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. 2021 Nov 18;97:105153. doi: 10.1016/j.meegid.2021.105153

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© 2021 The Authors

Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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Fig. 5 — A–E: Heatmap of variants observed in the A) Alpha, B) Beta, C) Gamma, D) Epsilon, variants of concern and the E) Iota variant of interest. Variants are listed on the y-axis, and time is categorized by week of collection date on the x-axis, beginning on January 5th, 2020, and ending on January 16th, 2021. Parentheses give the domain in which each variant appears, according to the domain ranges specified in Huang et al. 2020. Key for domain abbreviations: SP = signal peptide, NTD=N-terminal domain, RBD = receptor-binding domain, FP = fusion peptide, HR1 = heptad repeat 1, HR2 = heptad repeat 2, CD = cytoplasmic domain, ID = intracellular domain. The heatmap is colored based on a log-10 scale, with prevalence values of zero colored in white, and values less than or equal to 0.10% colored with the lightest shade. A) The ten mutations associated with the Alpha variant of concern have quickly increased in prevalence after appearing together in mid-September 2020 and are now observed in more than 50% of sequences worldwide. Some mutations associated with the Beta variant of concern (H69_V70del, Y145del, N501Y, D614G, P681H, and T716I) were present separately before the emergence of the variant in mid-September 2020, while others (A570D, S982A, and D1118H) appeared together at this point. Y144del sometimes appears as Y145del due to ambiguities in the alignment software with identical adjacent amino acids. B) The mutations associated with the Gamma variant of concern appeared together in mid-October 2020 and have increased in prevalence over time in samples worldwide, but to a lesser extent than the variants in the Alpha variant. C) The mutations associated with the Gamma variant of concern appeared together in mid-December 2020; all mutations except for T20N and K417T were present separately before the emergence of the variant. D) The mutations associated with the Epsilon variant of concern appeared together in mid-September 2020. The substitutions L452R and S13I appeared separately before the emergence of the variant, while W152C did not. E) The mutations associated with the Iota variant of interest consistently appear together after early October 2020. All mutations associated with this variant appeared separately before its emergence. Some mutations are present in multiple variants: the RBD substitution E484K is also observed in the Beta, Gamma, and Iota variants, and the RBD substitution N501Y is also observed in the Alpha, Beta, and Gamma variants.