In:
PLOS Pathogens, Public Library of Science (PLoS), Vol. 17, No. 2 ( 2021-2-26), p. e1009373-
Abstract:
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within and between individual hosts. Using domestic cats as a model, we show that SARS-CoV-2 consensus sequences remain largely unchanged over time within hosts, while dynamic sub-consensus diversity reveals processes of genetic drift and weak purifying selection. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats. It also becomes fixed following transmission in two of three pairs. These dynamics suggest this site may be under positive selection in this system and illustrate how a variant can quickly arise and become fixed in parallel across multiple transmission pairs. Transmission of SARS-CoV-2 in cats involved a narrow bottleneck, with new infections founded by fewer than ten viruses. In RNA virus evolution, stochastic processes like narrow transmission bottlenecks and genetic drift typically act to constrain the overall pace of adaptive evolution. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. Overall, our study suggests species- and context-specific adaptations are likely to continue to emerge. This underscores the importance of continued genomic surveillance for new SARS-CoV-2 variants as well as heightened scrutiny for signatures of SARS-CoV-2 positive selection in humans and mammalian model systems.
Type of Medium:
Online Resource
ISSN:
1553-7374
DOI:
10.1371/journal.ppat.1009373
DOI:
10.1371/journal.ppat.1009373.g001
DOI:
10.1371/journal.ppat.1009373.g002
DOI:
10.1371/journal.ppat.1009373.g003
DOI:
10.1371/journal.ppat.1009373.g004
DOI:
10.1371/journal.ppat.1009373.s001
DOI:
10.1371/journal.ppat.1009373.s002
DOI:
10.1371/journal.ppat.1009373.s003
DOI:
10.1371/journal.ppat.1009373.s004
DOI:
10.1371/journal.ppat.1009373.s005
DOI:
10.1371/journal.ppat.1009373.s006
DOI:
10.1371/journal.ppat.1009373.s007
DOI:
10.1371/journal.ppat.1009373.s008
DOI:
10.1371/journal.ppat.1009373.s009
DOI:
10.1371/journal.ppat.1009373.s010
DOI:
10.1371/journal.ppat.1009373.s011
DOI:
10.1371/journal.ppat.1009373.s012
DOI:
10.1371/journal.ppat.1009373.s013
DOI:
10.1371/journal.ppat.1009373.s014
DOI:
10.1371/journal.ppat.1009373.s015
DOI:
10.1371/journal.ppat.1009373.s016
DOI:
10.1371/journal.ppat.1009373.r001
DOI:
10.1371/journal.ppat.1009373.r002
DOI:
10.1371/journal.ppat.1009373.r003
DOI:
10.1371/journal.ppat.1009373.r004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2021
detail.hit.zdb_id:
2205412-1
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