Archives of Virology最新文献

A novel alphapartitivirus, tentatively named "Ceratobasidium alphapartitivirus 1" (CeAPV1), was identified in the phytopathogenic fungus Ceratobasidium anastomosis group (AG)-A strain SR-LN-10, which was isolated from diseased strawberry roots exhibiting typical symptom of root rot. The full genome of CeAPV1 consists of two linear double-stranded RNA (dsRNA) segments: dsRNA1 and dsRNA2. The larger segment, dsRNA1 (1891 bp), contains an open reading frame (ORF) predicted to encode a 578-amino-acid (aa) RNA-dependent RNA polymerase (RdRp). The smaller segment, dsRNA2 (1878 bp), contains an ORF encoding a 546-aa coat protein (CP). BLASTp analysis showed that the RdRp encoded by CeAPV1 had the highest sequence similarity (74.78% identity) to the RdRp of Leucocoprinus alphapartitivirus 1 (LeAPV1). The CP encoded by CeAPV1 showed the highest sequence similarity (44.24% identity) to the CP of Bondarzewia berkeleyi partitivirus 1 (BbPV1). Phylogenetic analysis revealed that CeAPV1 clustered together with mycoviruses belonging to the genus Alphapartitivirus within the family Partitiviridae. Taken together, this indicated that CeAPV1 is a novel alphapartitivirus. This is the first report of a full-genome sequence of a novel alphapartitivirus infecting AG-A.

In August 2021, begomovirus-like symptoms of yellow mosaic were observed on fiery tasselflower (Emilia coccinea) plants in Iguowan, Nigeria. Total DNA from symptomatic leaves was subjected to rolling-circle amplification and screened using degenerate primers targeting begomovirus DNA-A and DNA-B components, alphasatellites, and betasatellites. Subsequently, the complete nucleotide sequence of a monopartite begomovirus genome of 2802 nucleotides (nt) was determined. The novel virus, which we have named "tasselflower yellow mosaic virus" (TFYMV), was found to be associated with tomato leaf curl Cameroon alphasatellite (1,390 nt) and a novel 1271 nt betasatellite. The species names "Begomovirus emiliaflavi" and "Betasatellite emiliae" are proposed for TFYMV and the betasatellite, respectively.

Tilapia are susceptible to a number of viral diseases that have a severe economic impact in many countries. During a mass mortality event in lakes in central-western Gabon in 2019, the first rhabdoviruses infecting tilapia were identified. Two distinct and nearly complete viral genome sequences were obtained by combining whole-genome sequencing (WGS) and Sanger sequencing of amplicons. The two viruses, which we have named "tilapia rhabdovirus 1" (TiRV1) and "tilapia rhabdovirus 2" (TiRV2), were found coinfecting a single fish. These viruses are related to, but clearly distinct from, members of the subfamily Alpharhabdovirinae. The respective roles of TiRV1 and TiRV2 in the present disease outbreak remain to be clarified. Further studies are needed to evaluate whether these viruses pose a threat to the health of this fish species throughout the region.

Marseilleviruses are giant viruses that infect amoebas and have been isolated from various environments. Here, we describe a new strain, isolated from a water sample collected from the Paraguay River in the Brazilian Pantanal, which we have named "Marseillevirus pantanense". Transmission and scanning electron microscopy revealed icosahedral particles approximately 190 nm in diameter. Genomic and phylogenetic analyses show that M. pantanense has a 379,900-bp genome with 496 open reading frames, including 12 ORFans and two tRNAs. Furthermore, phylogenetic analysis places M. pantanense within Marseillevirus lineage A, group I. The findings of in this study underscore the importance of isolating new viruses to expand our understanding of the abundance and distribution of giant viruses in Brazilian biomes.

SARS-CoV-2, which emerged in Wuhan, China, in December 2019, caused one of the largest viral respiratory pandemics in history. As of February 1, 2025, Brazil had reported approximately 39 million cases and over 714,000 deaths. The Northeast region of Brazil, comprising the states of Alagoas, Paraíba, Pernambuco, and Rio Grande do Norte, is characterized by its socioeconomic and geographic diversity. Understanding the spread of SARS-CoV-2 in this region and identifying patterns of transmission, evolution, and pathogenicity are crucial for identifying vulnerable areas and planning effective interventions. In this study, to trace the spread of SARS-CoV-2 in the Brazilian Northeast, we analyzed 8,442 SARS-CoV-2 genome sequences from the states of Alagoas, Paraíba, Pernambuco, and Rio Grande do Norte, which were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Epidemiological data (cases, deaths, and vaccination records) from 2020 to 2024 were obtained from the Coronavirus Panel of the Ministry of Health and integrated with information from the IBGE (Instituto Brasileiro de Geografia e Estatística). The epidemiological analysis revealed three major and two minor waves of infection and mortality between 2020 and 2023, with a notable increase in cases in early 2024. Metropolitan regions, including Recife (PE), João Pessoa (PB), Maceió (AL), and Natal (RN), showed higher incidence and mortality rates. Vaccination data indicated high adherence to the initial doses but a significant drop in booster shots. Genomic characterization showed that 70.37% of the sequenced genomes were concentrated in metropolitan areas. A total of 43,594 single-nucleotide polymorphisms (SNPs) and 15,366 insertions/deletions (indels) were identified, with mutations concentrated in the ORF1a, ORF1b, S, and N genes. The lineage dynamics demonstrated the successive emergence and dominance of the variants Gamma, Delta, and Omicron, including its sublineages BA.1, BA.2, BA.5, XBB.1.16, and XBB.1.5. Phylogenetic analysis demonstrated the circulation of 27 distinct lineages in the region, with Delta (AY.99.2) and Gamma (P.1) being the most predominant. These results demonstrate the value of integrating epidemiological and genomic data for continuous surveillance and for adapting public-health strategies. Challenges such as low adherence to booster doses and the concentration of sequencing in urban centers must be addressed to improve pandemic control. Expanding genomic sequencing to inland regions would provide more detailed information about the circulation of SARS-CoV-2.

Yellow dwarf viruses (YDVs) are widespread and economically important pathogens of cereals globally. YDVs belong to the genus Luteovirus (family Tombusviridae) or the genus Polerovirus (family Solemoviridae). Despite their importance, information about the genetic diversity of YDVs is scarce, especially in an Australian context. Seventeen symptomatic cereal and grass plants from Australia were analysed using high-throughput sequencing (HTS). Twenty-five YDV genomes were revealed by HTS and were identified as barley yellow dwarf virus PAV (5/25), barley yellow dwarf virus PAS (3/25), cereal yellow dwarf virus RPV (6/25), barley virus G (3/25), cereal yellow dwarf virus RPS (1/25), and a novel luteovirus (7/25) that had likely been serologically misidentified previously as barley yellow dwarf virus MAV. The first full genome sequence of an Australian CYDV RPS isolate is also described. Despite the fact that this was only a snapshot of the virus profile in one region of Australia at one point in time, Australian YDVs were found to be surprisingly diverse. This information is critical for the development of virus-resistant cereal varieties and more-effective diagnostic tests and demonstrates the complex nature of YDV epidemiology and taxonomy.

“Jumbo phages” are tailed phages with genome sizes >200 kbp and physical dimensions reaching up to 0.45 μm. Although jumbo phages represent only a small fraction of the isolated phages to date, metagenomic surveys have shown that they are broadly distributed in a wide range of environments. In this study, we surveyed metagenomic data from aquatic systems and identified 25 genomes from a heretofore-undescribed lineage of jumbo phages with genomes reaching up to 307 kbp. We refer to these phages as “moraphages”, from the Gaelic word ‘mór’, for large. Moraphages represent a diverse lineage with inter-genome average amino acid identity (AAI) ranging from 39 to 95%, and our pan-genomic analysis identified only 26 viral orthologous groups (VOGs) found in at least 80% of the genomes. Our phylogenomic analysis suggests that moraphages are distant relatives of a recently described lineage of huge phages from marine sediment. Moraphages lack much of the genetic machinery found in other lineages of large phages, but they have a range of genes that may be used to take over host cellular machinery and subvert host defenses, such as glutamine synthetases, antitoxin genes, and chaperones. The predicted hosts of most moraphages are members of the phylum Bacteroidota, and some encode homologs of the chaperones DnaK and DnaJ that bear evidence of recent gene transfer from members of the order Flavobacteriales. Our work sheds light on the emerging diversity of large phages that are found across the biosphere.

Forty-two human-derived hepatitis E virus subtype 3f (HEV-3f) strains, identified in Japan between 1998 and 2024, were analyzed based on their genome sequences. Fourteen strains in the Kanto region and two in Mie Prefecture exhibited close genetic relatedness to each other but were distinct from European HEV-3f strains, suggesting possible endemic circulation in Japan. Conversely, seven strains from individuals without a history of travel shared identical nucleotide sequences with European HEV-3f, suggesting that these infections were potentially linked to imported pork. Comprehensive molecular and epidemiological studies are needed to clarify the relative contributions of local zoonotic transmission from domestic or wild animals versus foodborne introduction via imported pork products.

The soilborne phytopathogen Rhizoctonia solani (R. solani) infects multiple hosts and is capable of causing severe diseases in many economically important crops, including rice, potato, and wheat. This report describes the discovery and molecular characterization of a previously unrecognized mycovirus, tentatively named "Rhizoctonia solani partitivirus Rs31" (RsPV-Rs31), isolated from R. solani AG-4 HG III strain Rs31. Genome sequencing and analysis revealed that RsPV-Rs31 consists of two double-stranded RNA (dsRNA) segments with a length of 1991 bp (dsRNA1) and 1728 bp (dsRNA2), respectively. The larger segment, dsRNA1, contains a single open reading frame (ORF1) predicted to produce a 622-amino-acid RNA-dependent RNA polymerase (RdRp) with conserved functional motifs. The smaller dsRNA2 segment containing ORF2 was predicted to encode a 558-amino-acid capsid protein (CP). BLASTp analysis of the predicted RdRp revealed significant sequence similarity to viruses belonging to the genus Alphapartitivirus and other unclassified partitiviruses listed in the ICTV database. Phylogenetic analysis based on RdRp protein sequences suggested that RsPV-Rs31 is a novel member of the family Partitiviridae.

Porcine epidemic diarrhea virus (PEDV) is a major pathogen that causes severe diarrhea and high mortality in piglets. Immunoglobulin A (IgA) in milk provides more-effective protection for newborn piglets than immunoglobulin G (IgG). In this study, the heavy- and light-chain genes of IgA were cloned from peripheral blood mononuclear cells (PBMCs) and colostrum of pigs immunized with PEDV. Subsequently, the IgA was expressed in Chinese hamster ovary (CHO) cells and purified via affinity chromatography. Three IgA antibodies were obtained (5HV1, 1HV2, and 11HV2), and all three exhibited neutralizing activity against PEDV. The half-maximal effective inhibitory concentrations (IC₅₀) of 5HV1, 1HV2, and 11HV2 against PEDV were determined to be 0.7906 µg/mL, 4.113 µg/mL, and 1.026 µg/mL, respectively. A Western blot assay demonstrated that the IgA antibodies exhibited specific binding affinity for the S1 protein (aa 1-506) and the S1A protein (aa 1-239) of PEDV. While these IgA antibodies were susceptible to degradation in gastric fluid, Alg-CS gel effectively shielded them from degradation and preserved their immunoreactivity with the S protein in simulated gastric fluid. The results of this study provide useful information for the application of IgA against PEDV infections.