SARS-CoV-2’NİN SÜREGELEN EVRİMİ: PANDEMİNİN SONUNA NE KADAR YAKINIZ?

Year 2022, Volume: 6 Issue: 3, 201 - 212, 30.12.2022

Elmas Pınar Kahraman Kılbaş , Mustafa Altındiş

https://doi.org/10.34084/bshr.1200144

Abstract

Pandeminin başlangıcından bu yana SARS-CoV-2 genomunun dizilenmesi, viral evrimin anlaşılmasına katkıda bulunmakta ve COVID-19 hastalığının kökenleri ve yayılmasına yönelik genomik epidemiyoloji araştırmalarına olanak sağlamaktadır. SARS-CoV-2, diğer RNA virüslerine benzer şekilde sürekli mutasyona uğramakta ve yeni varyantlar ortaya çıkmaktadır. SARS-CoV-2 varyantları arasında, bunların yalnızca bir kısmı, daha bulaşıcı oldukları ve daha ağır hastalıklara neden oldukları için halk sağlığı açısından risk oluşturabilmektedir. Bu mutasyonlar virüse seçici bir avantaj sağlayabilirler. Varyantlar insan sağlığı açısıdan daha riskli hale geldiğinde, endişe verici varyantlar (VOC) olarak adlandırılmaktadırlar. 2021 yılının Kasım ayına kadar pandeminin hâkimi olan Delta varyantı, hastaneye yatış ve ölüm riskinin artmasına neden olmuştur, ancak mevcut aşılar bu varyanta karşı etkilidir. Son varyant olan Omicron, artan bulaşabilirlik ve azalmış antikor duyarlılığı ile karakterize edilmektedir. Bu derlemede, SARS-CoV-2 varyantlarının bulaşıcılıkları, hastalığın şiddeti ve bağışıklık duyarlılıkları ile ilgili bilgiler incelenecektir.

Keywords

COVID-19, SARS-CoV-2, Varyant, Mutasyon

THE CONTINUOUS EVOLUTION OF SARS-CoV-2: HOW CLOSE ARE WE TO THE END OF THE PANDEMIC?

Abstract

Sequencing the SARS-CoV-2 genome since the onset of the pandemic has contributed to the understanding of viral evolution and has enabled genomic epidemiology investigations into the origins and spread of COVID-19 disease. Similar to other RNA viruses, SARS-CoV-2 is constantly mutating and new variants appear. Among the SARS-CoV-2 variants, only some of them pose a public health risk because they are more contagious and cause more severe diseases. These mutations can give the virus a selective advantage. When variants become more risky to human health, they are called variants of concern (VOC). The Delta variant, which dominated the pandemic until November 2021, has resulted in an increased risk of hospitalization and death, but current vaccines are effective against this variant. The last variant, Omicron, is characterized by increased transmissibility and decreased antibody sensitivity. In this review, information about the contagiousness of SARS-CoV-2 variants, the severity of the disease and their immune susceptibility will be examined.

Keywords

COVID 19, SARS-CoV-2, Variant, Mutation

References

• 1. Ferron F, Subissi L, De Morais ATS, Le NTT, Sevajol M, Gluais L, et al. Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA. Proceedings of the National Academy of Sciences 2018;115(2): E162-E171.
• 2. Janik E, Niemcewicz M, Podogrocki M, Majsterek I, Bijak M. The Emerging Concern and Interest SARS-CoV-2 Variants. Pathogens 2021; 10(6): 633.
• 3. Burki T. Understanding variants of SARS-CoV-2. The Lancet 2021; 397(10273): 462.
• 4. Centers for Disease Control and Prevention (CDC). Erişim tarihi: 30.09.2021. Available from: https://www.cdc.gov/coronavirus/2019-ncov/variants/delta-variant.html
• 5. World Health Organization (WHO). Erişim tarihi: 24.07.2021. Available from: https://apps.who.int/iris/handle/10665/338480 adresinden 30 Eylül 2021 tarihinde alınmıştır (a)
• 6. 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. Nature communications 2020; 11(1): 1-9.
• 7. 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.
• 8. Becerra FM, Cardozo T. SARS‐CoV‐2 viral spike G614 mutation exhibits higher case fatality rate. International journal of clinical practice 2020; 74(8): e13525.
• 9. World Health Organization (WHO). Erişim tarihi: 19.03.2022. Available from: https://www.who.int/publications/m/item/update-74-addressing-the-challenges-of-sars-cov-2-variants-for-public-health
• 10. Cov-lineages. Erişim tarihi: 23.03.2022. Available from: https://cov-lineages.org/global_report_B.1.1.7.html
• 11. Kim JS, Jang JH, Kim JM, Chung YS, Yoo CK, Han MG. Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome. Osong Public Health Res Perspect 2020; 11(3): 101-111.
• 12. Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. CMMID COVID-19 Working Group; COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 2021; 372(6538): eabg3055.
• 13. Wang P, Nair MS, Liu L, Iketani S, Luo Y, Guo Y, et al. Antibody resistance of SARS-CoV-2 variants B. 1.351 and B. 1.1. 7. Nature 2021; 593(7857): 130-135.
• 14. Gu H, Chen Q, Yang G, He L, Fan H, Deng YQ, et al. Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science 2020; 369(6511): 1603-1607.
• 15. 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: 2020.12.29.424708; doi: https://doi.org/10.1101/2020.12.29.424708
• 16. Pereira F. SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Biochemical and biophysical research communications 2021; 550: 8-14.
• 17. Shen X, Tang H, McDanal C, Wagh K, Fischer W, Theiler J, et al. SARS-CoV-2 variant B. 1.1. 7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines. Cell host & microbe 2021; 29(4): 529-539.
• 18. Graham MS, Sudre CH, May A, Antonelli M, Murray B, Varsavsky T, et al. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B. 1.1. 7: an ecological study. The Lancet Public Health 2021; 6(5): e335-e345.
• 19. Grint DJ, Wing K, Williamson E, McDonald HI, Bhaskaran K, Evans D, et al. Case fatality risk of the SARS-CoV-2 variant of concern B. 1.1. 7 in England, 16 November to 5 February. Eurosurveillance 2021; 26(11): 2100256.
• 20. Davies NG, Jarvis CI, Edmunds WJ, Jewell NP, Diaz-Ordaz K, Keogh RH. Increased mortality in community-tested cases of SARS-CoV-2 lineage B. 1.1. 7. Nature 2021; 593(7858): 270-274.
• 21. Calistri P, Amato L, Puglia I, Cito F, Di Giuseppe A, Danzetta ML, et al. Infection sustained by lineage B. 1.1. 7 of SARS-CoV-2 is characterised by longer persistence and higher viral RNA loads in nasopharyngeal swabs. International Journal of Infectious Diseases 2021; 105: 753-755.
• 22. Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 2021; 593(7857): 136-141.
• 23. 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:2021.01.25.427948. doi: 10.1101/2021.01.25.427948.
• 24. Muik A, Wallisch AK, Sänger B, Swanson KA, Mühl J, Chen W, et al. Neutralization of SARS-CoV-2 lineage B. 1.1. 7 pseudovirus by BNT162b2 vaccine–elicited human sera. Science 2021; 371(6534): 1152-1153.
• 25. Mwenda M, Saasa N, Sinyange N, Busby G, Chipimo PJ, Hendry J, et al. (2021). Detection of B. 1.351 SARS-CoV-2 Variant Strain—Zambia, December 2020.
• 26. Cov-lineages. Erişim tarihi: 10.03.2022. Available from: https://cov-lineages.org/global_report_B.1.351.html
• 27. Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KH, Dingens AS, et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 2020; 182(5): 1295-1310.
• 28. Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, Chu HY, et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe 2021; 29(3): 463-476.
• 29. Cov-lineages. Erişim tarihi: 13.03.2022. Available from: https://cov-lineages.org/global_report_P.1.html
• 30. Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020; 5(11): 1403-1407.
• 31. Sabino EC, Buss LF, Carvalho MPS, Prete CA Jr, Crispim MAE, Fraiji NA, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet 2021; 397(10273): 452-455.
• 32. Wang P, Casner RG, Nair MS, Wang M, Yu J, Cerutti G, et al. Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe 2021; 29(5): 747-751.
• 33. De Souza WM, Amorim MR, Sesti-Costa R, Coimbra LD, Toledo-Teixeira DA, Parise PL, et al. Levels of SARS-CoV-2 lineage P.1 neutralization by antibodies elicited after natural infection and vaccination. SSRN 3793486 [Preprint]. 2021. http://dx.doi.org/10.2139/ ssrn.3793486
• 34. European Centre for Disease Prevention and Control (ECDC). Erişim tarihi: 22.06.2021. Available from: https://www.ecdc.europa.eu/en/publications-data/threat-assessment-emergence-and-impact-sars-cov-2-delta-variant adresinden 30 Eylül 2021 tarihinde alınmıştır.
• 35. American Society for Microbiology. Erişim tarihi: 30.12.2021. Available from: https://asm.org/Articles/2021/July/How-Dangerous-is-the-Delta-Variant-B-1-617-2
• 36. UpToDate. Erişim tarihi: 30.12.2021. Available from: https://www.uptodate.com/contents/covid-19-epidemiology-virology-and-prevention#H874583070
• 37. Riley S, Walters CE, Wang H, Eales O, Haw D, Ainslie KE, et al. REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant. medRxiv 2021.06.17.21259103; doi: https://doi.org/10.1101/2021.06.17.21259103
• 38. Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, et al. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022; 13(1): 460.
• 39. 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; 596(7871): 276-280.
• 40. Cov-lineages, Global Lineage Reports. Erişim tarihi: 15.03.2022. Available from: https://cov-lineages.org/global_report_B.1.617.2.html
• 41. Centers for Disease Control and Prevention (CDC). Erişim tarihi: 03.01.2022. Available from: https://www.cdc.gov/coronavirus/2019-ncov/variants/omicron-variant.html.
• 42. European Centre for Disease Prevention and Control (ECDC). Erişim tarihi: 03.01.2022. Available from: https://www.ecdc.europa.eu/en/news-events/epidemiological-update-omicron-variant-concern-voc-data-11-december-2021.
• 43. Liu L, Iketani S, Guo Y, Chan JF, Wang M, Liu L, et al. Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature 2022; 602(7898): 676-681.
• 44. McCreesh N, Dlamini V, Edwards A, Oliver S, Dayi N, Dikgale K, et al. Impact of the COVID-19 epidemic and related social distancing regulations on social contact and SARS-CoV-2 transmission potential in rural South Africa: Analysis of repeated cross-sectional surveys. BMC Infect Dis 2021; 21: 928. doi: 10.1186/s12879-021-06604-8.
• 45. Abbott S, Hellewell J, Thompson RN, Sherratt K, Gibbs HP, Bosse NI, et al. Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts. Wellcome Open Res 2020; 5: 112.
• 46. Dünya Sağlık Örgütü’nün 17.08.2022 Tarihli Yeni Koronavirüs (COVID-19) Haftalık Durum Raporu. https://www.seyahatsagligi.gov.tr/Site/HaberDetayi/3710 (21.09.2022)
• 47. World Health Organization. Weekly epidemiological update on covid-19. Jul 2022. https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19-27-july- 2022 (19.08.2022).
• 48. H. Tegally, M. Moir, J. Everatt, M. Giovanetti, C. Scheepers, E. Wilkinson, et al. Continued emergence and evolution of Omicron in South Africa: new BA.4 and BA.5 lineages [preprint] May 2, medRxiv (2022), https://doi.org/10.1101/2022.05.01.22274406.
• 49. D. Yamasoba, Y. Kosugi, I. Kimura, S. Fujita, K. Uriu, J. Ito, K. Sato, Sensitivity of novel SARS-CoV-2 Omicron subvariants, BA.2.11, BA.2.12.1, BA.4 and BA.5 to therapeutic monoclonal antibodies [preprint] May 3, bioRxiv (2022), https://doi.org/10.1101/2022.05.03.490409.
• 50. K. Khan, F. Karim, Y. Ganga, M. Bernstein, Z. Jule, K. Reedoy, et al. Omicron sub-lineages BA.4/BA.5 escape BA.1 infection elicited neutralizing immunity [preprint] May 1, medRxiv (2022), https://doi.org/10.1101/2022.04.29.22274477.
• 51. Saxena SK, Kumar S, Ansari S, Paweska JT, Maurya VK, Tripathi AK, et al. Characterization of the novel SARS-CoV-2 Omicron (B.1.1.529) variant of concern and its global perspective. J Med Virol 2022; 94(4): 1738-1744.
• 52. Mannar D, Saville JW, Zhu X, Srivastava SS, Berezuk AM, Tuttle KS, et al. SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science 2022; 375(6582): 760-764.
• 53. Song WJ, Hui CKM, Hull JH, Birring SS, McGarvey L, Mazzone SB, et al. Confronting COVID-19-associated cough and the post-COVID syndrome: role of viral neurotropism, neuroinflammation, and neuroimmune responses. Lancet Respir Med 2021; 9(5): 533-544.
• 54. Dong M, Zhang J, Ma X, Tan J, Chen L, Liu S, et al. ACE2, TMPRSS2 distribution and extrapulmonary organ injury in patients with COVID-19. Biomed Pharmacother 2020; 131: 110678.
• 55. McNamara LA, Wiegand RE, Burke RM, Sharma AJ, Sheppard M, Adjemian J, et al. Estimating the early impact of the US COVID-19 vaccination programme on COVID-19 cases, emergency department visits, hospital admissions, and deaths among adults aged 65 years and older: an ecological analysis of national surveillance data. Lancet 2022; 399(10320): 152-160.
• 56. Ioannou GN, Locke ER, O'Hare AM, Bohnert ASB, Boyko EJ, Hynes DM, et al. COVID-19 Vaccination Effectiveness Against Infection or Death in a National U.S. Health Care System: A Target Trial Emulation Study. Ann Intern Med 2021; 175(3): 352-361.
• 57. Xu S, Huang R, Sy LS, Glenn SC, Ryan DS, Morrissette K, et al. COVID-19 Vaccination and Non-COVID-19 Mortality Risk - Seven Integrated Health Care Organizations, United States, December 14, 2020-July 31, 2021. MMWR Morb Mortal Wkly Rep 2021; 70(43): 1520-1524.
• 58. Centers for Disease Control and Prevention (CDC). Erişim tarihi: 24.02.2022. Available from: https://www.cdc.gov/vaccines/covid-19/clinical-considerations/covid-19-vaccines-us.html
• 59. Centers for Disease Control and Prevention (CDC). Erişim tarihi: 20.11.2021. Available from: https://www.cdc.gov/media/releases/2021/s1119-booster-shots.html
• 60. Centers for Disease Control and Prevention (CDC). Erişim tarihi: 05.01.2022. Available from: https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2022-01-05/06_COVID_Oliver_2022-01-05.pdf
• 61. US Food and Drug Administration (FDA). Erişim tarihi: 03.01.2022. Available from: https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-takes-multiple-actions-expand-use-pfizer-biontech-covid-19-vaccine
• 62. Centers for Disease Control and Prevention (CDC). Erişim tarihi: 05.01.2022. Available from: https://www.cdc.gov/media/releases/2022/s0104-Pfizer-Booster.html
• 63. Klein NP, Stockwell MS, Demarco M, Gaglani M, Kharbanda AB, Irving SA, et al. Effectiveness of COVID-19 Pfizer-BioNTech BNT162b2 mRNA Vaccination in Preventing COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Nonimmunocompromised Children and Adolescents Aged 5–17 Years — VISION Network, 10 States, April 2021–January 2022. MMWR Morb Mortal Wkly Rep 2022; 71: 352–358.
• 64. Collie S, Champion J, Moultrie H, Bekker LG, Gray G. Effectiveness of BNT162b2 Vaccine against Omicron Variant in South Africa. N Engl J Med 2022; 386: 494.
• 65. Thompson MG, Natarajan K, Irving SA, Rowley EA, Griggs EP, Gaglani M, et al. Effectiveness of a Third Dose of mRNA Vaccines Against COVID-19-Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance - VISION Network, 10 States, August 2021-January 2022. MMWR Morb Mortal Wkly Rep 2022; 71: 139-145.
• 66. Johnson AG, Amin AB, Ali AR, Hoots B, Cadwell BL, Arora S, et al. COVID-19 Incidence and Death Rates Among Unvaccinated and Fully Vaccinated Adults with and Without Booster Doses During Periods of Delta and Omicron Variant Emergence - 25 U.S. Jurisdictions, April 4-December 25, 2021. MMWR Morb Mortal Wkly Rep 2022; 71: 132-138.
• 67. Danza P, Koo TH, Haddix M, Fisher R, Traub E, OYong K, et al. SARS-CoV-2 Infection and Hospitalization Among Adults Aged ≥18 Years, by Vaccination Status, Before and During SARS-CoV-2 B.1.1.529 (Omicron) Variant Predominance - Los Angeles County, California, November 7, 2021-January 8, 2022. MMWR Morb Mortal Wkly Rep 2022; 71: 177-181.
• 68. WHO. WHO SAGE roadmap for prioritizing uses of COVID-19 vaccines. https://www.who.int/publications/i/item/who-sage-roadmap-for-prioritizing-uses-of-covid-19-vaccines-in-the-context-of-limited-supply, accessed 20 January 2022).
• 69. Interim statement on decision-making considerations for the use of variant updated COVID-19 vaccines. https://www.who.int/news/item/17-06-2022-interim-statement-on-decision-making-considerations-for-the-use-of-variant-updated-covid-19-vaccines (18.06.2022)
• 70. Kannan S, Shaik Syed Ali P, Sheeza A. Omicron (B.1.1.529) - variant of concern - molecular profile and epidemiology: a mini review. Eur Rev Med Pharmacol Sci 2021; 25(24): 8019-8022.
• 71. UK Health Security Agency. Erişim tarihi: 07.03.2022. Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_dat a/file/1036324/Technical_Briefing_29_published_26_November_2021.pdf
• 72. Altarawneh H, Chemaitelly H, Tang P, Hasan MR, Qassim S, Ayoub HH, et al. Protection Afforded by Prior Infection against SARS-CoV-2 Reinfection with the Omicron Variant. Epidemiology; 2022. medRxiv 2022.01.05.22268782. doi:10.1101/2022.01.05.22268782
• 73. World Health Organization (WHO). Erişim tarihi: 07.03.2022. Available from: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
• 74. World Health Organization (WHO). Erişim tarihi: 22.07.2021. Available from: https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---22-june-2021
• 75. Böger B, Fachi MM, Vilhena RO, Cobre AF, Tonin FS, Pontarolo R. Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19. Am J Infect Control 2021; 49(1): 21-29.
• 76. Ziegler K, Steininger P, Ziegler R, Steinmann J, Korn K, Ensser A. SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene. Euro Surveill 2020; 25(39): 2001650.
• 77. Vecchio CD, Brancaccio G, Brazzale AR, Lavezzo E, Onelia F, Franchin E, et al. Emergence of N antigen SARS-CoV-2 genetic variants escaping detection of antigenic tests. medRxiv 2021.03.25.21253802. https://doi.org/10.1101/2021.03.25.21253802
• 78. US Food and Drug Administration (FDA). Erişim tarihi: 03.03.2022. Available from: https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests