Abstract
The worldwide burden of coronavirus disease 2019 (COVID-19) is still unremittingly prosecuting, with nearly 300 million infections and over 5.3 million deaths recorded so far since the origin of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic at the end of the year 2019. The fight against this new highly virulent beta coronavirus appears one of the most strenuous and long challenges that humanity has ever faced, since a definitive treatment has not been identified so far. The adoption of potentially useful physical preventive measures such as lockdowns, social distancing and face masking seems only partially effective for mitigating viral spread, though efficacy and continuation of such measures on the long term is questionable, due to many social and economic reasons. Many COVID-19 vaccines have been developed and are now widely used, though their effectiveness is challenged by several aspects such as low uptake and limited efficacy in some specific populations, as well as by continuous emergence of new mutations in the SARS-CoV-2 genome, accompanying the origin and spread of new variants, which in turn may contribute to further decrease the effectiveness of current vaccines and treatments. This article is hence aimed to provide an updated picture of SARS-CoV-2 variants and mutations that have emerged from November 2019 to present time (i.e., early December 2021).
-
Research funding: The authors received no funding for this work.
-
Author contributions: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.
-
Competing interests: The authors state no conflict of interest.
-
Informed consent: Not applicable.
-
Ethical approval: Not applicable.
References
1. John Hopkins University. Coronavirus Resource Center. https://coronavirus.jhu.edu/map.html [Accessed 6 Dec 2021].Search in Google Scholar
2. Lippi, G, Henry, BM, Plebani, M. Optimizing effectiveness of COVID-19 vaccination: will laboratory stewardship play a role? Clin Chem Lab Med 2021;59:1885–8. https://doi.org/10.1515/cclm-2021-0972.Search in Google Scholar PubMed
3. National Center for Biotechnology Information. NCBI SARS-CoV-2 resources. https://www.ncbi.nlm.nih.gov/sars-cov-2/ [Accessed 6 Dec 2021].Search in Google Scholar
4. World Health Organization. Tracking SARS-CoV-2 variants. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ [Accessed 6 Dec 2021].Search in Google Scholar
5. Centers for Disease Control and Prevention. SARS-CoV-2 variant classifications and definitions. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html [Accessed 6 Dec 2021].Search in Google Scholar
6. Carter, RW, Sanford, JC. A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918. Theor Biol Med Model 2012;9:42. https://doi.org/10.1186/1742-4682-9-42.Search in Google Scholar PubMed PubMed Central
7. Fischetti, M, Falconieri Hays, V, Glaunsinger, B, Christiansen, JS. A visual guide to the SARS-CoV-2 coronavirus. Sci Am 2020;323:32–7.Search in Google Scholar
8. Tao, K, Tzou, PL, Nouhin, J, Gupta, RK, de Oliveira, T, Kosakovsky Pond, SL, et al.. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021;22:757–73. https://doi.org/10.1038/s41576-021-00408-x.Search in Google Scholar PubMed PubMed Central
9. Corey, L, Beyrer, C, Cohen, MS, Michael, NL, Bedford, T, Rolland, M. SARS-CoV-2 variants in patients with immunosuppression. N Engl J Med 2021;385:562–6. https://doi.org/10.1056/nejmsb2104756.Search in Google Scholar PubMed PubMed Central
10. GISAID. Dataset of SARS-CoV-2 phylogeny. https://www.gisaid.org/phylodynamics/global/nextstrain/ [Accessed 6 Dec 2021].Search in Google Scholar
11. Pulliam, JRC, van Schalkwyk, C, Govender, N, von Gottberg, A, Cohen, C, Groome, MJ, et al.. Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa. MedRxiv 2021. https://doi.org/10.1101/2021.11.11.21266068.Search in Google Scholar
12. Lippi, G, Mattiuzzi, C, Bovo, C, Plebani, M. Current laboratory diagnostics of coronavirus disease 2019 (COVID-19). Acta Biomed 2020;91:137–45. https://doi.org/10.23750/abm.v91i2.9548.Search in Google Scholar PubMed PubMed Central
13. Machitani, M, Yasukawa, M, Nakashima, J, Furuichi, Y, Masutomi, K. RNA-dependent RNA polymerase, RdRP, a promising therapeutic target for cancer and potentially COVID-19. Cancer Sci 2020;111:3976–84. https://doi.org/10.1111/cas.14618.Search in Google Scholar PubMed PubMed Central
14. Rausch, JW, Capoferri, AA, Katusiime, MG, Patro, SC, Kearney, MF. Low genetic diversity may be an Achilles heel of SARS-CoV-2. Proc Natl Acad Sci USA 2020;117:24614–6. https://doi.org/10.1073/pnas.2017726117.Search in Google Scholar PubMed PubMed Central
15. Shen, Z, Xiao, Y, Kang, L, Ma, W, Shi, L, Zhang, L, et al.. Genomic diversity of severe acute respiratory syndrome-coronavirus 2 in patients with coronavirus disease 2019. Clin Infect Dis 2020;71:713–20. https://doi.org/10.1093/cid/ciaa203.Search in Google Scholar PubMed PubMed Central
16. Yao, H, Lu, X, Chen, Q, Xu, K, Chen, Y, Cheng, M, et al.. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell Discov 2020;6:76. https://doi.org/10.1038/s41421-020-00226-1.Search in Google Scholar PubMed PubMed Central
17. Voloch, CM, da Silva Francisco, RJr, de Almeida, LGP, Brustolini, OJ, Cardoso, CC, Gerber, AL, et al.. Intra-host evolution during SARS-CoV-2 prolonged infection. Virus Evol 2021;7:veab078. https://doi.org/10.1093/ve/veab078.Search in Google Scholar PubMed PubMed Central
18. Laskar, R, Ali, S. Differential mutation profile of SARS-CoV-2 proteins across deceased and asymptomatic patients. Chem Biol Interact 2021;347:109598. https://doi.org/10.1016/j.cbi.2021.109598.Search in Google Scholar PubMed PubMed Central
19. Otto, SP, Day, T, Arino, J, Colijn, C, Dushoff, J, Li, M, et al.. The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Curr Biol 2021;31:R918–29. https://doi.org/10.1016/j.cub.2021.06.049.Search in Google Scholar PubMed PubMed Central
20. Salleh, MZ, Derrick, JP, Deris, ZZ. Structural evaluation of the spike glycoprotein variants on SARS-CoV-2 transmission and immune evasion. Int J Mol Sci 2021;22:7425. https://doi.org/10.3390/ijms22147425.Search in Google Scholar PubMed PubMed Central
21. Bower, H, Smout, E, Bangura, MS, Kamara, O, Turay, C, Johnson, S, et al.. Deaths, late deaths, and role of infecting dose in Ebola virus disease in Sierra Leone: retrospective cohort study. BMJ 2016;353:i2403. https://doi.org/10.1136/bmj.i2403.Search in Google Scholar PubMed PubMed Central
22. Lippi, G, Plebani, M. The novel coronavirus (2019-nCoV) outbreak: think the unthinkable and be prepared to face the challenge. Diagnosis 2020;7:79–81. https://doi.org/10.1515/dx-2020-0015.Search in Google Scholar PubMed
23. Sarkar, R, Lo, M, Saha, R, Dutta, S, Chawla-Sarkar, M. S glycoprotein diversity of the Omicron variant. MedRxiv 2021. https://doi.org/10.1101/2021.12.04.21267284.Search in Google Scholar
24. Wilhelm, A, Widera, M, Grikscheit, K, Toptan, T, Schenk, B, Pallas, C, et al.. Reduced neutralization of SARS-CoV-2 Omicron variant by vaccine Sera and Monoclonal antibodies. MedRxiv 2021. https://doi.org/10.1101/2021.12.07.21267432.Search in Google Scholar
25. Cele, S, Jackson, L, Khan, K, Khoury, DS, Moyo-Gwete, T, Tegally, H, et al.. SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. MedRxiv 2021. https://doi.org/10.1101/2021.12.08.21267417.Search in Google Scholar PubMed PubMed Central
26. Zhang, L, Li, Q, Liang, Z, Li, T, Liu, S, Cui, Q, et al.. The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. Emerg Microb Infect 2022;11:1–5. https://doi.org/10.1080/22221751.2021.2017757.Search in Google Scholar PubMed PubMed Central
27. Gardner, BJ, Kilpatrick, AM. Estimates of reduced vaccine effectiveness against hospitalization, infection, transmission and symptomatic disease of a new SARS-CoV-2 variant, Omicron (B.1.1.529), using neutralizing antibody titers. MedRxiv 2021. https://doi.org/10.1101/2021.12.10.21267594.Search in Google Scholar
28. Syed, AM, Taha, TY, Tabata, T, Chen, IP, Ciling, A, Khalid, MM, et al.. Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles. Science 2021;374:1626–32. https://doi.org/10.1126/science.abl6184.Search in Google Scholar PubMed PubMed Central
29. Hassan, SS, Lundstrom, K, Serrano-Aroca, Á, Adadi, P, Aljabali, AAA, Redwan, EM, et al.. Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function. Int J Biol Macromol 2022;194:128–43. https://doi.org/10.1016/j.ijbiomac.2021.11.151.Search in Google Scholar PubMed PubMed Central
30. Callaway, E. The coronavirus is mutating – does it matter? Nature 2020;585:174–7. https://doi.org/10.1038/d41586-020-02544-6.Search in Google Scholar PubMed
31. Simonsen, L, Spreeuwenberg, P, Lustig, R, Taylor, RJ, Fleming, DM, Kroneman, M, et al.. Global mortality estimates for the 2009 influenza pandemic from the GLaMOR project: a modeling study. PLoS Med 2013;10:e1001558. https://doi.org/10.1371/journal.pmed.1001558.Search in Google Scholar PubMed PubMed Central
32. Toor, J, Echeverria-Londono, S, Li, X, Abbas, K, Carter, ED, Clapham, HE, et al.. Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world. Elife 2021;10:e67635. https://doi.org/10.7554/eLife.67635.Search in Google Scholar PubMed PubMed Central
33. US Centers for Disease Control and Prevention. Vaccine effectiveness: how well do flu vaccines work? https://www.cdc.gov/flu/vaccines-work/vaccineeffect.htm [Accessed 6 Dec 2021].Search in Google Scholar
34. Monto, AS. The future of SARS-CoV-2 vaccination – lessons from influenza. N Engl J Med 2021;385:1825–7. https://doi.org/10.1056/nejmp2113403.Search in Google Scholar
35. Lippi, G, Henry, BM, Plebani, M. Anti-SARS-CoV-2 antibodies testing in recipients of COVID-19 vaccination: why, when, and how? Diagnostics 2021;11:941. https://doi.org/10.3390/diagnostics11060941.Search in Google Scholar PubMed PubMed Central
© 2021 Walter de Gruyter GmbH, Berlin/Boston
