Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

Abstract

Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population. We identify recombination hot and cold spots that differ from those observed in inter-subtype recombinants. Furthermore, RAPR analysis of longitudinal samples from an individual with well-characterized neutralizing antibody responses shows that recombination helps carry forward resistance-conferring mutations in the diversifying quasispecies. These findings provide insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis and have implications for studies of HIV transmission and evolution in vivo.

Analysis of HIV-1 latent reservoir and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117

“…This rate is within range of that of reported HIV mutation rates (Abram et al, 2010; Ji and Loeb, 1992; Roberts et al, 1988). Recombination has been found to mediate escape from ART (Kellam and Larder, 1995; Moutouh et al, 1996), CD8 + T cells (Ritchie et al, 2014; Streeck et al, 2008), and autologous neutralizing antibodies (Chaillon et al, 2013; Moore et al, 2013; Song et al, 2018).…”

Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

“…To determine if potential recombination events could be identified in geographically regional data sets, we applied a computational method called RAPR (Song et al, 2018) that we had originally developed to explore the evolutionary role of within-patient HIV recombination in acute HIV infection-another situation of low viral diversity. RAPR enables the comparison of all triplets (sets of three sequences) in an alignment, and applies a run-length statistic to evaluate the possibility of recombination.…”

“…S8, we first did all triplet comparisons of all sequences from local region using the RAPR, and the raw pvalues based on a run-length statistic all the comparisons were rank-ordered to identify the triplet candidates with strongest evidence for recombination to be used as a basis for further exploration. Thus these p-values are uncorrected for multiple testing and not formally compared against the alternative hypotheses of stepwise convergent mutation, as we traditionally do in RAPR analysis (Song et al, 2018). However, given the very low overall mutation rate among SARS-CoV-2 pandemic, it is extremely unlikely that the mutational patterns seen in the recombinant sequences were a result of stepwise convergence.…”

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

“…The enrichment of libraries using multiplex PCR of tiled amplicons (tiling multiplex PCR) and/or capture probe enrichment has been successfully used for the genomic surveillance of EBOV 18,19 , ZIKV [20][21][22] and yellow fever virus (YFV) outbreaks 23 . Tiling multiplex PCR usually targets only a single circulating viral strain at a time; this requires that infection from that strain be established a priori (generally by previous virus-specific PCR testing) and it is thus less practical for viruses that exhibit high sequence divergence and/or recombination (for example HIV) 24 , are present as co-infections 25 or comprise multiple genotypes (for example, hepatitis C virus (HCV), dengue (DENV)). Large panels containing millions of probes have been developed to capture viral diversity and potentially enrich for hundreds of different viruses [26][27][28] , but the relatively high cost, complex protocols and prolonged turnaround times (6-24 h for the hybridization step alone) needed for efficient capture probe hybridization hinder the broad application of this approach.…”