Tweet From one of the authors explaining the use of `Bird' names
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We've another preprint study, published yesterday on MedRxiv, which identifies 7 recently emerged lineages of SARS-CoV-2 in the United States, all sharing an amino acid change at position 677 in the spike protein. While the significance and impact of this amino acid change is unknown, it occurs in a region of the spike protein that raises concerns.
We've seen other examples of `convergent evolutionary changes' in the SARS-CoV-2 genone - like E484K, which appears to reduce antibody recognition, and 501Y, which increases transmissibility - so researchers are eager to better understand this mutation.And the fact that it has shown up independently in at least 7 lineages in the United States over the last few months suggests it may contribute to the virus's biological fitness.
Carl Zimmer did a nice story on this study yesterday for the New York Times (see 7 Virus Variants Found in U.S. Carrying the Same Mutation). Below you'll find the abstract, and a link to the full 25-page PDF preprint.
Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677
Emma B Hodcroft, Daryl B Domman, Kasopefoluwa Oguntuyo, Daniel J Snyder, Maarten Van Diest, Kenneth H Densmore, Kurt C Schwalm, Jon Femling, Jennifer L Carroll, Rona S Scott, Martha M Whyte, Michael D Edwards, Noah C Hull, Christopher G Kevil, John A Vanchiere, Benhur Lee, Darrell L Dinwiddie, Vaughn S Cooper,Jeremy P Kamil
doi: https://doi.org/10.1101/2021.02.12.21251658
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing antibodies or are thought to enhance transmission through mechanisms such as increased affinity for the cell entry receptor, ACE2.
Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA.
Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid August to late November, 2020. Four 677H clades from clade 20G (B.1.2) , 20A (B.1.234), and 20B (B.1.1.220, and B.1.1.222) each contain roughly 100 or fewer sequenced cases, while a distinct pair of clade 20G clusters are represented by 754 and 298 cases, respectively.
Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission.
Taken together, our findings demonstrate simultaneous convergent evolution, thus providing an impetus to further evaluate S:677 polymorphisms for effects on proteolytic processing, cell tropism, and transmissibility.
