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 the authors deep-sequenced 1313 clinical samples from the UK. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high, and 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 which are readily observable on the phylogenetic tree. The authors concluded that their results suggest that transmission-enhancing and/or immune-escape variants are likely to arise infrequently, but could spread rapidly if successfully transmitted.
Lythgoe KA, et al. SARS-CoV-2 within-host diversity and transmission. Science. 2021 Mar 9:eabg0821. doi: 10.1126/science.abg0821