◐ Shell
reader mode source ↗
Skip to main page content
Advanced
User Guide
Full text links Cite
Display options

Abstract

We report the genome of a B.1.1.7+E484K severe acute respiratory syndrome coronavirus 2 from Southeastern Pennsylvania and compare it with all high-coverage B.1.1.7+E484K genomes (n = 235) available. Analyses showed the existence of at least 4 distinct clades of this variant circulating in the United States and the possibility of at least 59 independent acquisitions of the E484K mutation.

Keywords: B.1.1.7+E484K; convergent; escape mutation; vaccine; variant of concern.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Diversity of SARS-CoV-2 in Philadelphia and global diversity of sequenced B.1.1.7+E484K genomes. A, Stacked area plot showing the diversity of random genomes sequenced by our laboratory at Children’s Hospital of Philadelphia from January, February, and March 2021. Ten lineages that were represented by only 1 genome (B.1.1, B.1.1.106, B.1.1.129, B.1.1.197, B.1.1.281, B.1.1.296, B.1.119, B.1.234, B.1.350, B.1.409) were excluded from the plot. One B.1.526.1 isolate was counted with the parent B.1.526 for easier visualization. B, Stacked area plot showing the number of GISAID genomes (n = 250) that are B.1.1.7 (20I/501Y.V1) and have the E484K spike mutation over time in the United States and globally. C, Diversity of 236 isolates according to GNUVID. Stacked area plot showing relative abundance of circulating CCs for the 236 B.1.1.7+E484K isolates (typed by GNUVID). The bar plot shows that the isolates belong to 7 different CCs. Isolate EPI_ISL_1385215 was not assigned to any of the 7 CCs (CC255). Fourteen isolates were excluded from the plot as they had >5% nucleotides designated “N” in the sequence. Abbreviations: CCs, clonal complexes; GISAID, Global Initiative on Sharing All Influenza Data; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
Figure 2.
Figure 2.
SNP-based phylogeny showing the independent acquisitions of E484K in the B.1.1.7 lineage. Maximum likelihood tree of the B.1.1.7+E484K isolates. US isolates are in red. For the CHOP_204 isolate, the alternative allele was called a consensus if its frequency was at least 0.75. The tree was rooted with MN908947.3. The countries of the isolates are shown as a ring. The PA B.1.1.7+E484K isolates are represented with red stars. The red branches represent ancestral reconstruction of the E484K mutation in the B.1.1.7 lineage. Bootstrap values >70 are shown on the branches. Abbreviations: SNP, single nucleotide polymorphism; PA, Pennsylvania.
See this image and copyright information in PMC

Update of

References

    1. 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; eabg3055. - PMC - PubMed
    1. Tegally H, Wilkinson E, Giovanetti M, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv 2020.12.21.20248640 [Preprint]. 22 December 2020. Available at: 10.1101/2020.12.21.20248640. Accessed 25 May 2021. - DOI
    1. Faria NR, Mellan, TA, Whittaker C, et al. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Science 2021; 372:815–21. - PMC - PubMed
    1. Rambaut A, Loman N, Pybus O, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. 2020. Available at: https://virological.org/t/563. Accessed 25 May 2021.
    1. Chen RE, Zhang X, Case JB, et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat Med 2021; 27:717–26. - PMC - PubMed
Show all 26 references