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:	Katarina M Braun, Gage K Moreno, Peter J Halfmann, Emma B Hodcroft, David A Baker, Emma C Boehm, Andrea M Weiler, Amelia K Haj, Masato Hatta, Shiho Chiba, Tadashi Maemura, Yoshihiro Kawaoka, Katia Koelle, David H O'Connor, Thomas C Friedrich
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/07d679a1e6974eef85af99c958533244
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spelling	oai:doaj.org-article:07d679a1e6974eef85af99c9585332442021-12-02T20:00:18ZTransmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.1553-73661553-737410.1371/journal.ppat.1009373https://doaj.org/article/07d679a1e6974eef85af99c9585332442021-02-01T00:00:00Zhttps://doi.org/10.1371/journal.ppat.1009373https://doaj.org/toc/1553-7366https://doaj.org/toc/1553-7374The 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.Katarina M BraunGage K MorenoPeter J HalfmannEmma B HodcroftDavid A BakerEmma C BoehmAndrea M WeilerAmelia K HajMasato HattaShiho ChibaTadashi MaemuraYoshihiro KawaokaKatia KoelleDavid H O'ConnorThomas C FriedrichPublic Library of Science (PLoS)articleImmunologic diseases. AllergyRC581-607Biology (General)QH301-705.5ENPLoS Pathogens, Vol 17, Iss 2, p e1009373 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
spellingShingle	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5 Katarina M Braun Gage K Moreno Peter J Halfmann Emma B Hodcroft David A Baker Emma C Boehm Andrea M Weiler Amelia K Haj Masato Hatta Shiho Chiba Tadashi Maemura Yoshihiro Kawaoka Katia Koelle David H O'Connor Thomas C Friedrich Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.
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.
format	article
author	Katarina M Braun Gage K Moreno Peter J Halfmann Emma B Hodcroft David A Baker Emma C Boehm Andrea M Weiler Amelia K Haj Masato Hatta Shiho Chiba Tadashi Maemura Yoshihiro Kawaoka Katia Koelle David H O'Connor Thomas C Friedrich
author_facet	Katarina M Braun Gage K Moreno Peter J Halfmann Emma B Hodcroft David A Baker Emma C Boehm Andrea M Weiler Amelia K Haj Masato Hatta Shiho Chiba Tadashi Maemura Yoshihiro Kawaoka Katia Koelle David H O'Connor Thomas C Friedrich
author_sort	Katarina M Braun
title	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_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_sort	transmission of sars-cov-2 in domestic cats imposes a narrow bottleneck.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/07d679a1e6974eef85af99c958533244
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Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.

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