Virus Evolution最新文献

High numbers of reported mpox cases and recent identification of multiple sustained human outbreaks of mpox virus (MPXV) have highlighted the need for robust, best-practice genomic surveillance tools. In light of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, many labs across the globe developed the capacity to do virus genome sequencing; however, MPXV presents additional analytical challenges due to its large genome size, tracts of low-complexity or repeat regions, genetically distinct clades, and the need to perform bespoke apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3)-mutation reconstruction. We present squirrel (Some Quick Reconstruction to Resolve Evolutionary Links), an open source bioinformatic tool that can perform clade-aware alignment, mutation quality assessment, phylogenetic inference, and automated APOBEC3-mutation classification on branches of the phylogeny. Squirrel can be run on the command line or launched through the EPI2ME graphical user interface through the squirrel-nf workflow, enabling robust analysis without need for the command line. With the interactive output report produced and publication-ready APOBEC3-reconstruction visualization, squirrel enables researchers to distinguish between zoonotic and sustained human outbreaks and help accurately inform public health responses.

Understanding the viral diversity harboured by wildlife is essential for effective mapping and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several high-impact zoonotic viral pathogens, including coronaviruses responsible for Severe Acute Respiratory Syndrome (SARS), the rabies virus, diverse paramyxoviruses, Marburg, Ebola, Nipah, and Hendra viruses. However, a large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazilian ecosystems. We used a meta-transcriptomic approach to characterize new virus genomes found in blood, oral, and anal samples collected from cave- and noncave bats from Northeast Brazil, Caatinga, and Atlantic Forest biomes. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nobecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain from the C-terminal domai (CTD) region could not be identified due to high dissimilarity relative to known congeners. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests potential interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown, not just in Brazil but likely in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.

The virulence of Human Immunodeficiency Virus-1 (HIV-1) is partly determined by viral genetic variation. Finding individual genetic variants affecting virulence is important for our understanding of HIV pathogenesis and evolution of virulence; however, very few have been identified. To this end, within the "Bridging the Evolution and Epidemiology of HIV in Europe" (BEEHIVE) collaboration, we produced whole-genome HIV sequence data for 2294 seroconverters from European countries for a genome-wide association study (GWAS). We considered two phenotypes: (i) set-point viral load (SPVL), the approximately stable viral load from 6 to 24 months after infection, and (ii) the rate of CD4 cell count decline. We developed a GWAS method that corrects for population structure with random effects, accounts for two or more alleles at each locus, and tests for the effect of multiple genetic variants including single-nucleotide polymorphisms (SNPs), k-mers, insertions and deletions, within-host variant frequency, the number of rare point mutations, and drug resistance. We confirmed with this new approach that viral genomes explained 26% [95% CI 17%-35%] of the variance in SPVL, while they explained only 0.9% [0.0%-2.1%] of the variance in the rate of CD4 cell count decline. After correction for multiple testing, among all tested variants, only two significantly explained SPVL: an epitope mutation allowing escape from the host HLA-B^*57 allele and lowering SPVL by -0.26 [Formula: see text] copies/ml and an epitope mutation allowing escape from the host HLA-B^*35 allele and increasing SPVL by +0.22 [Formula: see text] copies/ml. We attempted to replicate these two large effects in two additional independent datasets together encompassing 2445 seroconverters, with mixed results. Overall, the inferred effects of all SNPs and amino-acid variants weakly correlated (R ² ranging from 0.08 to 0.87%, P-values from 0.001 to 0.32) between our main dataset and these two additional datasets. Lastly, a lasso regression of phenotypes on genetic variants confirmed the heritability of SPVL and explained up to 6% of variance in SPVL in cross-validation datasets. These findings suggest that HIV SPVL is determined by viral genomes through HLA escape variants with potentially large, host-dependent effects that may not always be detected at the population level and many other variants with effects too weak to reach genome-wide significance in our GWAS.

Rhinolophus bats harbour various alpha- and betacoronaviruses and are believed to be the progenitor host of SARS-CoV and SARS-CoV-2. These bats are widely distributed, with 38 species recognized in Africa. Although coronaviruses have been detected in several species in Africa, there is a lack of surveillance among South African rhinolophids. This study conducted longitudinal nucleic acid surveillance for Rhinolophus spp. coronaviruses from September 2021 to January 2024 in a mixed species cave in Limpopo, South Africa, using a hemi-nested RT-PCR assay. Among the 492 gastrointestinal samples collected, alphacoronavirus RNA was detected in 29.47% of samples, with betacoronavirus RNA identified among 7.11% of samples, with excretion peaks present in spring and summer (September-February). Based on GAMMs, the alphacoronavirus prevalence was strongly affected by season, total rainfall, and bat mass, whereas the betacoronavirus prevalence was influenced by forearm length, although the small sample size limits this finding. Rhinolophus acrotis contributed greatly to the interspecies sharing of alphacoronaviruses, and R. blasii was the primary origin of betacoronavirus interspecies sharing. This study expanded the known coronavirus diversity in African rhinolophids and highlighted the phylogeographic clustering of these viruses. The research emphasizes the need for more longitudinal studies involving African rhinolophids to better understand the ecological and behavioural factors that drive viral shedding for risk assessment and mitigation strategies.

Understanding the genetic and genomic underpinnings of infectious disease outbreaks has emerged as a frontier of epidemiology. Here, we argue that epistasis-where the phenotypic effects of mutations or gene variants are dictated by the presence of other mutations or genes-should become a focus of genomic epidemiology. To demonstrate this, we present the results of a systematic review of the literature on epistasis in viruses, focusing on three major human viral systems: (i) influenza, (ii) SARS-CoV-2, and (iii) human immunodeficiency virus, as well as two other bodies of the literature mainly focusing on nonhuman viruses: (iv) tobacco etch virus and (v) experimental evolution of viruses. Our systematic review of these five bodies of the literature highlights that epistasis is prevalent in host-virus systems of various kinds, manifesting within and between different loci, with effects of different magnitudes and directions, and shaping various phenotypic traits of epidemiological interest. At the same time, our systematic review demonstrates that our ability to draw general conclusions about the direction and magnitude of epistasis in viral evolution is constrained by several factors: the idiosyncrasies of virus-host systems, biases in the underlying data collection exercises, and the limitations of existing methods. Moving forward, we encourage collaborations between genomic epidemiologists and evolutionary biologists to identify and measure epistasis in studying the evolution of viral pathogens.

[This corrects the article DOI: 10.1093/ve/veaf056.].

The spread of a severe and often fatal form of lumpy skin disease (LSD) in cattle and water buffaloes has caused widespread mortality and morbidity of these animals in India. To track and understand the genetic changes occurring in the virus and to enable routine surveillance of the virus, multiplexed polymerase chain reaction (PCR) and sequencing methods were developed and validated in this study. Multiplexed nested PCR for LSD virus (LSDV) detection was optimized using skin lesion swabs and nasal samples collected from symptomatic and asymptomatic animals. For genotyping, overlapping PCRs to amplify the entire LSDV genome were developed and tested on field samples collected from the Maharashtra and Odisha states of India. Analysis of LSDV genomes from 41 field samples collected in 2022 and 2023 revealed the presence of highly conserved novel mutations. Phylogenetic analysis shows that a distinct genotype of LSDV has spread across India, which warrants genomic surveillance of the virus in the coming years to track the evolution and transmission of the virus. The non-invasive sample collection, detection, and genotyping methods described in this study can facilitate large-scale surveillance of LSDV in dairy animals.

This study investigates the genetic diversity of influenza A viruses (IAVs) in wild birds in Argentina prior to the 2023 outbreak of highly pathogenic avian influenza (HPAI) H5N1. Between 2017 and 2019, 2521 samples were collected from 39 bird species, and viral genomes (n = 44) were sequenced from nine duck species, including a newly identified host in South America, the ringed teal (Callonetta leucophrys). We detected five IAV subtypes for the first time in Argentina: H2N1, H3N8, H7N3, H8N4, and H11N9. Additionally, we identified a previously unrecognized South American H8 lineage that diverged from the North American lineage approximately 50 years ago. Phylogenetic analysis revealed a unique genetic profile: while the viruses' core internal segments were exclusively from the South American lineage, the surface segments (hemagglutinin and neuraminidase) exhibited reassortment between North and South American lineages. This resulted in novel, Argentina-specific genotypes not observed in other countries in the region. The recent arrival of HPAI H5N1 in South America raises serious concerns about potential reassortment with these unique Argentinian strains, which could create new HPAI viruses with unpredictable characteristics. This study highlights the unique evolutionary dynamics of IAVs in Argentina and emphasizes the need for ongoing influenza surveillance in under-studied regions in South America to monitor these evolving viral populations.

Galbut virus is a remarkably successful virus of the model organism Drosophila melanogaster. The ease of capturing galbut virus-infected wild flies presents an opportunity to study persistent virus-host interactions. To better understand galbut virus diversity, evolution, and genotype-phenotype relationships, we screened 957 flies collected from 13 locations across the USA. Galbut virus was detected in every population, and overall, 75% of flies tested positive. We selected 149 flies for shotgun RNA sequencing and recovered 368 coding-complete or near-complete sequences of galbut virus and its likely satellite, chaq virus. Galbut virus sequences clustered phylogenetically into three major clades. Two clades, termed melA and melB, comprised mainly viruses infecting D. melanogaster, while the third, simA, included D. simulans-infecting viruses. Between-clade pairwise nucleotide identity was as low as 75%, but diversity within clades was low. Geography partly explained phylogenetic clustering: some sequences from the same location were identical or nearly identical, while others were spread throughout trees. Several genotype-phenotype associations emerged, including higher average RNA levels in melA infections and an exclusive association of chaq virus with melA and simA infections. Coinfection was detected in 11% of samples and did not require complete sets of all three galbut virus segments. Coinfection is a prerequisite of reassortment, and there was evidence of reassortment involving all segments and chaq virus. However, reassortment did not occur between clades, despite coinfection, indicating that clades are reproductively isolated. Galbut virus RNA 3 sequences exhibited more involvement in coinfection, greater diversity, and stronger evidence of diversifying selection than the other segments, consistent with a possible role in host modulation. These findings corroborated the ecological success of galbut virus and reveal the need for experiments to uncover the mechanisms underlying reassortment incompatibility and clade-specific phenotypes.

The hemagglutinin of human influenza virus evolves rapidly to erode neutralizing antibody immunity. Twice per year, new vaccine strains are selected with the goal of providing maximum protection against the viruses that will be circulating when the vaccine is administered ~8-12 months in the future. To help inform this selection, here we quantify how the antibodies in recently collected human sera neutralize viruses with hemagglutinins from contemporary influenza strains. Specifically, we use a high-throughput sequencing-based neutralization assay to measure how 188 human sera collected from Oct 2024 to April 2025 neutralize 140 viruses representative of the H3N2 and H1N1 strains circulating in humans as of the summer of 2025. This data set, which encompasses 26 148 neutralization titre measurements, provides a detailed portrait of the current human neutralizing antibody landscape to influenza A virus. The full data set and accompanying visualizations are available for use in vaccine development and viral forecasting.