Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI. 2011 Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of Virology85157523-34 pubmed
SupplementalFigure1.tif InSites diagrams of genome sequences for transmission pair 4
SupplementalFigure4.tif InSites diagrams of genome sequences for transmission pair 3

Alignment of phylogenetically-informative sites identified in whole proteome sequences relative to the visit 1 consensus sequence in the seroconverter. Header row with visit 1 consensus sequence with HXB2 numbering is shaded in grey for positively selected sites (as detected by FEL or by a simulation approach (54, 42)) and purple for putative N-linked glycosylation sites. Footer row represents known or predicted epitopes:  AA sites within epitopes are shaded in black, AA sites located near known or predicted epitopes (up to 5 AA away) are shaded in grey. Green boxes surround HIV-1 segments recognized by IFN-γ ELISpot responses. Red boxes surround mutually exclusive mutation patterns. Orange cells represent forward mutations (decrease in database frequency of the AA by 50% or more), blue cells represent reverse mutations (increase in database frequency of the AA by 50% or more), green cells represent less substantial changes in database frequency. In addition, the upper part of the diagram corresponds to sequences from the transmitter, and sequences are also compared to the visit 1 consensus in the seroconverter; days post symptoms are displayed on the left of each row. Sites that differed between transmitter and seroconverter are highlighted. AA sites are highlighted in pink when the AA in the seroconverter was different from the AA found in the transmitter and the AA in the transmitter has a higher database frequency than the AA found in the seroconverter (by 50% or more). AA sites were highlighted in blue when the AA in the seroconverter is different from the AA found in the transmitter and the AA in the transmitter has a lower database frequency than the AA found in the seroconverter (by 50% or more).

SupplementalFigure2.tif

Dips in genetic diversity and APOBEC3F/G-induced mutations. The mean pairwise nucleotide diversity across genomes (corrected with the HKY substitution model) is represented by a black line. The mean number of APOBEC3G/F-mediated mutations is represented by a blue line; a dotted black line corresponds to the mean number of control mutations (as measured using Hypermut 2.0).

SupplementalFigure3.tif

InSites diagram of genome sequences for subject S3. Alignment of phylogenetically-informative sites identified in whole proteome coding sequences relative to the visit 1 consensus sequence in the seroconverter. Figure is as described in the legend for Supplemental Figures 1 and 4.

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School of Medicine
University of Washington
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