Skip to main content
SpringerLink
Log in

The Evolution of SARS-CoV-2

  • Chapter
  • First Online:
Studies to Combat COVID-19 using Science and Engineering

  • 189 Accesses

Abstract

Species evolve over time and viruses are no exception. Extensive genome sequencing of SARS-CoV-2 throughout the global pandemic has allowed for highly detailed and invaluable characterization of the molecular evolution in a virus population, to an extent that has never been seen before. Tracking of the molecular evolutionary changes in SARS-CoV-2 allows for (1) inference of important local and global transmission routes by tracking the distribution of specific genotypes, (2) identification of adaptive evolutionary changes with potential human health implications, and (3) generation of expectations/predictions for future evolutionary changes to better tailor detection, mitigation, and treatment strategies. In this chapter, we begin by outlining the key processes driving evolution in viruses, namely, random genetic drift and natural selection. We summarize the evolutionary history of SARS-CoV-2 within the context of other coronavirus species. Then we explore how ongoing genomic and epidemiological patterns have been used to identify the extent to which natural selection has played a role in the evolution of SAR-CoV-2 throughout the global pandemic. Next, an outline is provided for the World Health Organization’s criteria for identifying evolved Variants of Concern (VOC), along with a discussion about the impact of these evolved VOCs on human health. Finally, mechanisms are identified for extensive and rapid adaptive evolution in SARS-CoV-2 which suggest the need for closer monitoring. In addition, the possibilities for future evolution in SARS-CoV-2 are mentioned.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. McDonald, S. M., Nelson, M. I., Turner, P. E., & Patton, J. T. (2016). Reassortment in segmented RNA viruses: Mechanisms and outcomes. Nature Reviews. Microbiology, 14, 448–460.

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Abbasi, J. (2021). Researchers tie severe immunosuppression to chronic COVID-19 and virus variants. JAMA, 325, 2033–2035.

    CAS  PubMed  Google Scholar 

  3. Elena, S. F., & Sanjuán, R. (2005). Adaptive value of high mutation rates of RNA viruses: Separating causes from consequences. Journal of Virology, 79, 11555–11558.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Chao, L. (1990). Fitness of RNA virus decreased by Muller’s ratchet. Nature, 348, 454–455.

    CAS  PubMed  Google Scholar 

  5. Sanjuán, R., & Domingo-Calap, P. (2021). Genetic diversity and evolution of viral populations. In Encyclopedia of virology (pp. 53–61). Elsevier.

    Google Scholar 

  6. Dong, E., Du, H., & Gardner, L. (2020). An interactive web-based dashboard to track COVID-19 in real time. The Lancet Infectious Diseases, 20, 533–534.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Zanini, F., Brodin, J., Thebo, L., Lanz, C., Bratt, G., Albert, J., et al. (2015). Population genomics of intrapatient HIV-1 evolution. eLife, 4, e11282.

    PubMed  PubMed Central  Google Scholar 

  8. Braun, K. M., Moreno, G. K., Wagner, C., Accola, M. A., Rehrauer, W. M., Baker, D. A., et al. (2021). Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks. PLoS Pathogens, 17, e1009849.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Sender, R., Bar-On, Y. M., Gleizer, S., Bernshtein, B., Flamholz, A., Phillips, R., et al. (2021). The total number and mass of SARS-CoV-2 virions. Proceedings of the National Academy of Sciences of the United States of America, 118, e2024815118.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Sim, S., Aw, P. P. K., Wilm, A., Teoh, G., Hue, K. D. T., Nguyen, N. M., et al. (2015). Tracking dengue virus intra-host genetic diversity during human-to-mosquito transmission. PLoS Neglected Tropical Diseases, 9, e0004052.

    PubMed  PubMed Central  Google Scholar 

  11. Varble, A., Albrecht, R. A., Backes, S., Crumiller, M., Bouvier, N. M., Sachs, D., et al. (2014). Influenza A virus transmission bottlenecks are defined by infection route and recipient host. Cell Host & Microbe, 16, 691–700.

    CAS  Google Scholar 

  12. Bull, J. J. (1994). Virulence. Evolution, 48, 1423–1437.

    CAS  PubMed  Google Scholar 

  13. Anderson, R. M., & May, R. M. (1992). Infectious diseases of humans: Dynamics and control (Revised ed.). Oxford University Press.

    Google Scholar 

  14. Hanley, K. A., Azar, S. R., Campos, R. K., Vasilakis, N., & Rossi, S. L. (2019). Support for the transmission-clearance trade-off hypothesis from a study of Zika virus delivered by mosquito bite to mice. Viruses, 11, 1072.

    CAS  PubMed Central  Google Scholar 

  15. Blanquart, F., Grabowski, M. K., Herbeck, J., Nalugoda, F., Serwadda, D., Eller, M. A., et al. (2016). A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda. eLife, 5, e20492.

    PubMed  PubMed Central  Google Scholar 

  16. Ben-Shachar, R., & Koelle, K. (2018). Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context. Nature Communications, 9, 2355.

    PubMed  PubMed Central  Google Scholar 

  17. McKay, B., Ebell, M., Dale, A. P., Shen, Y., & Handel, A. (2020). Virulence-mediated infectiousness and activity trade-offs and their impact on transmission potential of influenza patients. Proceedings of the Royal Society B: Biological Sciences, 287, 20200496.

    PubMed  PubMed Central  Google Scholar 

  18. Holmes, E. C., Goldstein, S. A., Rasmussen, A. L., Robertson, D. L., Crits-Christoph, A., Wertheim, J. O., et al. (2021). The origins of SARS-CoV-2: A critical review. Cell, 184, 4848–4856.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Singh, D., & Yi, S. V. (2021). On the origin and evolution of SARS-CoV-2. Experimental & Molecular Medicine, 53, 537–547.

    Google Scholar 

  20. Rehman, S., Shafique, L., Ihsan, A., & Liu, Q. (2020). Evolutionary trajectory for the emergence of novel coronavirus SARS-CoV-2. Pathogens, 9, 240.

    PubMed Central  Google Scholar 

  21. Cui, J., Li, F., & Shi, Z.-L. (2019). Origin and evolution of pathogenic coronaviruses. Nature Reviews. Microbiology, 17, 181–192.

    CAS  PubMed  Google Scholar 

  22. Woo, P. C. Y., Lau, S. K. P., Lam, C. S. F., Lau, C. C. Y., Tsang, A. K. L., Lau, J. H. N., et al. (2012). 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. Journal of Virology, 86, 3995–4008.

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Weiss, S. R., & Leibowitz, J. L. (2011). Coronavirus pathogenesis. In Advances in virus research (pp. 85–164). Elsevier.

    Google Scholar 

  24. Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., et al. (2020). On the origin and continuing evolution of SARS-CoV-2. National Science Review, 7, 1012–1023.

    PubMed  PubMed Central  Google Scholar 

  25. Chen, B., Tian, E.-K., He, B., Tian, L., Han, R., Wang, S., et al. (2020). Overview of lethal human coronaviruses. Signal Transduction and Targeted Therapy, 5, 89.

    PubMed  PubMed Central  Google Scholar 

  26. de Wit, E., van Doremalen, N., Falzarano, D., & Munster, V. J. (2016). SARS and MERS: Recent insights into emerging coronaviruses. Nature Reviews. Microbiology, 14, 523–534.

    PubMed  PubMed Central  Google Scholar 

  27. Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford University Press.

    Google Scholar 

  28. Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Liu, Y., Hu, G., Wang, Y., Ren, W., Zhao, X., Ji, F., et al. (2021). Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2. Proceedings of the National Academy of Sciences, 118, 2025373118.

    Google Scholar 

  30. Vijgen, L., Keyaerts, E., Moës, E., Thoelen, I., Wollants, E., Lemey, P., et al. (2005). Complete genomic sequence of human coronavirus OC43: Molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. Journal of Virology, 79, 1595–1604.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Li, X., Luk, H. K. H., Lau, S. K. P., & Woo, P. C. Y. (2019). Human coronaviruses: General features. In Reference module in biomedical sciences (p. B9780128012383957000). Elsevier.

    Google Scholar 

  32. Schoeman, D., Gordon, B., & Fielding, B. C. (2021). Pathogenic human coronaviruses. In Reference module in biomedical sciences (p. B9780128187319001000). Elsevier.

    Google Scholar 

  33. Sharma, A., Ahmad Farouk, I., & Lal, S. K. (2021). COVID-19: A review on the novel coronavirus disease evolution, transmission, detection, control and prevention. Viruses, 13, 202.

    CAS  PubMed  PubMed Central  Google Scholar 

  34. WHO. (2020b). WHO Director-General’s opening remarks at the media briefing on COVID-19—11 March 2020. WHO.

    Google Scholar 

  35. Guan, Y., Zheng, B. J., He, Y. Q., Liu, X. L., Zhuang, Z. X., Cheung, C. L., et al. (2003). Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science, 302, 276–278.

    CAS  PubMed  Google Scholar 

  36. Kahn, J. S., & McIntosh, K. (2005). History and recent advances in coronavirus discovery. The Pediatric Infectious Disease Journal, 24, S223–S227.

    PubMed  Google Scholar 

  37. Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., et al. (2020). Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology, 5, 1408–1417.

    CAS  PubMed  Google Scholar 

  38. Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., et al. (2021). The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews. Genetics, 22, 757–773.

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Otto, S. P., Day, T., Arino, J., Colijn, C., Dushoff, J., Li, M., et al. (2021). The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Current Biology, 31, R918–R929. https://doi.org/10.1016/j.cub.2021.06.049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Zhang, W., Govindavari, J. P., Davis, B. D., Chen, S. S., Kim, J. T., Song, J., et al. (2020). Analysis of genomic characteristics and transmission routes of patients with confirmed SARS-CoV-2 in Southern California during the early Stage of the US COVID-19 pandemic. JAMA Network Open, 3, e2024191.

    PubMed  PubMed Central  Google Scholar 

  41. EMBL-EBI. (2021). Data sharing collaborations. EMBL-EBI.

    Google Scholar 

  42. Maxmen, A. (2021). Why US coronavirus tracking can’t keep up with concerning variants. Nature, 592, 336–337.

    CAS  PubMed  Google Scholar 

  43. Furuse, Y. (2021). Genomic sequencing effort for SARS-CoV-2 by country during the pandemic. International Journal of Infectious Diseases, 103, 305–307.

    CAS  PubMed  Google Scholar 

  44. Li, W., Moore, M. J., Vasilieva, N., Sui, J., Wong, S. K., Berne, M. A., et al. (2003). Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature, 426, 450–454.

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., et al. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579, 270–273.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., et al. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367, 1260–1263.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Carvalho, T., Krammer, F., & Iwasaki, A. (2021). The first 12 months of COVID-19: A timeline of immunological insights. Nature Reviews. Immunology, 21, 245–256.

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., et al. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581, 215–220.

    CAS  PubMed  Google Scholar 

  49. Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., et al. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581, 221–224.

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Baum, A., Fulton, B. O., Wloga, E., Copin, R., Pascal, K. E., Russo, V., et al. (2020). Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science, 369, 1014–1018.

    CAS  PubMed  Google Scholar 

  51. Schmidt, F., Weisblum, Y., Muecksch, F., Hoffmann, H.-H., Michailidis, E., Lorenzi, J. C. C., et al. (2020). Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric virusesSARS-CoV-2 neutralizing antibody activity. The Journal of Experimental Medicine, 217, e20201181.

    PubMed  PubMed Central  Google Scholar 

  52. Johnson, B. A., Xie, X., Bailey, A. L., Kalveram, B., Lokugamage, K. G., Muruato, A., et al. (2021). Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature, 591, 293–299.

    CAS  PubMed  PubMed Central  Google Scholar 

  53. McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., et al. (2021). N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell, 184, 2332–2347.e16.

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Jiang, H., Zhang, H., Meng, Q., Xie, J., Li, Y., Chen, H., et al. (2020). SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cellular & Molecular Immunology, 17, 998–1000.

    CAS  Google Scholar 

  55. Xia, H., Cao, Z., Xie, X., Zhang, X., Chen, J. Y.-C., Wang, H., et al. (2020). Evasion of type I interferon by SARS-CoV-2. Cell Reports, 33, 108234.

    CAS  PubMed  Google Scholar 

  56. Phillips, P. C. (2008). Epistasis—The essential role of gene interactions in the structure and evolution of genetic systems. Nature Reviews. Genetics, 9, 855–867.

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Rochman, N. D., Faure, G., Wolf, Y. I., Freddolino, P. L., Zhang, F. & Koonin, E. V. (2021). Epistasis at the SARS-CoV-2 RBD Interface and the propitiously boring implications for vaccine escape. In bioRxiv 2021.08.30.458225.

    Google Scholar 

  58. Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., et al. (2020). Tracking changes in SARS-CoV-2 spike: Evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182, 812–827.e19.

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Hodcroft, E. B., Domman, D. B., Snyder, D. J., Oguntuyo, K. Y., Van Diest, M., Densmore, K. H., et al. (2021). Emergence in late 2020 of multiple lineages of SARS-CoV-2 spike protein variants affecting amino acid position 677. In medRxiv 2021.02.12.21251658.

    Google Scholar 

  60. Konings, F., Perkins, M. D., Kuhn, J. H., Pallen, M. J., Alm, E. J., Archer, B. N., et al. (2021). SARS-CoV-2 variants of interest and concern naming scheme conducive for global discourse. Nature Microbiology, 6, 821–823.

    CAS  PubMed  Google Scholar 

  61. Bedford, T., Hodcroft, E. B. & Neher, R. A. (2021). Updated Nextstrain SARS-CoV-2 clade naming strategy. https://nextstrain.org/blog/2021-01-06-updated-SARS-CoV-2-clade-naming

    Google Scholar 

  62. GISAID. (2021). Clade and lineage nomenclature aids in genomic epidemiology studies of active hCoV-19 viruses. GISAID.

    Google Scholar 

  63. Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5, 1403–1407.

    CAS  PubMed  PubMed Central  Google Scholar 

  64. WHO. (2021). Tracking SARS-CoV-2 variants. WHO.

    Google Scholar 

  65. Rambout, A., Loman, N., Pybus, O., Barclay, W., Barrett, J., Carabelli, A., et al. (2020). Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel. 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

  66. Chand, M., Hopkins, S., Achison, C., Anderson, C., Allen, H., Blomquist, P., et al. (2020). Investigation of novel SARS-CoV-2 variant: Variant of concern 202012/01. Public Health England Technical Briefing 2. https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/959361/Technical_Briefing_VOC202012-2_Briefing_2.pdf

  67. Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., et al. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373, 889–895.

    CAS  PubMed  Google Scholar 

  68. Alpert, T., Brito, A. F., Lasek-Nesselquist, E., Rothman, J., Valesano, A. L., MacKay, M. J., et al. (2021). Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States. Cell, 184, 2595–2604.e13.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. O’Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., et al. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Research.

    Google Scholar 

  70. Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., et al. (2021a). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372, eabg3055.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Leung, K., Shum, M. H., Leung, G. M., Lam, T. T., & Wu, J. T. (2021). Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Eurosurveillance, 26, 2002106.

    PubMed Central  Google Scholar 

  72. Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., et al. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593, 266–269.

    CAS  PubMed  Google Scholar 

  73. Teruel, N., Mailhot, O., & Najmanovich, R. J. (2021). Modelling conformational state dynamics and its role on infection for SARS-CoV-2 spike protein variants. PLoS Computational Biology, 17, e1009286.

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Jones, T. C., Biele, G., Mühlemann, B., Veith, T., Schneider, J., Beheim-Schwarzbach, J., et al. (2021). Estimating infectiousness throughout SARS-CoV-2 infection course. Science, 373, eabi5273.

    CAS  PubMed  Google Scholar 

  75. Kidd, M., Richter, A., Best, A., Cumley, N., Mirza, J., Percival, B., et al. (2021). S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral load in samples tested by TaqPath polymerase chain reaction. The Journal of Infectious Diseases, 223, 1666–1670.

    CAS  PubMed  Google Scholar 

  76. Wargo, A. R., & Kurath, G. (2012). Viral fitness: Definitions, measurement, and current insights. Current Opinion in Virology, 2, 538–545.

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Challen, R., Brooks-Pollock, E., Read, J. M., Dyson, L., Tsaneva-Atanasova, K., & Danon, L. (2021a). Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: Matched cohort study. British Medical Journal, 372, n579.

    PubMed  Google Scholar 

  78. Davies, N. G., Jarvis, C. I., Edmunds, W. J., Jewell, N. P., Diaz-Ordaz, K., & Keogh, R. H. (2021b). Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature, 593, 270–274.

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Grint, D. J., Wing, K., Williamson, E., McDonald, H. I., Bhaskaran, K., Evans, D., et al. (2021). Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February. Eurosurveillance, 26, 2100256.

    CAS  PubMed Central  Google Scholar 

  80. Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsavsky, T., et al. (2021). Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: An ecological study. The Lancet Public Health, 6, e335–e345.

    PubMed  PubMed Central  Google Scholar 

  81. Abu-Raddad, L. J., Chemaitelly, H., & Butt, A. A. (2021). Effectiveness of the BNT162b2 Covid-19 vaccine against the B.1.1.7 and B.1.351 variants. The New England Journal of Medicine, 385, 187–189.

    CAS  PubMed  Google Scholar 

  82. Emary, K. R. W., Golubchik, T., Aley, P. K., Ariani, C. V., Angus, B., Bibi, S., et al. (2021). Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): An exploratory analysis of a randomised controlled trial. The Lancet, 397, 1351–1362.

    CAS  Google Scholar 

  83. Heath, P. T., Galiza, E. P., Baxter, D. N., Boffito, M., Browne, D., Burns, F., et al. (2021). Safety and efficacy of NVX-CoV2373 Covid-19 vaccine. The New England Journal of Medicine, 385, 1172–1183.

    CAS  PubMed  Google Scholar 

  84. Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., et al. (2021). Detection of a SARS-CoV-2 variant of concern in South Africa. Nature, 592, 438–443.

    CAS  PubMed  Google Scholar 

  85. Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D., Mishra, S., et al. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, 372, 815–821.

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Pearson, C. A., Russell, T. W., Davies, N. G., Kucharski, A. J., CMMID COVID-19 Working Group, Edmunds, W. J., et al. (2021). Estimates of severity and transmissibility of novel SARS-CoV-2 variant 501Y.V2 in South Africa. UpToDate.

    Google Scholar 

  87. Cele, S., Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., et al. (2021). Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature, 593, 142–146.

    CAS  PubMed  Google Scholar 

  88. Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., et al. (2021). SARS-CoV-2 501Y.V2 escapes neutralization by south African COVID-19 donor plasma. Nature Medicine, 27, 622–625.

    CAS  PubMed  Google Scholar 

  89. Jassat, W., Mudara, C., Ozougwu, L., Tempia, S., Blumberg, L., Davies, M.-A., et al. (2021). Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: A cohort study. The Lancet Global Health, 9, e1216–e1225.

    PubMed  PubMed Central  Google Scholar 

  90. Challen, R., Dyson, L., Overton, C. E., Guzman-Rincon, L. M., Hill, E. M., Stage, H. B., et al. (2021b). Early epidemiological signatures of novel SARS-CoV-2 variants: Establishme.06.05.21258365.

    Google Scholar 

  91. Riley, S., Wang, H., Eales, O., Haw, D., Walters, C. E., Ainslie, K. E. C., et al. (2021). REACT-1 round 12 report: Resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant. In MedRxiv 2021.06.17.21259103.

    Google Scholar 

  92. Bolze, A., Cirulli, E. T., Luo, S., White, S., Wyman, D., Rossi, A. D., et al. (2021). SARS-CoV-2 variant Delta rapidly displaced variant alpha in the United States and led to higher viral loads. In MedRxiv 2021.06.20.21259195.

    Google Scholar 

  93. Grant, R., Charmet, T., Schaeffer, L., Galmiche, S., Madec, Y., Platen, C. V., et al. (2021). Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France. Lancet Regional Health—Europe, 13, 100278.

    PubMed  PubMed Central  Google Scholar 

  94. Li, B., Deng, A., Li, K., Hu, Y., Li, Z., Xiong, Q., et al. (2021). Viral infection and transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant—SARS-CoV-2 coronavirus/nCoV-2019 genomic epidemiology. Virological.

    Google Scholar 

  95. Ong, S. W. X., Chiew, C. J., Ang, L. W., Mak, T.-M., Cui, L., Toh, M. P. H., et al. (2021). Clinical and virological features of SARS-CoV-2 variants of concern: A retrospective cohort study comparing B.1.1.7 (alpha), B.1.315 (Beta), and B.1.617.2 (Delta). Social Science Research Network.

    Google Scholar 

  96. Planas, D., Veyer, D., Baidaliuk, A., Staropoli, I., Guivel-Benhassine, F., Rajah, M. M., et al. (2021). Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature, 596, 276–280.

    CAS  PubMed  Google Scholar 

  97. TAG-VE. (2021). Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern.

    Google Scholar 

  98. Shah, A. S. V., Gribben, C., Bishop, J., Hanlon, P., Caldwell, D., Wood, R., et al. (2021). Effect of vaccination on transmission of SARS-CoV-2. The New England Journal of Medicine, 385, 1718–1720.

    CAS  PubMed  Google Scholar 

  99. Polack, F. P., Thomas, S. J., Kitchin, N., Absalon, J., Gurtman, A., Lockhart, S., et al. (2020). Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. The New England Journal of Medicine, 383, 2603–2615.

    CAS  PubMed  Google Scholar 

  100. Chung, H., He, S., Nasreen, S., Sundaram, M. E., Buchan, S. A., Wilson, S. E., et al. (2021). Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: Test negative design study. BMJ, 374, n1943.

    PubMed  Google Scholar 

  101. Sadoff, J., Gray, G., Vandebosch, A., Cárdenas, V., Shukarev, G., Grinsztejn, B., et al. (2021). Safety and efficacy of single-dose Ad26.COV2.S vaccine against Covid-19. The New England Journal of Medicine, 384, 2187–2201.

    CAS  PubMed  Google Scholar 

  102. Sheikh, A., McMenamin, J., Taylor, B., & Robertson, C. (2021). SARS-CoV-2 Delta VOC in Scotland: Demographics, risk of hospital admission, and vaccine effectiveness. The Lancet, 397, 2461–2462.

    CAS  Google Scholar 

  103. Tang, P., Hasan, M. R., Chemaitelly, H., Yassine, H. M., Benslimane, F. M., Al Khatib, H. A., et al. (2021). BNT162b2 and mRNA-1273 COVID-19 vaccine effectiveness against the SARS-CoV-2 Delta variant in Qatar. Nature Medicine, 1–8.

    Google Scholar 

  104. Liu, W.-D., Chang, S.-Y., Wang, J.-T., Tsai, M.-J., Hung, C.-C., Hsu, C.-L., et al. (2020). Prolonged virus shedding even after seroconversion in a patient with COVID-19. The Journal of Infection, 81, 318–356.

    PubMed  PubMed Central  Google Scholar 

  105. Wölfel, R., Corman, V. M., Guggemos, W., Seilmaier, M., Zange, S., Müller, M. A., et al. (2020). Virological assessment of hospitalized patients with COVID-2019. Nature, 581, 465–469.

    PubMed  Google Scholar 

  106. Avanzato, V. A., Matson, M. J., Seifert, S. N., Pryce, R., Williamson, B. N., Anzick, S. L., et al. (2020). Case study: Prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with cancer. Cell, 183, 1901–1912.e9.

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Bazykin, G. A., Stanevich, O., Danilenko, D., Fadeev, A., Komissarova, K., Ivanova, A., et al. (2021). Emergence of Y453F and Δ69-70HV mutations in a lymphoma patient with long-term COVID-19—SARS-CoV-2 coronavirus/nCoV-2019 genomic epidemiology. Virological.

    Google Scholar 

  108. Choi, B., Choudhary, M. C., Regan, J., Sparks, J. A., Padera, R. F., Qiu, X., et al. (2020). Persistence and evolution of SARS-CoV-2 in an immunocompromised host. The New England Journal of Medicine, 383, 2291–2293. https://doi.org/10.1056/NEJMc2031364

    Article  PubMed  Google Scholar 

  109. Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., et al. (2021). SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592, 277–282.

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Borges, V., Isidro, J., Cunha, M., Cochicho, D., Martins, L., Banha, L., et al. (2021). Long-term evolution of SARS-CoV-2 in an immunocompromised patient with non-Hodgkin Lymphoma. mSphere, 6, e0024421.

    PubMed  Google Scholar 

  111. Bosco-Lauth, A. M., Root, J. J., Porter, S. M., Walker, A. E., Guilbert, L., Hawvermale, D., et al. (2021). Peridomestic mammal susceptibility to severe acute respiratory syndrome coronavirus 2 infection. Emerging Infectious Diseases, 27, 2073–2080.

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Fischhoff, I. R., Castellanos, A. A., Rodrigues, J. P. G. L. M., Varsani, A., & Han, B. A. (2021). Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2. Proceedings of the Royal Society B: Biological Sciences, 288, 20211651.

    CAS  PubMed  PubMed Central  Google Scholar 

  113. WHO. (2020a). SARS-CoV-2 mink-associated variant strain—Denmark. WHO.

    Google Scholar 

  114. Bas, B., Munnink, O., Sikkema, R. S., Nieuwenhuijse, D. F., Molenaar, R. J., Munger, E., et al. (2021). Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science, 371, 172–177.

    Google Scholar 

  115. Larsen, H. D., Fonager, J., Lomholt, F. K., Dalby, T., Benedetti, G., Kristensen, B., et al. (2021). Preliminary report of an outbreak of SARS-CoV-2 in mink and mink farmers associated with community spread, Denmark, June to November 2020. Eurosurveillance, 26, 2100009.

    CAS  PubMed Central  Google Scholar 

  116. Hoffmann, M., Zhang, L., Krüger, N., Graichen, L., Kleine-Weber, H., Hofmann-Winkler, H., et al. (2021). SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Cell Reports, 35, 109017.

    CAS  PubMed  Google Scholar 

  117. Koopmans, M. (2021). SARS-CoV-2 and the human-animal interface: Outbreaks on mink farms. The Lancet Infectious Diseases, 21, 18–19.

    CAS  PubMed  Google Scholar 

  118. Chandler, J. C., Bevins, S. N., Ellis, J. W., Linder, T. J., Tell, R. M., Jenkins-Moore, M., et al. (2021). SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus). Proceedings of the National Academy of Sciences, 118, e2114828118.

    CAS  Google Scholar 

  119. Kuchipudi, S. V., Surendran-Nair, M., Ruden, R. M., Yon, M., Nissly, R. H., Nelli, R. K., et al. (2021). Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer. Proceedings of the National Academy of Sciences of the United States of America, 119, e2121644119.

    Google Scholar 

  120. Egeren, D. V., Novokhodko, A., Stoddard, M., Tran, U., Zetter, B., Rogers, M., et al. (2021). Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein. PLoS One, 16, e0250780.

    PubMed  PubMed Central  Google Scholar 

  121. Rella, S. A., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. A. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports, 11, 15729.

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. W., Choudhary, M. C., Dingens, A. S., et al. (2021). Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science, 371, 850–854.

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., Neher, R. A., (2018). Nextstrain: real-time tracking of pathogen evolution, Bioinformatics, 34, 4121–4123, https://doi.org/10.1093/bioinformatics/bty407.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biology, Clarkson University, Potsdam, NY, USA

    Susan F. Bailey & Mahfuza Akter

Authors
  1. Susan F. Bailey
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mahfuza Akter
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Susan F. Bailey .

Editor information

Editors and Affiliations

  1. Department of Electrical & Computer Engineering, Clarkson University, Potsdam, NY, USA

    Dana Barry

  2. National Institute of Technology, Suzuka College, Shiroko-cho, Suzuka, Mie, Japan

    Hideyuki Kanematsu

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Bailey, S.F., Akter, M. (2022). The Evolution of SARS-CoV-2. In: Barry, D., Kanematsu, H. (eds) Studies to Combat COVID-19 using Science and Engineering. Springer, Singapore. https://doi.org/10.1007/978-981-19-1356-3_5

Download citation

Publish with us

Policies and ethics

Search

Navigation