Virus Evolution最新文献

Migratory birds may carry emerging viruses over long distances. Regular surveillance and metagenomic analysis were employed to explore the diversity of avian coronaviruses at Hong Kong's Mai Po Wetland. We tested a total of 3239 samples collected from 2018 to 2024, among which the prevalence rate of viruses of the genus Gammacoronavirus (64.4%) was higher than that of Deltacoronavirus (35.6%). The host species were identified for 79.8% of the coronavirus-positive samples. Two deltacoronaviruses with full-genome sequences and one nearly complete gammacoronavirus genome were identified in faecal samples of three bird species. We also predicted putative transcriptional regulatory sequences and 3CLpro and PLpro cleavage sites for these viruses. Results from our phylogenetic analysis and pairwise amino acid identity comparisons, using the International Committee on Taxonomy of Viruses classification criteria based on the DEmARC framework, indicate that black-faced spoonbill coronavirus (BSCoV, strain MP22-1474) prototypes a new subgenus. Great cormorant coronavirus (GCCoV, strain MP18-1070) and falcated duck coronavirus (FDCoV, strain MP22-196) belong to two previously known species while diverging most profoundly from known viruses of these species. Two recombination events may have contributed to the evolution of FDCoV MP22-196 in genome regions from ORF1b to the S gene and from the M gene to the N gene. The cophylogenetic analysis between avian hosts and coronaviruses provides evidence for a strong linkage between viruses of the genus Gammacoronavirus and the birds of order Anseriformes. This study highlights the importance of ongoing surveillance for coronaviruses in wild migratory birds.

Ticks are obligate hematophagous arthropods that can transmit pathogens and are important vectors of diseases affecting wild and domestic animals, as well as humans, thus representing a serious risk to public health. Despite the growing concern about arboviruses, our understanding of tick-borne viruses remains limited compared to those transmitted by mosquitoes. We performed metagenomic analysis, focusing on the virome of ticks collected from wild animals in the countryside of the state of São Paulo, Brazil. The experimental analysis highlighted important molecular evidence of a potential new virus from the Jingmenvirus group in ticks collected from wild animals. The four pools that were positive included Amblyomma sculptum and A. nodosum ticks, collected from Myrmecophaga tridactyla, Callithrix penicillata, and Cerdocyon thous. These data suggest that it is a new member of the Jingmenvirus group, which we propose to be named Rio Preto tick virus (RPTV). In addition, the RPTV genome was analysed in silico, and proteins with high homology to those of the Jingmenvirus group were identified. Here, we report the identification of a potentially novel virus found in ticks from wild animals in southeastern Brazil. This study contributes to the epidemiological surveillance of the region and helps to understand the potential risks of the emergence of zoonoses, which can impact human health, in addition to the potential impacts on the fauna.

The evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has profoundly influenced the trajectory of the COVID-19 pandemic. In late 2020, the Alpha variant (Pango lineage B.1.1.7) emerged in South East England, characterized by enhanced transmissibility, increased mortality, and rapid geographic expansion. Here, we studied the evolutionary history and migration dynamics of Alpha across Europe using genomic data sourced from 38 European countries. Our findings reveal that Alpha was introduced to over 25 European countries within 90 days of its emergence, with the UK accounting for 61% of early exportation events. However, as the epidemic progressed, several mainland European countries, including France, Denmark, and the Czech Republic, became significant hubs of onward transmission. Social mixing during the December holiday period and air travel facilitated the variant's rapid dissemination, as corroborated by air passenger flight volumes and viral introductions. Notably, genomic surveillance intensified after Alpha was designated a variant of concern, reducing the detection lag in countries with later introductions. Our study highlights the critical interplay between international mobility, surveillance efforts, and regional connectivity in shaping the epidemiology of SARS-CoV-2 variants and underscores the need for coordinated genomic surveillance and timely interventions to mitigate the spread of emerging pathogens.

[This corrects the article DOI: 10.1093/ve/veae107.].

In rare individuals with a severely immunocompromised system, chronic infections of SARS-CoV-2 may develop, where the virus replicates in the body for months. Sequencing of some chronic infections has uncovered dramatic adaptive evolution and fixation of mutations reminiscent of lineage-defining mutations of variants of concern (VOCs). This has led to the prevailing hypothesis that VOCs emerged from chronic infections. To examine the mutation dynamics and intra-host genomic diversity of SARS-CoV-2 during chronic infections, we focused on a cohort of nine immunocompromised individuals with chronic infections and performed longitudinal sequencing of viral genomes. We showed that sequencing errors may cause erroneous inference of genetic variation, and to overcome this, we used duplicate sequencing across patients and time points, allowing us to distinguish errors from low-frequency mutations. We further found recurrent low-frequency mutations that we flagged as most likely sequencing errors. This stringent approach allowed us to reliably infer low-frequency mutations and their dynamics across time. We applied a generalized linear model that accounts for gradual mutation accumulation and episodic divergence shifts to infer a synonymous mutation rate of 1.9 × 10^-6 mutations/site/day. Using the same framework, we inferred patient-specific non-synonymous divergence rates that exhibited marked heterogeneity across individuals. This framework also uncovered episodes of high non-synonymous rates consistent with selective sweeps or subpopulation replacement. Overall, we observed diverse evolutionary dynamics across chronic infections, highlighting variation in patient-specific selection pressures and within-host demographic histories that shape intra-host viral evolution.

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the COVID-19 pandemic, has produced unprecedented numbers of structures of the Spike protein. In this study, we present a comprehensive analysis of 1560 published structures, covering most major variants that emerged throughout the pandemic, diverse heteromerization, and interacting complexes. Using interaction-energy-informed geometric clustering, we identify 14 structurally distinct epitopes based on their conformational specificity, shared interface with angiotensin-converting enzyme 2 (ACE2), and glycosylation patterns. Our per-residue interaction evaluations accurately predict antibody recognition sites and correlate strongly with deep mutational scanning data, enabling immune escape predictions for future variants. To complement this structural analysis, we integrate longitudinal genomic data from nearly 3 million viral sequences, linking mutational patterns to changes in Spike's conformational dynamics. Our findings reveal two distinct evolutionary trade-offs driving immune escape. First, we confirm an enthalpic trade-off, where mutations in the receptor-binding motif (RBM) enhance immune escape at the cost of weakened ACE2 binding. Second, we introduce an entropic trade-off, showing that mutations outside the RBM modulate Spike's conformational equilibrium, reducing open-state occupancy to evade immune detection-without directly altering the ACE2-binding interface. With these analyses, this work not only highlights the different functional effects of mutations across SARS-CoV-2 Spike variants but also reveals the complex interplay of evolutionary forces shaping the evolution of the SARS-CoV-2 Spike protein over the course of the pandemic.

Identifying traits that make a host a good reservoir for virus emergence is central to understanding virus ecology, host range evolution and mitigating virus epidemics, but is often hindered by a lack of knowledge on the infection dynamics of the virus in the reservoir population. Here we analyse traits that determine the reservoir potential of the wild plant Nicotiana glauca for tobacco mild green mosaic virus (TMGMV), an important pathogen of pepper (Capsicum annuum) crops, using epidemiological, experimental and population genetic approaches. We show that TMGMV is maintained at high prevalence in N. glauca populations that share the space with pepper crops in South eastern Spain. High prevalence may be explained by low virulence associated with TMGMV behaving as a conditional mutualist, which is in part explained by increased survival of infected plants under drought conditions. We also show maintenance in N. glauca populations of TMGMV genotypes that have a within-host fitness advantage in pepper and a disadvantage in N. glauca. This is explained by pleiotropic effects of host range mutations that result in higher vertical transmission through the seeds of N. glauca of isolates adapted to pepper. Last, high migration from N. glauca prevents fixation of pepper-adapted genotypes in pepper populations. Our results underscore the need to analyse the effects of infection on a range of host life-history traits, and effects of host range mutations on different components of virus fitness, to understand dynamics of infection and virus host range evolution.

Cancer-inducing viruses (oncogenic viruses) are linked to over 10% of cancer cases. Although the molecular details of viral oncogenesis are well-documented, the evolutionary mechanisms by which viruses have acquired oncogenic properties remain poorly understood. Here, we investigate the evolutionary conditions affecting viral oncogenicity across both within- and between-host scales using mathematical models of oncovirus-immune system interactions, conceptualized as an extended shared enemy-victim relationship. We begin by examining how oncogenic traits impact within-host viral dynamics, focusing on the transformation rate of infected cells into pre-cancerous states and the pre-cancerous cell proliferation rate. In various scenarios reflecting different within-host conditions, we then identify the transformation and proliferation rates that maximize within- and between-host viral fitness. We find that the transformation rate maximizing the viral load depends on the viral production rate, immunogenicity, and the immune-mediated elimination rate of pre-cancerous cells. We also identify conditions under which an intermediate proliferation rate minimizes within- and between-host viral fitness: in that scenario, a lower or higher proliferation rate leads to a higher viral load, providing a possible explanation for the diversity of oncogenic viruses. The analyses presented here provide insights into the evolutionary drivers affecting viral oncogenicity and highlight the complexity of oncogenic virus-immune system interactions.

Shrews are primary hosts for mammalian hantaviruses and are thus considered to be important reservoirs for viruses, similar to rodents and bats. To explore the diversity of hantaviruses in Swedish common shrews (Sorex araneus), we investigated lung tissue from shrews collected between 2015 and 2017. The collection took place at three separate locations in south-central Sweden. Screening for hantaviruses was performed using two different approaches. (i) A total of 113 common shrews were investigated for hantaviruses by a pan-hantavirus L-gene reverse transcriptase PCR, and Sanger sequencing was performed on the 13 positive samples. (ii) In addition, 88 RNA samples were pooled into eight libraries subjected to RNA sequencing. The RNA sequencing data analysis, which focused specifically on identifying hantaviruses, revealed two divergent hantaviruses: the complete genome of an Altai virus (ALTV) and the partial genome of the Seewis virus. Evolutionary analysis revealed that Swedish ALTVs are closely related to Russian ALTVs but distinct from Finnish strains. On the contrary, the Swedish Seewis virus shares closer ancestry with Finnish Seewis virus strains. Given that these viruses were identified in several pools, Seewis virus and ALTV are likely circulating in Swedish common shrews. Supported by earlier studies, common shrews are probably a natural host for at least these two distinct hantaviruses.

Epidemics are often initiated by emerging and re-emerging infectious diseases caused by viruses of animal origin. It is thus important to identify the reservoirs of potentially zoonotic viruses and understand the dynamics of their host shifts. The flu viruses belong to the virus family Orthomyxoviridae, which also contains Isavirus, Quaranjavirus, and Thogotovirus. Many members of this virus family are known to be pathogenic to humans. For initial surveillance of animal-originated or zoonotic Orthomyxoviridae, unclassified viruses were screened by the use of high-throughput transcriptomes as a data source because of their wide species and lineage coverage. We identified 96 novel or unclassified Orthomyxoviridae members with the discovery of three new lineages of the virus, possibly new genera, one sister to Influenza + Thogotovirus, one to Influenza + Thogotovirus + Quaranjavirus, and another one to all orthomyxoviruses except Isavirus. Throughout the evolution of Orthomyxoviridae, there might be multiple host-shifting incidences, shifting between six different animal host phyla. The most common host shifts seemed to be between Arthropoda and Chordata; however, further evidence would be needed to fully support this statement. Nonetheless, Orthomyxoviridae viruses can infect a wide range of animal phyla, while some members hold a higher risk of shifting back to Chordates and humans that warrants surveillance.