Archives of Virology最新文献

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.

Hepacivirus is a genus of RNA viruses within the family Flaviviridae of which hepatitis C virus (HCV) is the prototype. Several hepaciviruses have been identified in mammals, including rodents of multiple families. Each rodent hepacivirus described so far has been found only in members of a single rodent species. Here, we report the discovery and characterization of a putative new genotype of an unclassified rodent hepacivirus in a wild cavy (Cavia aperea aperea) that was reported previously in Proechimys semispinosus. This virus was detected in one out of 14 (7.14%) wild cavy sera tested by RT-PCR. The complete genome sequence was obtained by high-throughput sequencing using an Illumina MiSeq platform. This is the first report of a hepacivirus in a member of the family Caviidae. Our findings show that members of different rodent species and even families can be infected by hepaciviruses of the same species. The identification and characterization of novel hepaciviruses might lead to the discovery of reservoirs of viruses that are genetically related to human pathogens, and this can help to elucidate the evolutionary origins of HCV and other hepaciviruses.

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 virus was found in Sauropus androgynus plants with curled and yellow leaves in China and tentatively named "Sauropus androgynus virus" (SaV). The complete genome of SaV is an 8007-nucleotide-long (+)RNA, excluding the 3’-poly(A) tail, and contains five open reading frames. Both pairwise comparisons and phylogenetic analysis of the putative replicase and coat proteins showed that SaV has a high level of sequence similarity to members of the genus Allexivirus of the family Alphaflexiviridae. This is the first report of an allexivirus in Sauropus androgynus.

The families Naryaviridae (order Rivendellvirales), Nenyaviridae (order Rohanvirales), and Vilyaviridae (order Cirlivirales), all within the class Arfiviricetes of the phylum Cressdnaviricota, include single-stranded DNA viruses associated with protozoan parasites of the genera Entamoeba and Giardia as well as viruses found in various environmental samples, also likely infecting protozoans. Here, we provide a taxonomic update for these three families, which were recently expanded with multiple new members. In particular, we established seven new genera and nine new species in the family Naryaviridae, one new genus with one new species in the family Nenyaviridae, and three new genera and nine new species in the family Vilyaviridae. We also summarize the genomic properties and protein characteristics, including conserved motifs of the rolling-circle replication initiation proteins, of the viruses in the three families. Notably, the high GC content of vilyavirids (51–61%) and considerably lower GC content of naryavirids and nenyavirids (33–44%) appear to represent an adaptation to their hosts, Giardia and Entamoeba species, respectively.

Lumpy skin disease (LSD) has emerged as a threat to cattle production in Asia, and India has been facing LSD epidemics since 2019. Although water buffalo (Bubalus bubalis) is susceptible to natural LSDV infection, there have been no confirmed reports of LSDV infection in water buffalo in India. In this study, we investigated suspected cases of LSD in water buffaloes from 12 Indian states and one union territory during 2020–2023. Buffaloes showed mild to moderate clinical disease with fever and nodular skin lesions, but most remained asymptomatic. Eighteen of 177 (10.18%) buffaloes in 12 districts in three states tested positive for LSDV by real-time PCR, while 22 of 57 (38.59%) from nine districts in six states tested positive for LSDV-neutralizing antibodies, demonstrating the prevalence of LSDV infection in buffaloes over a wider geographic area. Successful virus isolation and nucleotide sequencing confirmed natural LSDV infection in buffaloes. Phylogenetic analysis of complete GPCR, RPO30, and EEV gene sequences revealed the presence of wild-type strains of two divergent LSDV lineages (1.2.1 and 1.2.2) in buffaloes. The 1.2.2 strains were closely related to the dominant LSDV strain (subcluster 1.2.2, KSGP-like) circulating in India, while the 1.2.1 strains clustered with strains from the Middle East, Europe, and the Balkans, confirming that there have been multiple introductions of LSDV into India. The detection of viruses with identical sequences in buffaloes and local cattle implied that the LSDV strain found in buffaloes is probably of cattle origin. We also found evidence of cocirculation of LSDV 1.2.1 and 1.2.2 wild-type strains in the same area, highlighting the importance of LSDV surveillance and genetic analysis. This is the first confirmed report of natural LSDV infection in water buffaloes in India. Further investigations are needed to assess the impact of LSDV infection in buffalo production and the role of buffalo in LSD epidemiology.

Here, we report the complete genome sequence of Jasminum polyanthum nepovirus 1 (JPV1), a novel virus associated with foliar ringspot symptoms in Jasminum polyanthum (Oleaceae). The genome of JPV1 consists of RNA1 and RNA2, both of which are monocistronic and are 7081 nt and 4212 nt in length, respectively. RNA1 encodes six functional proteins, including the X1 protein, X2 protein, NTP-binding protein (NTB), VPg protein, protease cofactor (Pro), and RNA-dependent RNA polymerase (RdRp), while RNA2 encodes three functional proteins: the 2A protein, movement protein (MP), and capsid protein (CP). Pairwise sequence comparisons showed that the JPV1 protease-polymerase (Pro-Pol) and CP proteins each shared less than 40% aa sequence identity with those of other nepoviruses. Phylogenetic analysis indicated that JPV1 is a putative member of the genus Nepovirus. Based on these results, we propose that JPV1 is a member of subgroup B of the genus Nepovirus.

A new badnavirus was discovered in nettle plants (Urtica dioica L., family Urticaceae) with vein banding symptoms using high-throughput sequencing. This virus was provisionally named "nettle badnavirus 1" (NBV 1). The complete NBV 1 genome consists of 7598 bp and contains three overlapping open reading frames. NBV 1 found to be was most closely related to green Sichuan pepper vein clearing-associated badnavirus, sharing 73.9% nucleotide sequence identity in the whole genome. These two viruses showed 76.3% nucleotide sequence identity in the region of the genome encoding RT-RNase H. This is lower than the species demarcation cutoff (80%) for the genus Badnavirus of the family Caulimoviridae, suggesting that NBV 1 is a new member of this genus. Phylogenetic analysis based on full-length badnavirus genome sequences showed that NBV 1 belongs to the same clade as a badnavirus whose genome was found to be integrated into chromosome 6 of the nettle genome, sharing 78% identity. Using PCR, NBV 1 was detected in a symptomless nettle plant growing next to symptomatic ones. It is therefore likely that the observed vein banding was due to an idaeovirus or a partitivirus, which were shown to be coinfecting the symptomatic plant. These findings expand the list of viruses infecting nettle.

The coronavirus disease of 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can alter the expression levels of host microRNAs (miRNAs). Increasing evidence suggests that circulating miRNAs can potentially play an important role in the diagnosis and prognosis of respiratory infectious diseases, especially COVID-19, and might serve as sensitive indicators of disease before the emergence of clinical symptoms. Here, we review the potential of circulatory microRNAs as novel biomarkers for different aspects of COVID-19. Recent studies have suggested that they can be useful not only for COVID‐19 prognosis but also for prediction of disease severity and mortality among intensive care unit (ICU) and ward patients. Moreover, extracellular vesicle (EV) miRNAs can be associated with antibody titer after COVID-19 vaccination. This review provides an overview of miRNA‐based biomarkers.

Penicillium exsudans strain RCEF7900, obtained from leaf litter, was found to harbor two double-stranded RNA (dsRNA) elements, designated as dsRNA1 and dsRNA2, with lengths of 1,816 bp and 1,625 bp, respectively. dsRNA1 encodes a 572-amino-acid RNA-dependent RNA polymerase (RdRp) protein (65.29 kDa), while dsRNA2 encodes a 503-amino-acid coat protein (CP) (56.73 kDa). A BLASTp search indicated that dsRNA1 and dsRNA 2 together constitute the genome of a novel partitivirus, which we have named "Penicillium exsudans partitivirus 1" (PePV1). Phylogenetic analysis based on RdRp amino acid sequences revealed that these genome segments belong to a member of a new species within the proposed genus “Zetapatitivirus” of the family Partitiviridae, with the RdRp showing the most sequence similarity (79.72% identity) to that of Sonifin virus. This is the first report of a zetapatitivirus from P. exsudans, expanding our understanding of mycoviral diversity in this fungal species.