Virus Evolution最新文献

N-linked glycosylation of flavivirus envelope proteins is widely viewed as being required for optimal folding, processing and/or transit of envelope proteins, and the assembling virons, through the endoplasmic reticulum (ER) and the Golgi. Zika virus (ZIKV) has a single N-linked envelope glycan located adjacent to the fusion loop. Herein we show that independent serial passage of ZIKV_Natal in Rag1 ^-/- mice for 223 or 386 days generated two unique envelope glycan-deficient mutants, ZIKV-V153D and ZIKV-N154D, respectively. Surprisingly, these mutants grew to titres ∼1 to 2.6 logs higher than the glycosylated parental ZIKV_Natal in Vero E6 cells and human brain organoids. RNA-Seq of infected organoids suggested that this increased replication fitness was associated with upregulation of the unfolded protein response (UPR). Cell death, cellular viral RNA, and viral protein levels were not significantly affected, arguing that these glycan mutants enjoyed faster ER/Golgi folding, processing, assembly, transit, and virion egress, assisted by an upregulated UPR. Thus, ZIKV envelope N-linked glycosylation is not essential for promoting envelope folding, assembly, and transit through the ER/Golgi, since aspartic acid (D) substitutions in the glycosylation motif can achieve this with significantly greater efficiency. Instead, the evolution of glycan mutants in Rag1 ^-/- mice indicates that such envelope glycosylation can have a fitness cost in an environment devoid of virus-specific antibody responses. The V153D and N154D mutations, generated by natural selection in Rag1 ^-/- mice, have to date not been employed in orthoflavivirus envelope glycosylation studies. Instead, genetic engineering has been used to generate mutant viruses that, for instance, contain a N154A substitution. The latter may impart confounding unfavourable properties, such as envelope protein insolubility, that have a detrimental impact on virus replication. The V153D and N154D substitutions may avoid imparting unfavourable properties by preserving the surface negative charge provided by the glycan moiety in the parental ZIKV_Natal envelope protein. In Ifnar1 ^-/- mice ZIKV-V153D and -N154D showed faster viremia onsets, but reduced viremic periods, than the parental ZIKV_Natal, consistent with an established contention that such glycans have evolved to delay neutralizing antibody activity.

Jingmenviruses are a distinct group of flavi-like viruses characterized by a genome consisting of four to five segments. Here, we report the discovery of three novel putative jingmenviruses, identified by mining publicly available metagenomics data from mosquito and arachnid samples. Strikingly, these novel jingmenvirus sequences contain up to six genomic segments, with pairs of homologous segments coding for putative structural proteins. Following this discovery, we found an additional homologous segment for two other jingmenvirus genomes, which had gone unnoticed in the initial publications. The presence of a single version of the segments coding for non-structural proteins suggests that we have indeed identified jingmenviruses with infectious units that contain up to six segments. We compared these novel jingmenvirus sequences to published sequences, in particular the segments with multiple open reading frames (ORFs), and we propose that the putative translation initiation mechanisms involved for these segments are ribosomal frameshift resulting in the fusion of ORFs and leaky scanning for overlapping ORFs. These putative mechanisms, conserved for all jingmenvirus sequences analysed, including in homologous segments, require biological confirmation. We also generated structural models of two putative structural proteins in the duplicated segments, and the corresponding alignments enabled us to confirm or identify the homologous relationship between sequences that shared limited nucleotide or amino acid identity. Altogether, these results highlight the fluid nature of jingmenviruses, which is a hallmark of multipartite viruses. Different combinations of segments packaged in different virus particles could facilitate the acquisition or loss of genomic segments and a segment duplication following genomic drift. Our data therefore contribute to the evidence of the multipartite nature of jingmenviruses and the evolutionary role this organization may play.

Mammalian hepadnaviruses have likely been evolving alongside their hosts for millions of years. Domestic cat HBV (DCHBV) has been detected in cats from several countries, but its genealogy, epidemiology, and host range remain unclear. Besides DCHBV, the only hepadnavirus identified among carnivores is the ringtail HBV (RtHBV). Because there is a gap in the felid fossil record of approximately 5-7 million years between the late Oligocene and the early Miocene, carnivore-derived viruses might help to shed light on Felidae evolution. Here, we screened 2260 sera and 154 paraffin-embedded liver samples from cats and 2123 sera from dogs sampled in Europe and South and Central America between 2018 and 2020 by PCR for DCHBV. We identified DCHBV genotype A (GtA) in 0.6% (7/1,195; 95% CI, 0.2-1.2) of cats sampled in Germany, France, Croatia, and Bulgaria and a genetically divergent DCHBV genotype B (GtB; 10.8% genomic sequence distance) in 0.2% of cats (2/1,065; 95% CI, 0.0-0.7) from Brazil. The detection rates of the two genotypes did not differ significantly (Fisher, P = .19). Viral loads ranged from 4 × 10¹-6 × 10⁶ for DCHBV GtA to 5-7 × 10³ for DCHBV GtB DNA copies per milliliter of serum. None of the cat livers or dog sera tested positive by PCR. Immunoglobulin G against the DCHBV core antigen (anti-DCHBc) was detected in 8/504 cat sera (1.6%; 95% CI, 0.7-3.1), without significant variation between countries (χ², P = .17), and in none of 180 dog sera by indirect immunofluorescence assay (IFA). Neither IFA (Fisher, P = .11; n = 311) nor PCR (Fisher, P = .63; n = 699) positivity was significantly associated with increased liver enzymes in cats, respectively. Coevolutionary reconciliations of virus and host phylogenies and Bayesian hypothesis testing suggested evolutionary origins of DCHBV during the Miocene, ∼8-17 million years ago (mya) from ancestral carnivores, consistent with long-term evolution. The long-term association of DCHBV with felines aids in elucidating orthohepadnaviral infection patterns and felid genealogy.

Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy-hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies have failed to detect Onchocerca volvulus in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A viral particle-based shotgun sequencing approach was used to detect viral sequences in 55 pools of 10 blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the haematophagous blackfly, which also could be present in their nematode host O. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.

Phytophthora cinnamomi stands out as one of the most devastating plant pathogens worldwide, rapidly expanding its range and impacting a wide range of host species. In this study, we investigated the virome of P. cinnamomi across 222 isolates from Africa, Asia, Europe, Oceania, and the Americas using stranded total RNA sequencing, reverse transcription polymerase chain reaction screening, and Sanger sequencing of selected isolates. Our analysis revealed that virus infections were prevalent across all sampled populations, including RNA viruses associated with the orders Ghabrivirales, Martellivirales, and Tolivirales, and the classes Amabiliviricetes, Bunyaviricetes, and the recently proposed Orpoviricetes. Viruses were mainly found in East and Southeast Asian populations, within the geographic origin of P. cinnamomi but have also spread to new regions where the pathogen has emerged as a clonal destructive pathogen. Among the identified viruses, eight species, including two bunya-like viruses, one narna-like virus, and five ormycoviruses, exhibit a global distribution with some genetic divergence between continents. The interaction between P. cinnamomi and its virome indicates a dynamic coevolution across diverse geographic regions. Indonesia is indicated to be the viral epicentre of P. cinnamomi, with the highest intra- and interspecies diversity of viruses. Viral diversity is significantly enhanced in regions where sexual recombination of P. cinnamomi occurs, while regions with predominantly asexual reproduction harbour fewer viral species. Interestingly, only the partially self-fertile mating type (MAT) A2, associated with the global pandemic, facilitates the spread of viruses across different biogeographic regions, whereas viruses are absent in the self-sterile MAT A1 in its areas of introduction like Australia and South Africa. Intriguingly, the presence of a plant tombusvirus suggests a potential cross-kingdom infection among Chilean isolates and a plant host. This study sheds further light on the geographical origin of P. cinnamomi from a novel virome perspective.

Since its first academic record in 1978, dengue epidemics have occurred in all provinces of China, except Xizang. The epidemiological and molecular features of the whole genome of dengue virus (DENV) have not yet been completely elucidated, interfering with prevention and control strategies for dengue fever in China. Here, we obtained 553 complete genomes of the four serotypes of DENV (DENV1-4) isolated in China from the GenBank database to analyze the phylogeny, recombination, genomic variants, and selection pressure and to estimate the substitution rates of DENV genomes. Phylogenetic analyses indicated that DENV sequences from China did not cluster together and were genetically closer to those from Southeast Asian countries in the maximum likelihood trees, indicating that DENV was not endemic in China. Thirty intra-serotype recombinant sequences were identified for DENV1-4, with the highest frequency in DENV4. Selection pressure analyses revealed that 13 codons under positive selection were located in the C, NS1, NS2A, NS3, and NS5 proteins. For DENV1 to DENV3, the substitution rates evaluated in this study were 9.23 × 10^-4, 7.59 × 10^-4, and 7.06 × 10^-4 substitutions per site per year, respectively. These findings improve our understanding of the evolution of DENV in China.

Mutations within the N-terminal domain (NTD) of the spike (S) protein are critical for the emergence of successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral lineages. The NTD has been repeatedly impacted by deletions, often exhibiting complex and dynamic patterns, such as the recurrent emergence and disappearance of deletions in dominant variants. This study investigates the influence of repair of NTD lineage-defining deletions found in the BA.1 lineage (Omicron variant) on viral success. We performed comparative genomic analyses of >10 million SARS-CoV-2 genomes from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCov database to evaluate the detection of viruses lacking S:ΔH69/V70, S:ΔV143/Y145, or both. These findings were contrasted against a screening of publicly available raw sequencing data, revealing substantial discrepancies between data repositories, suggesting that spurious deletion repair observations in GISAID may result from systematic artifacts. Specifically, deletion repair events were approximately an order of magnitude less frequent in the read-run survey. Our results suggest that deletion repair events are rare, isolated events with limited direct influence on SARS-CoV-2 evolution or transmission. Nevertheless, such events could facilitate the emergence of fitness-enhancing mutations. To explore potential drivers of NTD deletion repair patterns, we characterized the viral phenotype of such markers in a surrogate in vitro system. Repair of the S:ΔH69/V70 deletion reduced viral infectivity, while simultaneous repair with S:ΔV143/Y145 led to lower fusogenicity. In contrast, individual S:ΔV143/Y145 repair enhanced both fusogenicity and susceptibility to neutralization by sera from vaccinated individuals. This work underscores the complex genotype-phenotype landscape of the spike NTD in SARS-CoV-2, which impacts viral biology, transmission efficiency, and immune escape potential, offering insights with direct relevance to public health, viral surveillance, and the adaptive mechanisms driving emerging variants.

Transmission of influenza A viruses (IAVs) between pigs and humans can trigger pandemics but more often cease as isolated infections without further spread in the new host species population. In Denmark, a major pig-producing country, the first two detections of human infections with swine-like IAVs were reported in 2021. These zoonotic IAVs were reassortants of the H1N1 pandemic 2009 lineage ("H1N1pdm09," H1 lineage 1A, clade 1A.3.3.2) introduced to swine farms in Denmark through humans approximately 11 years prior. However, predicting the likelihood and outcome of such IAV spillovers is challenging without a better understanding of the viral determinants. This study traced the evolution of H1N1pdm09 from 207 sequenced genomes as the virus propagated across Danish swine farms over a decade. H1N1pdm09 diverged into several genetically distinct viral populations, largely prompted by reassortments with neuraminidase (NA) segments from other enzootic IAV lineages. The genomic segments encoding the viral envelope glycoproteins, hemagglutinin (HA) and NA, evolved at the fastest rates, while the M and NS genomic segments were among the lowest evolutionary rates. The two zoonotic IAVs emerged from separate viral populations and shared the highest number of amino acid mutations in the PB2 and HA proteins. Acquisition of additional predicted glycosylation sites on the HA proteins of the zoonotic IAVs may have facilitated infection of the human patients. Ultimately, the analysis provides a foundation from which to further explore viral genetic indicators of host adaptation and zoonotic risk.

Over the past century, Influenza A virus (IAV) has caused four of the five reported pandemics, all of which originated from viruses possessing genome segments of avian origin. The recent spread of highly pathogenic avian influenza (HPAI) viruses, particularly the clade 2.3.4.4b A(H5N1) subtype, has led to an alarming increase in mammalian infections, raising concerns about the potential for future pandemics. In response to this, we developed FluMut, an open-source, cross-platform tool designed to identify molecular markers with potential impacts on H5N1 virus phenotypes. FluMut leverages an up-to-date database, FluMutDB, to rapidly analyze thousands of nucleotide sequences, identifying mutations associated with host adaptation, increased virulence, and antiviral resistance. The tool is available both as a command-line interface and a user-friendly graphical interface, making it accessible to researchers with varying levels of computational expertise. FluMut provides comprehensive outputs, including tables of detected markers, their biological effects, and corresponding literature references. This tool fills a critical gap in the genomic surveillance of HPAI H5N1, facilitating real-time monitoring of viral evolution and aiding in the identification of mutations that may signal increased pandemic potential. Future updates will extend FluMut's capabilities to other influenza subtypes.

Endogenous viral elements (EVEs) have been found in diverse eukaryotic genomes. These elements are particularly frequent in the genomes of brown algae (Phaeophyceae) because these seaweeds are infected by viruses (Phaeovirus) of the phylum Nucleocytoviricota (NCV) that are capable of inserting into their host's genome as part of their infective cycle. A search for inserted viral sequences in the genome of the freshwater brown alga Porterinema fluviatile identified seven large EVEs, including four complete or near-complete proviruses. The EVEs, which all appear to have been derived from independent insertion events, correspond to phylogenetically diverse members of the Phaeovirus genus and include members of both the A and B subgroups of this genus. This latter observation is surprising because the two subgroups were thought to have different evolutionary strategies and were therefore not expected to be found in the same host. The EVEs contain a number of novel genes including a H4 histone-like sequence but only one of the EVEs possesses a full set of NCV core genes, indicating that the other six probably correspond to nonfunctional, degenerated viral genomes. The majority of the genes within the EVEs were transcriptionally silent and most of the small number of genes that showed some transcriptional activity were of unknown function. However, the existence of some transcriptionally active genes and several genes containing introns in some EVEs suggests that these elements may be undergoing some degree of endogenization within the host genome over time.