Summary SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2 1 , and is a major antibody target. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences over 23 time points spanning 101 days. Little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days. However, following convalescent plasma therapy we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro , the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type, possibly compensating for the reduced infectivity of D796H. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with evidence of reduced susceptibility to neutralising antibodies.

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Extensive global sampling and sequencing of the pandemic virus 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 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. Our results suggest that transmission-enhancing and/or immune-escape variants are likely to arise infrequently, but could spread rapidly if successfully transmitted.

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019 causing a global pandemic, with the United Kingdom (UK) one of the hardest hit countries. Rapid sequencing and publication of consensus genomes have enabled phylogenetic analysis of the virus, demonstrating SARS-CoV-2 evolves relatively slowly 1 , but with multiple sites in the genome that appear inconsistent with the overall consensus phylogeny 2 . To understand these discrepancies, we used veSEQ 3 , a targeted RNA-seq approach, to quantify minor allele frequencies in 413 clinical samples from two UK locations. We show that SARS-CoV-2 infections are characterised by extensive within-host diversity, which is frequently shared among infected individuals with patterns consistent with geographical structure. These results were reproducible in data from other sequencing locations around the UK, where we find evidence of mixed infection by major circulating lineages with patterns that cannot readily be explained by artefacts in the data. We conclude that SARS-CoV-2 diversity is transmissible, and propose that geographic patterns are generated by co-circulation of distinct viral populations. Co-transmission of mixed populations could open opportunities for resolving clusters of transmission and understanding pathogenesis. symptomatic individuals who tested positive for COVID-19 within two geographically-separate hospital trusts (Oxford University Hospitals and Basingstoke and North Hampshire Hospital, located 37 miles (60 km) apart; Supplementary Table 1) . Using veSEQ, a sequencing protocol based on a quantitative targeted enrichment strategy 3 , which we previously validated for other viruses 3 , 11 , 12 , we characterised the full spectrum of within-host diversity in SARS-CoV-2 and contextualised our findings within other high-quality, publicly available deep-sequencing datasets from the UK generated on the high-fidelity Illumina platform 13 , 14 . All genomic data has been made publicly available as part of the COVID-19 Genomics UK (COG-UK) Consortium [cogconsortium.uk] via GISAID 15 and the European Nucleotide Archive (ENA) study PRJEB37886. Within-host diversity is extensive and shared between individualsTo examine patterns of within-host diversity, we first considered the distribution of minor allele frequencies (MAFs) in the mapped reads at every position along the genome. This analysis was supported by data curation to ensure that only high-confidence variants were examined, which included analysis of in-batch quantification controls as well as a stringent computational clean-up to eliminate any residual cross-mapping 16 , previously validated for targeted metagenomics 11 (see Methods and Supplementary Text for a full description). In combination with unique dual indexing (UDI), these procedures generated highly robust minority variant calls, which were reproducible in independent replicates and distinguishable from methodological noise above a threshold of 2% of reads at a given position (Supplementary Figure 1). The distribution of MAFs was a...