Virus Evolution最新文献

[This corrects the article DOI: 10.1093/ve/vead053.].

Understanding the dispersal patterns of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) lineages is crucial to public health decision-making, especially in countries with limited access to viral genomic sequencing. This study provides a comprehensive epidemiological and phylodynamic perspective on SARS-CoV-2 lineage dispersal in Iran from February 2020 to July 2022. We explored the genomic epidemiology of SARS-CoV-2 combining 1281 genome sequences with spatial data in a phylogeographic framework. Our analyses shed light on multiple international imports seeding subsequent waves and on domestic dispersal dynamics. Lineage B.4 was identified to have been circulating in Iran, 29 days (95% highest probability density interval: 21-47) before non-pharmaceutical interventions were implemented. The importation dynamics throughout subsequent waves were primarily driven from the country or region where the variant was first reported and gradually shifted to other regions. At the national level, Tehran was the main source of dissemination across the country. Our study highlights the crucial role of continuous genomic surveillance and international collaboration for future pandemic preparedness and efforts to control viral transmission.

Animal genomes are characterized by extensive variation in size. RNA viruses similarly exhibit substantial genomic diversity, with genome lengths ranging from 1.7 to ∼64 kb. Despite the myriad of novel viruses discovered by metagenomics, we know little of the factors that shape the evolution of the genome size in RNA viruses. We analyzed the variation in genome sizes across orders and families of animal RNA viruses. We found that RNA viruses can have highly variable genome sizes within and among orders, with the Nidovirales (including the Coronaviridae) exhibiting both significantly larger genomes and a greater range of genome sizes than other orders. In the Bunyavirales, Amarillovirales, Nidovirales, and Picornavirales, the genome sizes of invertebrate-associated RNA viruses were significantly larger than those that infect vertebrates, in contrast to their animal hosts in which vertebrates commonly have larger genomes than invertebrates. However, in the Mononegavirales, vertebrate viruses were significantly larger than those viruses associated with invertebrates. There were similarly complex associations between genome size and patterns of genome segmentation. In the Bunyavirales, Reovirales, and Nidovirales, viruses with segmented genomes, or that possessed a large number of segments, had significantly larger genome sizes than viruses with nonsegmented genomes or a small number of segments, while in Articulavirales, there were no significant differences in genome size among viruses possessing any number of genome segments. More broadly, our analysis revealed that taxonomic position (i.e. RNA virus order) had a greater impact on genome size than whether viruses infected vertebrates or invertebrates or their pattern of genome segmentation. Hence, the phylogenetic constraints on genome size are of sufficient magnitude to shape some other aspects of virus evolution.

Anelloviruses are a group of small, circular, single-stranded DNA viruses that are found ubiquitously across mammalian hosts. Here, we explored a large number of publicly available human microbiome datasets and retrieved a total of 829 anellovirus genomes, substantially expanding the known diversity of these viruses. The majority of new genomes fall within the three major human anellovirus genera: Alphatorquevirus, Betatorquevirus, and Gammatorquevirus, while we also present new genomes of the under-sampled Hetorquevirus, Memtorquevirus, and Samektorquevirus genera. We performed recombination analysis and show evidence of extensive recombination across all human anelloviruses. Interestingly, more than 95% of the detected events are between members of the same genus and only 15 inter-genus recombination events were detected. The breakpoints of recombination cluster in hotspots at the ends and outside of the ORF1 gene, while a recombination coldspot was detected within the gene. Our analysis suggests that anellovirus evolution is governed by homologous recombination; however, events between distant viruses or ones producing chimaeric ORF1s likely lead to nonviable recombinants. The large number of genomes further allowed us to examine how essential genomic features vary across anelloviruses. These include functional domains in the ORF1 protein and the nucleotide motif of the replication loop region, required for the viruses' rolling-circle replication. A subset of the genomes assembled in both this and previous studies are completely lacking these essential elements, opening up the possibility that anellovirus intracellular populations contain nonstandard viral genomes. However, low-read depth of the metagenomically assembled contigs may partly explain the lack of some features. Overall, our study highlights key features of anellovirus genomics and evolution, a largely understudied group of viruses whose potential in virus-based therapeutics is recently being explored.

Advancements in high-throughput sequencing and associated bioinformatics methods have significantly expanded the RNA virus repertoire, including novel viruses with highly divergent genomes encoding "orphan" proteins that apparently lack homologous sequences. This absence of homologs in routine sequence similarity search complicates their taxonomic classification and raises a fundamental question: Do these orphan viral genomes represent bona ide viruses? In 2022, an orphan viral genome encoding a large polyprotein was identified in alfalfa (Medicago sativa) and thrips (Frankliniella occidentalis), and named Snake River alfalfa virus (SRAV). SRAV was initially proposed as an uncommon flavi-like virus identified in a plant host distantly related to family Flaviviridae. Subsequently, another research group showed its common occurrence in alfalfa but challenged its taxonomic position, suggesting it belongs to the family Endornaviridae. In this study, a large-scale analysis of 77 publicly available small RNA datasets indicates that SRAV could be detected across various tissues and cultivars of alfalfa, and has a broad geographical distribution. Moreover, profiles of the SRAV-derived small interfering RNAs (vsiRNAs) exhibited typical characteristics of viruses in plant hosts. The evolutionary analysis suggests that SRAV represents a unique class of plant-hosted flavi-like viruses with an unusual genome organization and evolutionary status, distinct from previously identified flavi-like viruses documented to infect plants. The latter shows a close evolutionary relationship to flavi-like viruses primarily found in plant-feeding invertebrates and lacks evidence of triggering host RNA interference (RNAi) responses so far. Moreover, mining the transcriptome shotgun assembly (TSA) database identified two novel viral sequences with a similar genome organization and evolutionary status to SRAV. In summary, our study resolves the disagreement regarding the taxonomic status of SRAV and suggests the potential existence of two distinct clades of plant-hosted flavi-like viruses with independent evolutionary origins. Furthermore, our research provides the first evidence of plant-hosted flavi-like viruses triggering the host's RNAi antiviral response. The widespread occurrence of SRAV underscores its potential ecological significance in alfalfa, a crop of substantial economic importance.

Despite the increasing burden of dengue in Kenya and Africa, the introduction and expansion of the virus in the region remain poorly understood. The objective of this study is to examine the genetic diversity and evolutionary histories of dengue virus (DENV) serotypes 1 and 3 in Kenya and contextualize their circulation within circulation dynamics in the broader African region. Viral RNA was extracted from samples collected from a cohort of febrile patients recruited at clinical sites in Kenya from 2013 to 2022. Samples were tested by polymerase chain reaction (PCR) for DENV presence. Five DENV-positive samples were serotyped, and complete viral genomes for phylogenetic inference were obtained via sequencing on Illumina platforms. Sequences generated in our study were combined with global datasets of sequences, and Bayesian and maximum likelihood methods were used to infer phylogenetic trees and geographic patterns of spread with a focus on Kenya and Africa as a whole. Four new DENV-1 and one new DENV-3 genomes were successfully sequenced and combined with 328 DENV-1 and 395 DENV-3 genomes from elsewhere for phylogenetic analyses. The DENV-1 sequences from our study formed a monophyletic cluster with an inferred common ancestor in 2019 (most recent common ancestor 2019 and 95% high posterior density 2018-19), which was closely related to sequences from Tanzania. The single DENV-3 sequence clustered with sequences from Tanzania and Kenya, was collected between 2017 and 2019 and was related to recent outbreaks in the region. Phylogenetic trees resolved multiple clades of DENV-1 and DENV-3 concurrently circulating in Africa, introduced in the early-to mid-2000s. Three DENV-1 and four DENV-3 clades are highlighted, introduced between 2000 and 2015. Phylogeographic models suggest frequent, independent importations of DENV lineages into Kenya and Africa from East and South-East Asia via distinct geographic pathways. DENV-1 and DENV-3 evolutionary dynamics in Africa are characterized by the cocirculation of multiple recently introduced lineages. Circulating lineages are introduced via distinct geographic pathways that may be centered around regional nexus locations. Increased surveillance is required to identify key regional locations that drive spread, and dengue interventions should focus on interrupting spread at these locations.

Infectious disease transmission to different host species makes eradication very challenging and expands the diversity of evolutionary trajectories taken by the pathogen. Since the beginning of the ongoing COVID-19 pandemic, SARS-CoV-2 has been transmitted from humans to many different animal species, in which viral variants of concern could potentially evolve. Previously, using available whole genome consensus sequences of SARS-CoV-2 from four commonly sampled animals (mink, deer, cat, and dog), we inferred similar numbers of transmission events from humans to each animal species. Using a genome-wide association study, we identified 26 single nucleotide variants (SNVs) that tend to occur in deer-more than any other animal-suggesting a high rate of viral adaptation to deer. The reasons for this rapid adaptive evolution remain unclear, but within-host evolution-the ultimate source of the viral diversity that transmits globally-could provide clues. Here, we quantify intra-host SARS-CoV-2 genetic diversity across animal species and show that deer harbor more intra-host SNVs (iSNVs) than other animals, providing a larger pool of genetic diversity for natural selection to act upon. Mixed infections involving more than one viral lineage are unlikely to explain the higher diversity within deer. Rather, a combination of higher mutation rates, longer infections, and species-specific selective pressures are likely explanations. Combined with extensive deer-to-deer transmission, the high levels of within-deer viral diversity help explain the apparent rapid adaptation of SARS-CoV-2 to deer.

In North America, raccoon rabies virus (RRV) is a public health concern due to its potential for rapid spread, maintenance in wildlife, and impact on human and domesticated animal health. RRV is an endemic zoonotic pathogen throughout the eastern USA. In 1991, an outbreak of RRV in Fairfield County, Connecticut, spread through the state and eventually throughout the Northeast and into Canada. Factors that contribute to, or curb, RRV transmission should be explored and quantified to guide targeted rabies control efforts, including the size and location of buffer zones of vaccinated animals. However, population dynamics and potential underlying determinants of rabies virus diversity and circulation in Connecticut have not been fully studied. In this study, we aim to (i) investigate RRV source-sink dynamics between Connecticut and surrounding states and provinces, (ii) explore the impact of the Connecticut River as a natural barrier to transmission, and (iii) characterize the genomic diversity and transmission dynamics in Connecticut. Using RRV whole-genome sequences collected from various host species between 1990 and 2020, we performed comparative genetic and Bayesian phylodynamic analyses at multiple spatial scales. We analyzed 71 whole-genome sequences from Connecticut, including 21 recent RRV specimens collected at the Connecticut Veterinary Medical Diagnostic Laboratory that we sequenced for this study. Our analyses revealed evidence of RRV incursions over the US-Canada border, including bidirectional spread between Quebec and Vermont. Additionally, we highlighted the importance of Connecticut and New York in seeding RRV transmission in eastern North America, including two introduction events from New York to Connecticut that resulted in sustained local transmission. While RRV transmission does occur across the Housatonic and Connecticut Rivers, we demonstrated the distinct presence of spatial structuring in the phylogenetic trees and characterized the directionality of RRV migration. The significantly higher mean transition rates from locations east to west of the Connecticut River, compared to west to east, may be leveraged in directing interventions to fortify these natural barriers. Ultimately, the findings of these international, regional, and state analyses can inform targeted control programs, vaccination efforts, and enhanced surveillance at borders of key viral sources and sinks.

Reverse-transcribing viruses (RTVs) characterized by reverse transcription required for their replication infect nearly all the eukaryotes. After decades of extensive analyses and discoveries, the understanding of the diversity of RTVs has largely stagnated. Herein, we discover a previously neglected lineage of RTVs, designated Kuafuorterviruses, in animals. Through screening over 8000 eukaryote genomes, we identify the presence of endogenous Kuafuorterviruses in the genomes of 169 eumetazoans dispersed across 11 animal phyla. Phylogenetic analyses and sequence similarity networks indicate that Kuafuorterviruses constitute a novel major lineage of RTVs. The discovery of Kuafuorterviruses refines our understanding of the diversity, evolution, and classification of RTVs and has implications in annotating animal genomes.