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Little is known about the insect viruses in wheat sawfly, Dolerus tritici , which is an important agricultural insect feeding on wheat leaves. Here, we used RNA sequencing to identify a novel single positive-strand RNA virus from the larvae of wheat sawfly collected in northern China and then determined its complete genome sequence by rapid amplification of cDNA ends. The complete genome is 9,594 nt in length, including a polyA tail at its 3′ terminus, and it is predicted to encode a 326.3-kDa polyprotein. Phylogenetic analysis based on deduced amino acid sequences of the polyprotein revealed that this RNA virus clustered in a clade with deformed wing virus of the genus Iflavirus , family Iflaviridae. The full genome of this RNA virus shows 42.0–50.0% sequence identity with other iflaviruses. Comparisons of amino acid sequences showed that the coat protein of this RNA virus is most similar to that of slow bee paralysis virus, with 33.6% identity, suggesting that this virus is a new member in the genus Iflavirus . Thus, we have tentatively designated it as “Dolerus tritici iflavirus 1” (DtIV1). To our knowledge, this is the first report of an insect virus in wheat sawfly.

In this study, a novel virus isolated from Nigrospora oryzae, tentatively named \"Nigrospora oryzae mycovirus 1\" (NoMyV1), was identified. NoMyV1 has a non-segmented dsRNA genome that is 2891 bp in length and contains two non-overlapping open reading frames (ORF1 and 2). ORF1 encodes a protein with sequence similarity to the putative capsid proteins or hypothetical proteins of other unclassified viruses, while ORF2 encodes an RNA-dependent RNA polymerase (RdRp). Sequence comparisons showed that NoMyV1 was most similar to Penicillium janczewskii Beauveria bassiana-like virus 1 (PjBblV1), with 76.12% amino acid sequence identity in the RdRp. In a phylogenetic analysis based on RdRp sequences, NoMyV1 was found to cluster with several other unclassified viruses for which a new genus, \"Unirnavirus\", which is distinct from the family Partitiviridae, has been proposed. Thus, we conclude that NoMyV1 is a novel member of the proposed genus \"Unirnavirus\".

Conidiobolus sensu lato, a genus within the family Ancylistaceae, encompasses a diverse range of fungal species that are widely distributed in plant debris and soil. In this study, we identified three double-stranded RNA (dsRNA) viruses coinfecting a strain of Conidiobolus taihushanensis. These viruses were identified as Conidiobolus taihushanensis totivirus 1 (CtTV1), Conidiobolus nonsegmented RNA virus 1–2 (CNRV1-2), and Conidiobolus taihushanensis virus 1 (CtV1). Through high-throughput sequencing and RNA-ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we determined their complete genome sequences. The genome of CtTV1 is 6,921 nucleotides in length, containing two open reading frames (ORFs). ORF1 encodes a 1,124-amino-acid capsid protein (CP) with a molecular weight of 125.07 kDa, and ORF2 encodes a 780-amino-acid RNA-dependent RNA polymerase (RdRp) with a molecular weight of 88.05 kDa. CNRV1-2, approximately 3.0 kb in length, also contains two ORFs, which are predicted to encode a 186-amino-acid hypothetical protein (HP) and a 758-amino-acid RdRp. CtV1 has a smaller genome consisting of 3,081 base pairs (bp) with two ORFs: one encoding a 244-amino-acid HP (26.85 kDa) and the other encoding a 707-amino-acid RdRp (80.64 kDa). Phylogenetic analysis based on RdRp sequences revealed that CtTV1 shows the highest similarity to Phytophthora pluvialis RNA virus 1, with 38.79% sequence identity, and clusters with members of the family Orthototiviridae, and it is most closely related to Utsjoki toti-like virus. In contrast, CtV1 formed a unique branch and might represent a new genus. The genome sequence of CNRV1-2 is 99.74% identical to that of the previously described Conidiobolus non-segmented RNA virus 1 (CNRV1). Our findings indicate that CtTV1 and CtV1 are distinct novel viruses, while CNRV1-2 appears to be a variant of CNRV1. This study enhances our understanding of the genetic diversity and evolutionary relationships among mycoviruses associated with C. taihushanensis.

Here, we identified a new mycovirus infecting the phytopathogenic fungus Nigrospora oryzae, which we have designated \"Nigrospora oryzae partitivirus 2\" (NoPV2). The genome of NoPV2 consists of two dsRNA segments (dsRNA 1 and dsRNA 2), measuring 1771 and 1440 bp in length, respectively. dsRNA 1 and dsRNA 2 each contain a single open reading frame (ORF) that encodes the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP), respectively. A BLASTp search showed that the RdRp of NoPV2 had significant sequence similarity to the RdRps of other partitiviruses, including Nigrospora sphaerica partitivirus 1 (75.61% identity) and Magnaporthe oryzae partitivirus 1 (67.53% identity). Phylogenetic analysis revealed that NoPV2 is a new member of the genus Gammapartitivirus in the family Partitiviridae. This study provides important information for understanding the diversity of mycoviruses in N. oryzae.

Human blood-associated partitivirus (HuBPV) was first identified through metagenomic analysis of serum samples from two Peruvians, but its natural host remains unknown. Here, we report the detection of an HuBPV strain (HuBPV-Bm) in the phytopathogenic fungus Bipolaris maydis strain HN11 in Hubei Province, China. The dsRNA1 and dsRNA2 of HuBPV-Bm show more than 97.6% and 98.8% nucleotide sequence identity, respectively, to those from the metagenomically discovered HuBPV strain (HuBPV-M). Notably, HuBPV-Bm contains a third dsRNA segment that was not reported for HuBPV-M. All mycelia derived from individual asexual spores of HN11 tested positive for HuBPV-Bm, as did nine out of 293 B. maydis strains collected across Hubei.

A new double-stranded RNA (dsRNA) virus, tentatively named \"Valeriana jatamansi cryptic virus 1\" (VJCV1, GenBank accession nos. PP482519 and PP482520), was isolated from diseased Valeriana jatamansi Jones plants exhibiting vein-banding in Yunnan. Its complete genome sequence was determined using metatranscriptomic and Sanger sequencing. The genome of VJCV1 consists of two dsRNA of different size, namely dsRNA1 (2,026 bp) and dsRNA2 (1,754 bp), which are predicted to encode an RNA-dependent RNA polymerase (RdRp, 616 aa) with molecular weight of 72.6 kDa and coat protein (CP, 491 aa) with molecular weight of 55.8 kDa, respectively. The non-coding region of dsRNA in VJCV1 is predicted to have a stem-loop structure and a poly(A) tail that are unique to the members of the genus Alphapartitivirus . Multiple sequence alignments showed that the RdRp and CP of VJCV1 shared the highest amino acid sequence identity (86.2% and 56.1%, respectively) with red clover cryptic virus 1 (RCCV1). These values are below the threshold for creating new species within the genus Alphapartitivirus . Phylogenetic analysis based on RdRp and CP sequences showed that VJCV1 clustered independently from members of the genus Alphapartitivirus , with RCCV1 being the closest relative. It is therefore suggested that VJCV1 should be considered a member of a new species of the genus Alphapartitivirus in the family Partitiviridae . This is the first report of a member of the genus Alphapartitivirus infecting a plant of the genus Valeriana .

Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by a lack of efficient methods for searching this corpus, which (at the time of writing) exceeds 20 petabases and is growing exponentially 1 . Here we developed a cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at the petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) for the hallmark gene RNA-dependent RNA polymerase and identified well over 10 5 novel RNA viruses, thereby expanding the number of known species by roughly an order of magnitude. We characterized novel viruses related to coronaviruses, hepatitis delta virus and huge phages, respectively, and analysed their environmental reservoirs. To catalyse the ongoing revolution of viral discovery, we established a free and comprehensive database of these data and tools. Expanding the known sequence diversity of viruses can reveal the evolutionary origins of emerging pathogens and improve pathogen surveillance for the anticipation and mitigation of future pandemics. Serratus, an open-source cloud-computing infrastructure, can be used to screen millions of nucleic acid sequencing libraries at the petabase scale, and has enabled many new RNA viruses to be identified efficiently.

Our understanding of the diversity and evolution of vertebrate RNA viruses is largely limited to those found in mammalian and avian hosts and associated with overt disease. Here, using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated viruses in reptiles, amphibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts. We establish a long evolutionary history for most groups of vertebrate RNA virus, and support this by evaluating evolutionary timescales using dated orthologous endogenous virus elements. We also identify new vertebrate-specific RNA viruses and genome architectures, and re-evaluate the evolution of vector-borne RNA viruses. In summary, this study reveals diverse virus–host associations across the entire evolutionary history of the vertebrates. Around 200 new vertebrate-specific viruses are discovered, and every vertebrate-specific viral family known to infect mammals and birds is also present in amphibians, reptiles or fish, suggesting that evolution of vertebrate viruses mirrors that of vertebrate hosts.

Deformed wing virus (DWV) and its vector, the mite Varroa destructor, are a major threat to the world's honeybees. Although the impact of Varroa on colony-level DWV epidemiology is evident, we have little understanding of wider DWV epidemiology and the role that Varroa has played in its global spread. A phylogeographic analysis shows that DWV is globally distributed in honeybees, having recently spread from a common source, the European honeybee Apis mellifera. DWV exhibits epidemic growth and transmission that is predominantly mediated by European and North American honeybee populations and driven by trade and movement of honeybee colonies. DWV is now an important reemerging pathogen of honeybees, which are undergoing a worldwide manmade epidemic fueled by the direct transmission route that the Varroa mite provides.

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.