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SARS-CoV-2 within-host diversity and transmission


Patterns and bottlenecks
A year into the severe acute respiratory syndrome coronavirus 2 pandemic, we are experiencing waves of new variants emerging. Some of these variants have worrying functional implications, such as increased transmissibility or antibody treatment escape. Lythgoe
et al. have undertaken in-depth sequencing of more than 1000 hospital patients isolates to find out how the virus is mutating within individuals. Overall, there seem to be consistent and reproducible patterns of within-host virus diversity. The authors observed only one or two variants in most samples, but a few carried many variants. Although the evidence indicates strong purifying selection, including in the spike protein responsible for viral entry, the authors also saw evidence for transmission clusters associated with households and other possible superspreader events. After transmission, most variants fizzled out, but occasionally some initiated ongoing transmission and wider dissemin ....

United Kingdom , Takara Bio , Beckman Coulter , United Kingdom Research Innovation , Royal Society , Melinda Gates Foundation , Virus Network , Genome Research , Oxford Biomedical Research Centre , Oxford University Hospitals , Department Of Health , Oxford Genomics Centre , Research Computing , Research Council , Public Health England Research Ethics , National Institute For Biological Standards , National Institute Of Health Research , Genomics Consortium , Wellcome Sanger Institute , Reference Reagent Program , Global Initiative On Sharing All Influenza Data , Li Ka Shing Foundation , Analysis Group , Genomics United Kingdom Consortium , Fleming Fund , Governance Group ,