Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%-43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical "Brownian motion" model and another model ("Ornstein-Uhlenbeck") that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%-43%) is consistent with other studies based on regression of viral load in donor-recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation.Peer reviewe

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between-and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.Peer reviewe

Decreased Time to Viral Suppression After Implementation of Targeted Testing and Immediate Initiation of Treatment of Acute Human Immunodeficiency Virus Infection Among Men Who Have Sex With Men in Amsterdam

BACKGROUND: Men who have sex with men (MSM) with acute human immunodeficiency virus (HIV) infection (AHI) are a key source of new infections. To curb transmission, we implemented a strategy for rapid AHI diagnosis and immediate initiation of combination antiretroviral therapy (cART) in Amsterdam MSM. We assessed its effectiveness in diagnosing AHI and decreasing the time to viral suppression. METHODS: We included 63 278 HIV testing visits in 2008-2017, during which 1013 MSM were diagnosed. Standard of care (SOC) included HIV diagnosis confirmation in < 1 week and cART initiation in < 1 month. The AHI strategy comprised same-visit diagnosis confirmation and immediate cART. Time from diagnosis to viral suppression was assessed for 3 cART initiation periods: (1) 2008-2011: cART initiation if CD4 < 500 cells/μL (SOC); (2) January 2012-July 2015: cART initiation if CD4 < 500 cells/μL, or if AHI or early HIV infection (SOC); and (3a) August 2015-June 2017: universal cART initiation (SOC) or (3b) August 2015-June 2017 (the AHI strategy). RESULTS: Before implementation of the AHI strategy, the proportion of AHI among HIV diagnoses was 0.6% (5/876); after implementation this was 11.0% (15/137). Median time (in days) to viral suppression during periods 1, 2, 3a, and 3b was 584 (interquartile range [IQR], 267-1065), 230 (IQR, 132-480), 95 (IQR, 63-136), and 55 (IQR, 31-72), respectively (P < .001). CONCLUSIONS: Implementing the AHI strategy was successful in diagnosing AHI and significantly decreasing the time between HIV diagnosis and viral suppression

Summary of model fit for GSVL, for subtype B, for each gene.

<p>Parameters as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2001855#pbio.2001855.t001" target="_blank">Table 1</a>.</p

Summary of model fit for the subset of subtype B viruses and for all subtypes.

<p>Summary of model fit for the subset of subtype B viruses and for all subtypes.</p

Predictions from the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models of evolution.

<p><b>(A)</b> Illustration of the models of character evolution on a phylogeny (top panel), showing unconstrained neutral evolution leading to increasing genetic variance under the BM model (middle panel) versus stabilizing selection around an optimum θ under the OU model, which results in stable variance over time (bottom panel). Edges of the phylogeny were arbitrarily colored for illustrative purposes. <b>(B)</b> The distribution of gold standard viral load (GSVL) over evolutionary time (as quantified by root-to-tip distance [i.e., distance from the common ancestor as assessed by the phylogeny]). Points are the data; boxplots show the median, lower, and upper quartiles, and the whiskers are the lower and upper quartile minus or plus 1.5 times the interquartile range for 8 bins of equal size. <b>(C)</b> The correlation coefficient of GSVL across 511 phylogenetic cherries in the subtype B phylogeny as a function of the patristic distance between cherries. Phylogenetic cherries were grouped by patristic distance in 10 bins of equal size. Points are the data, the dashed line is a decreasing exponential fit on the data, and thick lines show predictions from the maximum likelihood (ML) BM and OU models. The large points at patristic distance 0 show the population-level heritability estimated under the BM (blue) and OU (red) model. The data used in the figure are provided as <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2001855#pbio.2001855.s014" target="_blank">S1 Data</a>.</p

Decreased Time to Viral Suppression after Implementation of Targeted Testing and Immediate Initiation of Treatment of Acute Human Immunodeficiency Virus Infection among Men Who Have Sex with Men in Amsterdam

Background: Men who have sex with men (MSM) with acute human immunodeficiency virus (HIV) infection (AHI) are a key source of new infections. To curb transmission, we implemented a strategy for rapid AHI diagnosis and immediate initiation of combination antiretroviral therapy (cART) in Amsterdam MSM. We assessed its effectiveness in diagnosing AHI and decreasing the time to viral suppression. Methods: We included 63 278 HIV testing visits in 2008-2017, during which 1013 MSM were diagnosed. Standard of care (SOC) included HIV diagnosis confirmation in &lt; 1 week and cART initiation in &lt; 1 month. The AHI strategy comprised same-visit diagnosis confirmation and immediate cART. Time from diagnosis to viral suppression was assessed for 3 cART initiation periods: (1) 2008-2011: cART initiation if CD4 &lt; 500 cells/μL (SOC); (2) January 2012-July 2015: cART initiation if CD4 &lt; 500 cells/μL, or if AHI or early HIV infection (SOC); and (3a) August 2015-June 2017: universal cART initiation (SOC) or (3b) August 2015-June 2017 (the AHI strategy). Results: Before implementation of the AHI strategy, the proportion of AHI among HIV diagnoses was 0.6% (5/876); after implementation this was 11.0% (15/137). Median time (in days) to viral suppression during periods 1, 2, 3a, and 3b was 584 (interquartile range [IQR], 267-1065), 230 (IQR, 132-480), 95 (IQR, 63-136), and 55 (IQR, 31-72), respectively (P &lt;. 001). Conclusions: Implementing the AHI strategy was successful in diagnosing AHI and significantly decreasing the time between HIV diagnosis and viral suppression.</p

Maximum likelihood estimates of heritability across the genome.

<p>Heritability was inferred for overlapping windows of 1,000 bp separated by 500 bp for the Ornstein–Uhlenbeck (OU) model (black bullets) and the Brownian motion (BM) model (grey bullets). The horizontal dashed lines are the whole-genome heritability estimates. The 3 colored segments show heritability for <i>gag</i>, <i>pol</i>, and <i>env</i> genes in blue, green, red (for OU only). Confidence intervals (grey and colored regions) reflect phylogenetic uncertainty. The largest heritability is in the region where <i>gag</i> and <i>pol</i> overlap. We also show entropy—a measure of genetic diversity—along the genome (dashed curve and right axis). Entropy at a position was calculated as −Σ_{<i>i</i> ∈ {<i>A</i>,<i>C</i>,<i>G</i>,<i>T</i>}}<i>p</i>_<i>i</i> log(<i>p</i>_<i>i</i>), and we show the average entropy over 200-bp windows. The data used in the figure are provided as <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2001855#pbio.2001855.s014" target="_blank">S1 Data</a>.</p