Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic “signatures” within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission

Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.

<p>Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.</p

Mean average pairwise Hamming distance (APHD) of HIV-1 Env SGA/S sequences distinguishes between single and multiple founder viruses.

<p><b>(A)</b> A training set of SGA/S Env sequences derived from 127 previously published acute HIV-1 infected subjects illustrating a wide range of <i>env</i> diversity. The APHD is calculated using a sliding window of 120bp with a step size of 21bp. The mean APHD is plotted according to Fiebig stages as defined by HIV-1 clinical laboratory test results. <b>(B)</b> A classifier based on a logistic regression segregated 127 subjects into single or multiple infections and correctly assigned 97% of subjects into the respective groups. Each point corresponds to an individual subject with the number of subjects denoted on the x-axis in parenthesis under each Fiebig stage.</p

Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.

<p>Multiplicity of HIV-1 infection in HSX, MSM and IDU subjects.</p

Previously described signature sites enriched in HSX Founder viruses.

<p>Previously described signature sites enriched in HSX Founder viruses.</p

Mapping of signature sites on the three-dimensional structure of gp120 shows clustering around the CD4-binding site.

<p>A ribbon representation of the crystal structure from the JRFL gp120 molecule (grey) bound to CD4 molecule (green) (PDBID: 2B4C). The CD4 binding site is highlighted in transparent green while signature sites 283, 343, 362, 389, 429, 465 and 471 are all depicted as <i>red</i> space-filling residues.</p

Selection bias intensified for HSX founder viruses compared to MSM founder viruses.

<p>The transmission index of a sequence was calculated using logistic regression with model weights taken from [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005619#ppat.1005619.ref012" target="_blank">12</a>]. Black lines represent the median transmission index for the two risk groups. The overall transmission index of HSX (red circles) viruses is significantly higher than from MSM (blue circles) founder viruses (<i>P</i> = 0.00003, Mann-Whitney two-tailed test). The number of subjects in each category is denoted under each group.</p

Signature sites identified between MSM and HSX Founder viruses in Env using a phylogenetic corrected method.

<p>Signature sites identified between MSM and HSX Founder viruses in Env using a phylogenetic corrected method.</p