SARS-CoV-2 within-host diversity and transmission
Lythgoe KA., Hall M., Ferretti L., de Cesare M., MacIntyre-Cockett G., Trebes A., Andersson M., Otecko N., Wise EL., Moore N., Lynch J., Kidd S., Cortes N., Mori M., Williams R., Vernet G., Justice A., Green A., Nicholls SM., Ansari MA., Abeler-Dörner L., Moore CE., Peto TEA., Eyre DW., Shaw R., Simmonds P., Buck D., Todd JA., Connor TR., Ashraf S., da Silva Filipe A., Shepherd J., Thomson EC., Bonsall D., Fraser C., Golubchik T.
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 dissemination. Science , this issue p. eabg0821