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

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.

SUBMITTER: Lythgoe KA 

PROVIDER: S-EPMC8128293 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

Lythgoe Katrina A KA   Hall Matthew M   Ferretti Luca L   de Cesare Mariateresa M   MacIntyre-Cockett George G   Trebes Amy A   Andersson Monique M   Otecko Newton N   Wise Emma L EL   Moore Nathan N   Lynch Jessica J   Kidd Stephen S   Cortes Nicholas N   Mori Matilde M   Williams Rebecca R   Vernet Gabrielle G   Justice Anita A   Green Angie A   Nicholls Samuel M SM   Ansari M Azim MA   Abeler-Dörner Lucie L   Moore Catrin E CE   Peto Timothy E A TEA   Eyre David W DW   Shaw Robert R   Simmonds Peter P   Buck David D   Todd John A JA   Connor Thomas R TR   Ashraf Shirin S   da Silva Filipe Ana A   Shepherd James J   Thomson Emma C EC   Bonsall David D   Fraser Christophe C   Golubchik Tanya T  

Science (New York, N.Y.) 20210309 6539

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 char  ...[more]

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