Immune-driven recombination and loss of control after HIV superinfection

After acute HIV infection, CD8+ T cells are able to control viral replication to a set point. This control is often lost after superinfection, although the mechanism behind this remains unclear. In this study, we illustrate in an HLA-B27+ subject that loss of viral control after HIV superinfection coincides with rapid recombination events within two narrow regions of Gag and Env. Screening for CD8+ T cell responses revealed that each of these recombination sites (∼50 aa) encompassed distinct regions containing two immunodominant CD8 epitopes (B27-KK10 in Gag and Cw1-CL9 in Env). Viral escape and the subsequent development of variant-specific de novo CD8+ T cell responses against both epitopes were illustrative of the significant immune selection pressures exerted by both responses. Comprehensive analysis of the kinetics of CD8 responses and viral evolution indicated that the recombination events quickly facilitated viral escape from both dominant WT- and variant-specific responses. These data suggest that the ability of a superinfecting strain of HIV to overcome preexisting immune control may be related to its ability to rapidly recombine in critical regions under immune selection pressure. These data also support a role for cellular immune pressures in driving the selection of new recombinant forms of HIV

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development

Evolutionary Fingerprinting of Genes

Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change—an “evolutionary fingerprint” of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify genetic features of potential biological interest; however, no framework exists for comparing evolutionary fingerprints between genes. We hypothesize that protein-coding genes with similar protein structure and/or function tend to have similar evolutionary fingerprints and that comparing evolutionary fingerprints can be useful for discovering similarities between genes in a way that is analogous to, but independent of, discovery of similarity via sequence-based comparison tools such as Blast

Molecular and functional consequences of immune-mediated evolution in HIV-1 Nef during the North American epidemic.

Background: HLA-restricted CTL responses drive evolution of the highly immunogenic Nef protein, but the extent and functional consequences of population-level adaptation remain unclear. We have used novel historic Nef data to estimate the date and reconstruct the founder virus sequence of the North American epidemic, compare patterns of population-level HLA-associated polymorphisms over time, and assess CD4 downregulation activity of historic and modern Nef sequences. Methods: Plasma HIV-1 RNA Nef sequencing and HLA typing was performed on 241 historic specimens (1979–89). Modern published HLA/HIV datasets served as controls. Timing and sequence reconstruction of the founder Nef was performed using BEAST and HyPhy. HLA-associated polymorphisms were identified using phylogenetically-corrected methods. CD4 downregulation capacity of 52 historic vs. 52 modern Nef sequences was compared using flow cytometric methods. Results: Based on Nef sequences, the most recent common ancestor of the North American epidemic was dated to 1965. The consensus of the reconstructed founder Nef sequence differed from 2004 subtype B consensus at codons 15, 22, 51 and 178, while additional sites remained ambiguous in the reconstruction. Patterns and statistical strengths of HLA-associated polymorphisms remained generally consistent over time (e.g. A*24-associated Y135F, B*07-R71K, B*08-K94Q and B*57-H116N ranked among the strongest in historic and modern cohorts); however, a small number of polymorphisms were identified as candidates for population-level accumulation. Functional assessment of Nef revealed a modest yet statistically significant increase in CD4 downregulation capacity over time (median 0.93 vs. 1.00 in historic vs. modern sequences; p = 0.005). Conclusion: Modest population-level immune adaptation in Nef, potentially leading to modest increases in CD4 downregulation capacity, may have occurred in North America since 1979. However, the relatively high similarity between the estimated founder and modern consensus B, and the observation that CTL escape patterns have remained largely consistent over time, support Nef as a suitable target for vaccine consideration

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.ISSN:2057-585