SARS-CoV-2 within-host diversity and transmission.


Lythgoe, Katrina A ORCID: 0000-0002-7089-7680, Hall, Matthew ORCID: 0000-0002-2671-3864, Ferretti, Luca ORCID: 0000-0001-7578-7301, de Cesare, Mariateresa ORCID: 0000-0002-9847-1526, MacIntyre-Cockett, George, Trebes, Amy ORCID: 0000-0002-3715-9109, Andersson, Monique ORCID: 0000-0003-0619-1074, Otecko, Newton ORCID: 0000-0002-9149-4776, Wise, Emma L ORCID: 0000-0002-0279-3900, Moore, Nathan ORCID: 0000-0002-4279-2443 et al (show 28 more authors) (2021) SARS-CoV-2 within-host diversity and transmission. Science (New York, N.Y.), 372 (6539). eabg0821-. ISSN 0036-8075, 1095-9203

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Abstract

Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted.

Item Type: Article
Uncontrolled Keywords: Oxford Virus Sequencing Analysis Group (OVSG), COVID-19 Genomics UK (COG-UK) Consortium, Humans, Coronavirus OC43, Human, Coronavirus Infections, RNA, Viral, Viral Load, Family Characteristics, Phylogeny, Mutation, Genome, Viral, Genetic Variation, Selection, Genetic, Immune Evasion, Coinfection, Spike Glycoprotein, Coronavirus, United Kingdom, RNA-Seq, COVID-19, SARS-CoV-2
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 10 Jan 2023 16:16
Last Modified: 07 Dec 2024 23:18
DOI: 10.1126/science.abg0821
Open Access URL: https://doi.org/10.1126/science.abg0821
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3166977
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