Inferred neighbour-joining phylogenetic tree of single genome derived HIV-1 env sequences.

<p>Two APOBEC hypermutated sequences found in the third rebound have been removed. Pre melphalan HIV DNA (-27 to -38, orange open diamonds), first rebound HIV RNA (+6, blue closed diamonds), first rebound HIV DNA (+6, blue open diamonds), second rebound HIV RNA (+515, magenta closed diamonds), third rebound HIV DNA (+643 to +958, green open diamonds). Rooted on MJ4 (black square), branches with bootstrap support > 75% are indicated by black asterisk. Overall population APD is 1.5%. The scale represents 0.005 nucleotide substitutions per site, equivalent to 4.5nt. The tips in the boxed grey area representative sequences predicted to confer CXCR4 tropism by both Geno2Pheno and Phenoseq genotypic algorithms.</p

Diversity measured as average pairwise distance at longitudinal time points.

<p>APD measured pre- ASCT and during subsequent viral rebounds. Numbers in parentheses indicate the number of single genomes acquired at each time point. Significance was determined by two-tailed.</p

Non-parametric geographic subdivision tests comparing pre- ASCT viruses with those at each rebound.

<p>Non-parametric geographic subdivision tests comparing pre- ASCT viruses with those at each rebound.</p

Genotypically defined co-receptor usage following HIV rebounds.

<p>Tropism testing of the HIV V3 loop was performed in both Geno2Pheno and Phenoseq online genotypic algorithms. Percentage of CXCR4 sequences is plotted on the Y-axis. Only sequences found to be X4 in both programs were designated as X4. Significance was determined using a two-tailed Fishers Exact test.</p

SARS-CoV-2 evolution during treatment of chronic infection

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals