Extended Data Fig. 3: QVOA wells with exponential outgrowth contain proviruses with and without the recurrent deletions. | Nature Microbiology

Extended Data Fig. 3: QVOA wells with exponential outgrowth contain proviruses with and without the recurrent deletions.

From: Superinfection promotes replication and diversification of defective HIV-1 proviruses in people with non-suppressible viraemia

Extended Data Fig. 3

(a and b) (Left) Neighbour-joining phylogenetic trees of single genome sequences obtained from outgrowth wells. Coloured boxes represent multiple sequences obtained from the same outgrowth well. The sequenced amplicon coordinates refer to the reference genome HXB2. Tree nodes with bootstrap values above 80 are marked with asterisks. (Right) Highlighter plot with black lines representing nucleotide changes compared to the top sequence of each tree. Gray vertical bars represent deletions compared to HXB2. Boxed regions represent recurrent deletion patterns of 1417 nt, 313 nt (P1), and 270 nt (P2).

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