SARS-CoV-2 Within-host Diversity and Transmission

Overview

Journal Science

Specialty Science

Date 2021 Mar 10

PMID 33688063

Citations 220

Authors

Katrina A Lythgoe

Matthew Hall

Luca Ferretti

Mariateresa de Cesare

George MacIntyre-Cockett

Amy Trebes

Monique Andersson

Newton Otecko

Emma L Wise

Nathan Moore

Jessica Lynch

Stephen Kidd

Nicholas Cortes

Matilde Mori

Rebecca Williams

Gabrielle Vernet

Anita Justice

Angie Green

Samuel M Nicholls

M Azim Ansari

Lucie Abeler-Dorner

Catrin E Moore

Timothy E A Peto

David W Eyre

Robert Shaw

Peter Simmonds

David Buck

John A Todd

Thomas R Connor

Shirin Ashraf

Ana da Silva Filipe

James Shepherd

Emma C Thomson

David Bonsall

Christophe Fraser

Tanya Golubchik

Affiliations

Soon will be listed here.

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.

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