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Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

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 sequenc...

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Autores principales: Braun, Katarina M., Moreno, Gage K., Halfmann, Peter J., Hodcroft, Emma B., Baker, David A., Boehm, Emma C., Weiler, Andrea M., Haj, Amelia K., Hatta, Masato, Chiba, Shiho, Maemura, Tadashi, Kawaoka, Yoshihiro, Koelle, Katia, O’Connor, David H., Friedrich, Thomas C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946358/
https://www.ncbi.nlm.nih.gov/pubmed/33635912
http://dx.doi.org/10.1371/journal.ppat.1009373
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author Braun, Katarina M.
Moreno, Gage K.
Halfmann, Peter J.
Hodcroft, Emma B.
Baker, David A.
Boehm, Emma C.
Weiler, Andrea M.
Haj, Amelia K.
Hatta, Masato
Chiba, Shiho
Maemura, Tadashi
Kawaoka, Yoshihiro
Koelle, Katia
O’Connor, David H.
Friedrich, Thomas C.
author_facet Braun, Katarina M.
Moreno, Gage K.
Halfmann, Peter J.
Hodcroft, Emma B.
Baker, David A.
Boehm, Emma C.
Weiler, Andrea M.
Haj, Amelia K.
Hatta, Masato
Chiba, Shiho
Maemura, Tadashi
Kawaoka, Yoshihiro
Koelle, Katia
O’Connor, David H.
Friedrich, Thomas C.
author_sort Braun, Katarina M.
collection PubMed
description 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.
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spelling pubmed-79463582021-03-22 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck Braun, Katarina M. Moreno, Gage K. Halfmann, Peter J. Hodcroft, Emma B. Baker, David A. Boehm, Emma C. Weiler, Andrea M. Haj, Amelia K. Hatta, Masato Chiba, Shiho Maemura, Tadashi Kawaoka, Yoshihiro Koelle, Katia O’Connor, David H. Friedrich, Thomas C. PLoS Pathog Research Article 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. Public Library of Science 2021-02-26 /pmc/articles/PMC7946358/ /pubmed/33635912 http://dx.doi.org/10.1371/journal.ppat.1009373 Text en © 2021 Braun et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Braun, Katarina M.
Moreno, Gage K.
Halfmann, Peter J.
Hodcroft, Emma B.
Baker, David A.
Boehm, Emma C.
Weiler, Andrea M.
Haj, Amelia K.
Hatta, Masato
Chiba, Shiho
Maemura, Tadashi
Kawaoka, Yoshihiro
Koelle, Katia
O’Connor, David H.
Friedrich, Thomas C.
Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
title Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
title_full Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
title_fullStr Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
title_full_unstemmed Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
title_short Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck
title_sort transmission of sars-cov-2 in domestic cats imposes a narrow bottleneck
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946358/
https://www.ncbi.nlm.nih.gov/pubmed/33635912
http://dx.doi.org/10.1371/journal.ppat.1009373
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