Virus Evolution最新文献

Comparative complete genome analyses were conducted on 173 field outbreak strains of foot-and-mouth disease virus (FMDV) serotype A, collected from various regions worldwide, including strains that have circulated in India in recent years. Phylogenetic analyses revealed that the majority of isolates included in this study belonged to the Asia (n = 108), followed by EURO-SA (n = 41) and Africa (n = 24) topotypes. The mean rate of evolutionary change in FMDV serotype A was estimated to be 2.369 × 10^-3 substitutions/site/year for the Open Reading Frame (ORF). Faster substitution rates in the Asia topotype suggests heightened selective pressures, likely driven by pre-existing host immune responses due to prior infections or vaccination. The periodic emergence and subsequent dominance of notable genotypes or lineages within the Asia topotype such as genotype 18 (ASIA/VII), genotype 20 (Sea-97), and genotype 26 (Iran-05) underscore the ongoing diversification, adaptation, and selection of the virus in the field across Asia. Monophyletic clustering within the Asia and Africa topotypes suggests region-specific evolutionary trajectories, while the diversity observed within EURO-SA indicates an older and more genetically varied lineage pattern. The presence of amino acid insertions and deletions in some of the isolates points to potential hotspots for genetic change, particularly in regions such as L, VP1, and 3A, reflecting high genetic volatility. Positive selection across the protein-coding regions excluding VP4 and 2A highlights the virus's adaptive potential, likely contributing to immune evasion, host adaptation, and enhanced fitness for replication and transmission. Evidence of recombination events, particularly in five isolates with spatio-temporal overlaps, indicates dynamic viral evolution potentially favourable for emergence of new variants. These findings are crucial for understanding foot-and-mouth disease (FMD) epidemiology and may have implications for global FMD control strategies.

Background: Human immunodeficiency virus type 1 (HIV-1) is one of the fastest-evolving human pathogens. Understanding HIV-1 transmission, within-host adaptation, and evolutionary dynamics is pivotal for development of interventions and vaccines. HIV-1 infection is generally caused by a single transmitted founder virus (TFV), and TFV sequences are typically obtained using single genome amplification (SGA). However, suboptimal sample quality can cause sequencing failures, representing considerable losses considering the scarcity of acute HIV-1 infection (AHI) samples. Sequencing failures may be mitigated by molecular cloning (MC), which can be less vulnerable to sample quality but more susceptible to polymerase chain reaction (PCR) errors. Here, we explore the feasibility of supplementing SGA with MC data using samples from clinical and research cohorts to determine whether sequence diversity and evolutionary rate estimates are comparable between the techniques.

Methods: Plasma samples were selected from participants with documented AHI from an East African research cohort (the International AIDS Vaccine Initiative, 2006-2011) and a clinical cohort from Sweden (1983-2011). SGA and MC sequencing were done on the HIV-1 env V1-V3 region (~940 base pairs). Within-host sequence diversity was determined from maximum likelihood phylogenetic trees, and evolutionary rate by Bayesian phylogenetic analysis. Highlighter plots, Hamming distances, and assessment of star phylogenies were used to quantify TFVs.

Results: One hundred participants (median age 30.3 years, 15% female), contributing 350 samples from four longitudinal time points, 10-540 days post-infection, met the inclusion criteria. SGA succeeded on 90% of research cohort and 48% of clinical cohort samples. Comparative analysis of linked SGA and MC data from 10 samples indicated that approximately eight sequences were necessary for diversity estimates. Consistently higher sequence diversity was observed among MC relative to SGA sequences (median [IQR]: 0.009 [0.003, 0.015] and 0.004 [0.001, 0.012] substitutions/site, P = .002), whereas evolutionary rates were comparable between the two methods (0.016 [0.012, 0.019] and 0.011 [0.008, 0.020] substitutions/site/year, P = .232). Five participants with samples obtained within 45 days post-infection were eligible for TFV quantification, and all found to have one TFV using both techniques.

Conclusion: MC data is a suitable supplement for SGA-based HIV-1 studies to preserve the value of precious samples for analysis of evolutionary rate, but not for sequence diversity.

Human noroviruses are genetically diverse and over 30 different genotypes, mainly from genogroups GI and GII, are known to infect humans. Understanding of human norovirus diversity is still incomplete, and this large genetic diversity across and even within genotypes raises important questions about the origins of this diversity and how it is shaped within and between infected individuals. To gain insight into the origin of this genetic diversity, we analysed intra-host norovirus evolution from individuals experimentally infected with the prototype norovirus strain, Norwalk virus (GI.1[P1]). We investigated intra-host viral dynamics, the impact of antibody responses on intra-host viral evolution, inoculum-to-host viral evolution, and whether detected intra-host mutations have evidence of global (population-level) circulation. Notably, most intra-inoculum mutations detected in two GI.1 norovirus inoculum pools were not detected in individuals challenged with those inocula. Likewise, the majority of all intra-host mutations detected in challenged individuals were not detected in the inoculum and thus likely arose de novo within these individuals. Most of them were detected only once during shedding and have not been circulating at appreciable levels at the population level. Structural analyses confirmed that there was no significant difference in the distribution of intra-host mutations on the proteins among specimens with or without positive serum antibody responses. Our analyses suggest that stochastic processes, rather than host immune pressure, govern patterns of intra-host viral diversity in experimental, acute human norovirus infections. They further suggest that strong fitness constraints act to purify the majority of mutations during infection. Further studies that investigate structural and chemical constraints of this virus as well as fitness effects of mutations across the viral genome could help in our understanding of norovirus evolution.

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.