of a nosocomial outbreak of severe acute respiratory syn- drome (SARS) in Toronto, Canada. CMAJ. 2003; 169 (4), 285-292.
  79. Virlogeux V, Fang VJ, Park M, Wu JT, Cowling BJ. Comparison of incubation period distribution of hu- man infections with MERS-CoV in South Korea and Saudi Arabia. Sci Rep. 2016; 6 (1), 1-7.
  80. Lauer SA, Grantz KH, Bi Q, et al. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and ap- plication. Ann Intern Med. 2020; 172 (9), 577-582.
  81. Homma Y, Katsuta T, Oka H, et al. The incubation period of the SARS-CoV-2 B1. 1.7 variant is shorter than that of other strains. J Infect. 2021; 83 (2), e15-e17.
  82. Grant R, Charmet T, Schaeffer L, et al. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a na- tionwide case-control study in France. The Lancet Re- gional Health-Europe. 2022; 13, 100278.
  83. Kremer C, Braeye T, Proesmans K, André E, Torneri A, Hens N. Observed serial intervals of SARS-CoV-2 for the Omicron and Delta variants in Belgium based on contact tracing data, 19 November to 31 December 2021. medRxiv. 2022.
  84. Hsu L, Grüne B, Buess M, et al. COVID-19 Break- through infections and transmission risk: real-world data analyses from Germany's largest public health de- partment (Cologne). Vaccines. 2021; 9 (11), 1267.
  85. Vitiello A, Ferrara F, Troiano V, La Porta R. COV- ID-19 vaccines and decreased transmission of SARS- CoV-2. Inflammopharmacology. 2021; 29 (5), 1357-1360.
  86. Prunas O, Warren JL, Crawford FW, et al. Vaccina- tion with BNT162b2 reduces transmission of SARS- CoV-2 to household contacts in Israel. Science. 2022, eabl4292.
  87. Harris RJ, Hall JA, Zaidi A, Andrews NJ, Dunbar JK, Dabrera G. Impact of vaccination on household transmission of SARS-COV-2 in England. medRxiv. 2021.
  88. Lyngse FP, Mølbak K, Denwood M, et al. Effect of Vaccination on household transmission of SARS-CoV-2 Delta VOC. medRxiv. 2022.
  89. Levine-Tiefenbrun M, Yelin I, Katz R, et al. Initial report of decreased SARS-CoV-2 viral load after inocu- lation with the BNT162b2 vaccine. Nat Med. 2021; 27 (5), 790-792.
  90. de Gier B, Andeweg S, Backer JA, et al. Vaccine ef- fectiveness against SARS-CoV-2 transmission to house- hold contacts during dominance of Delta variant (B. 1.617. 2), the Netherlands, August to September 2021. Euro Surveill. 2021; 26 (44), 2100977.
  91. Eyre DW, Taylor D, Purver M, et al. Effect of Cov- id-19 vaccination on transmission of alpha and delta variants. N Engl J Med. 2022; 386 (8), 744-756.
  92. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wu- han, China. The Lancet. 2020; 395 (10223), 497-506.
  93. Lei J, Li J, Li X, Qi X. CT imaging of the 2019 novel coronavirus (2019-nCoV) pneumonia. Radiology. 2020; 295 (1), 18.
  94. Hu Z, Huang X, Zhang J, Fu S, Ding D, Tao Z. Dif- ferences in clinical characteristics between Delta Vari- ant and Wild-Type SARS-CoV-2 Infected Patients. Front Med. 2021; 8.
  95. Ong SW, Chiew CJ, Ang LW, et al. Clinical and vi- rological features of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern: a ret- rospective cohort study comparing B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta). Clin Infect Dis. 2021; ciab721.
  96. Taha SI, Samaan SF, Shata AK, Baioumy SA, Abdal- geleel SA, Youssef MK. Baseline characteristics and out- comes of 180 Egyptian COVID-19 patients admitted to quarantine hospitals of Ain Shams University: a retro- spective comparative study. Afro-Egypt J Infect Endem Dis. 2021; 11 (3), 295-305.
  97. Fouad SH, Allam MF, Ibrahim S, et al. ICU admis- sion of COVID-19 patients: identification of risk factors. Egypt. J. Anaesth. 2021; 37 (1), 202-207.
  98. Luna-Muschi A, Borges IC, de Faria E, et al. Clinical features of COVID-19 by SARS-CoV-2 Gamma variant: A prospective cohort study of vaccinated and unvacci- nated healthcare workers. J Infect. 2022; 84 (2), 248-288.
  99. Kim M-K, Lee B, Choi YY, et al. Clinical Character- istics of 40 Patients Infected With the SARS-CoV-2 Omi- cron Variant in Korea. J Korean Med Sci. 2022; 37 (3).
  100. Lee JJ, Choe YJ, Jeong H, et al. Importation and transmission of SARS-CoV-2 B. 1.1. 529 (omicron) vari- ant of concern in Korea, November 2021. J Korean Med Sci. 2021; 36 (50).