Archives of Virology最新文献

Here, we describe a novel mycovirus, tentatively designated as “Nigrospora sphaerica fusarivirus 2” (NsFV2), which was isolated from the phytopathogenic fungus Nigrospora sphaerica strain HNXX-Ns20. NsFV2 has a single-stranded positive-sense RNA (+ ssRNA) genome of 6,156 nucleotides, excluding the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a large polypeptide of 1,509 amino acids (aa) containing a conserved RNA-dependent RNA polymerase (RdRp) domain and a viral helicase domain. The ORF1-encoded polypeptide shares 29.40-68.48% sequence identity with other fusariviruses and shares the highest sequence identity (68.48%) with Nigrospora sphaerica fusarivirus 1 (NsFV1). The small ORF2 encodes a polypeptide of 483 aa that contains a conserved chromosome segregation ATPase (Smc) domain. Multiple sequence alignments and phylogenetic analysis based on the ORF1-encoded polypeptide indicated that NsFV2 should be considered a new member of the genus Alphafusarivirus of the family Fusariviridae.

A lytic Proteus mirabilis phage, PmP19, was isolated from sewage on a farm. PmP19 has an icosahedral head (60 ± 3 nm in diameter) and a short tail (15 ± 2 nm long). Its genome, a linear, double-stranded DNA molecule 44,305 bp in length with an average GC content of 51.93%, has 52 putative open reading frames (ORFs). BLASTn comparisons and phylogenetic analysis revealed a close relationship between Pmp19 and Klebsiella phage vB_KpnP_ZK1. Bioinformatic analysis revealed that PmP19 belongs to the phage subfamily Molineuxvirinae.

A significant proportion of the highly divergent and novel proteins of giant viruses are termed “hypothetical” due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.

Zucchini tigre mosaic virus (ZTMV) is a positive-sense single-stranded RNA virus belonging to the genus Potyvirus. In this study, a full-length infectious cDNA clone of a ZTMV strain infecting snake gourd (Trichosanthes cucumerina var. anguina L.) was constructed and shown to infect snake gourd, chieh-qua, zucchini, ridge gourd, and bitter melon. The complete genome sequence of ZTMV-FS7 (PP291701) showed the highest nucleotide sequence similarity to ZTMV-TW (86.2% identity). Genetic diversity analysis of 12 ZTMV isolates showed that the P1 gene had the highest variability. Selection pressure analysis indicated that all of the ZTMV genes were under negative selection. However, some sites, particularly within the P1 gene, were under positive selection.

Acute lower respiratory tract infections (ALRTIs) are a leading cause of mortality in young children worldwide due to human respiratory syncytial virus (RSV). The aim of this study was to monitor genetic variations in RSV and provide genomic data support for RSV prevention and control. A total of 105 complete RSV genome sequences were determined during 2017-2020. Phylogenetic analysis showed that all of the RSVA sequences were of genotype ON1, and all of the RSVB sequences were of genotype BA9. Notably, a phylogenetic tree based on the whole genome had more branches than a tree based on the G gene. In comparison to the RSV prototype sequences, 71.43% (50/70) of the ON1 sequences had five amino acid substitutions (T113I, V131N, N178G, H258Q, and H266L) that occurred simultaneously, and 68.57% (24/35) of the BA9 genotype sequences had 12 amino acid substitutions, four of which (A131T, T137I, T288I, and T310I) occurred simultaneously. In the F gene, there were 19 amino acid substitutions, which were mainly located in the antigenic sites Ø, II, V, and VII. Other amino acid substitutions were found in the NS1, NS2, P, SH, and L proteins. No significant evidence of recombination was found in any of the sequences. These findings provide important data that will be useful for prevention, control, and vaccine development against RSV.

In this study, a novel positive-sense single-stranded RNA (+ ssRNA) mycovirus, Alternaria tenuissima mitovirus 1 (AtMV1), was identified in Alternaria tenuissima strain YQ-2-1, a phytopathogenic fungus causing leaf blight on muskmelon. The genome of AtMV1 is a single RNA molecule that is 3013 nt in length with an A + U content of 66.58% and contains a single open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF was predicted to encode a 313-amino-acid RNA-dependent RNA polymerase (RdRp) with a molecular mass of 35.48 kDa, which contains six conserved motifs with the highly conserved GDD tripeptide in motif IV. The 5ʹ and 3ʹ untranslated regions were predicted to fold into stem-loop and panhandle secondary structures. The results of a BLASTp search revealed that the amino acid (aa) sequence of RdRp of AtMV1 shared the highest sequence similarity (51.04% identity) with that of Sichuan mito-like virus 30, a member of the genus Duamitovirus within the family Mitoviridae. Phylogenetic analysis based on the aa sequence of the RdRp suggested that AtMV1 is a novel member of the genus Duamitovirus. To our knowledge, this is the first report of the complete genome sequence of a new mitovirus infecting A. tenuissima.

Porcine epidemic diarrhea virus (PEDV) causes the third most important disease in the pig industry, after African swine fever and porcine reproductive and respiratory syndrome, and leads to illness or death of the entire litter, causing significant economic losses. In this study, three PEDV strains (HN-1, HN-2, and SC2023) were isolated from swine farms with suspected PEDV infections in Sichuan and Henan provinces. Phylogenetic analysis based on complete S gene sequences showed that all three strains belonged to the G2c subgroup. HN-1 adapted readily to cell culture, grew to a viral titer as high as 2 × 10⁸ TCID₅₀/mL in Vero cells, and caused the formation of large syncytia. We analyzed the amino acid sequence of the HN-1 isolate and found that its S1 subunit contained a three-amino-acid insertion (³⁵⁵KRL³⁵⁸). A seven-amino-acid-deletion (¹³⁷⁷FEKVHVQ¹³⁸³) in the S2 subunit resulted in the partial deletion of the endocytosis signal YxxΦ and the complete deletion of the endoplasmic reticulum retrieval signal (ERRS) KVHVQ in the cytoplasmic tail of the S protein. Consequently, HN-1 is predicted to be less pathogenic than its parent strain, an attribute that facilitates rapid cell-to-cell spread by enhancing syncytium formation. In addition, strain HN-1 was found to have the mutation ^884–885SG→RR, which may favor adaptation to cell culture by providing new trypsin cleavage sites. These results suggest that HN-1 is a G2c subtype variant that adapts well to cell culture and can be used to study the adaptive mechanisms of PEDV and develop attenuated vaccines.

Soybean dwarf virus (SbDV; family Tombusviridae, genus Luteovirus, species Luteovirus glycinis) is an RNA plant virus that is transmitted solely by aphids in a persistent, circulative and non-propagative manner. SbDV causes significant losses in cultivated Fabaceae, especially in subterranean clover (Trifolium subterraneum) pastures of mainland Australia. SbDV isolates are classified into four phenotypically distinguishable strains: YP, YS, DP, and DS. Y and D strains differ primarily in their host range, and P and S strains in their primary vector species. Genetically, Y and D strains separate into two clades in every genomic region except for the N-terminal region of the readthrough domain (N-RTD), in which P and S strains separate. SbDV diversity in Australia has yet to be investigated, so in this study, 41 isolates were collected from six different host species across two production regions of Australia: the south coast of Western Australia (‘south-west’) and northern New South Wales/southern Queensland (‘north-east’). A near-complete genome sequence of each isolate was obtained, and together with all 50 whole-genome sequences available in the GenBank database, underwent phylogenetic analysis of the whole genome nt and the N-RTD aa sequences. At the whole-genome level, the isolates separated into D and Y clades. At the N-RTD level, most of the isolates separated into P and S clades. All south-west isolates and 11 of the 31 north-east isolates were in the Y clade, and the remaining 20 north-east isolates were in the D clade. Except for one isolate that fell outside the P and S clades, all south-west and north-east isolates were in the P clade, suggesting that they are transmitted by Acyrthosiphon pisum and Myzus persicae. Available biological data largely supported the phenotypic inferences made from the phylogenetic analysis, suggesting that genetic data can provide critical epidemiological insights, provided that sufficient biological data have been collected.

Triatomines are infamous as vectors of the parasite Trypanosoma cruzi, the causative agent of Chagas disease. However, climate-driven range expansion and urbanization adaptation of triatomine populations, coupled with their highly diverse feeding strategies (vertebrate haematophagy, kleptohaematophagy, and coprophagy), and has elevated interest in triatomines as potential arboviral vectors. Information on the triatomine virome is scant, with prior records including only eight insect-specific viruses: Triatoma virus (TrV) and Rhodnius prolixus viruses 1–7. Here, we leverage publicly available transcriptome datasets to assess viral diversity in 122 wild and colony kissing bugs representing eight species from six countries. In total, six viruses were detected (including Rhodnius prolixus viruses 4–6), and TrV was detected in almost half of all screened triatomines. This is the first report of TrV in Triatoma brasiliensis and in members of the genus Mepraia (M. gajardoi, M. spinolai, and M. parapatrica), and this effort has vastly expanded the publicly available genomic resources of TrV, adding 39 genome sequences to the single genome sequence currently available in the GenBank database. Furthermore, two additional viruses—Meccus longipennis virus 1 and Drosophila melanogaster Nora virus—are herein reported for the first time from kissing bugs. Meccus longipennis virus 1 was detected in Triatoma infestans from Argentina, Brazil, Chile, and Peru, and Drosophila melanogaster Nora virus was found in T. infestans from Argentina. Our results illustrate the advantage and utility of low-cost transcriptome data mining for the discovery of known and novel arboviruses in triatomines and other potential insect vectors.

Pigeon paramyxovirus type 1 (PPMV-1) poses significant economic challenges to the pigeon industry in China. However, information about the prevalence, genetic diversity, and epidemiology of PPMV-1 in China is still lacking. In this study, we isolated six strains of PPMV-1 from Hubei and Zhejiang provinces in 2022. All six isolates were found to belong to subgenotype VI.2.1.1.2.2. Five of them were identified as mesogenic and one as lentogenic. Multiple mutations were observed in the F and HN proteins of these isolates. Comprehensive analysis of global PPMV-1 strains highlighted the dominance of genotype VI, showing that VI.2.1.1.2.2 has been the dominant subgenotype since 2011. We also identified 36 host-specific amino acid substitutions that are unique to PPMV-1 in comparison to chicken-origin NDVs. The data reported here contribute to our understanding of the epidemiology, genetic diversity, and prevalence of PPMV-1 and serve as a valuable reference for the prevention and control of PPMV-1.