Archives of Virology最新文献

The first member of the family Pithoviridae (Pithovirus sibericum) was isolated from ancient Siberian permafrost and characterized in 2014. Since then, many relatives have been isolated, characterized, and classified as members of the genera Alphapithovirus, Alphacedratvirus, and Alphaorpheovirus. In addition, one complete circular genome sequence was assembled from metagenomic data (hydrivirus). All of these viruses form distinctive giant elongated ovoid particles, up to 2 µm in length, but they differ significantly in the size of their genome, their nucleotide composition, and their gene content. Based on their shared ovoid virion shape, common replication strategy, and core gene similarity, we recently proposed to update their taxonomic status by classifying them in three distinct families (Pithoviridae, Orpheoviridae, and Hydriviridae) within a new suborder, the Ocovirineae, to separate them clearly from the other more distant families (Marseilleviridae, Ascoviridae, Iridoviridae) of the order Pimascovirales. This new taxonomy, validated by the last ICTV Ratification vote held in March 2025, extends the previous partition from three clades to four (to include hydrivirus) while keeping the genera Alphacedratvirus and Alphapithovirus in the same family, Pithoviridae (but split into two subfamilies), due to their much greater similarity to each other than to orpheovirus and hydrivirus.

A new alphasatellite was discovered via high-throughput sequencing in mixed infections with five distinct tomato-infecting begomoviruses in central Brazil, and the presence of this alphasatellite in tomato leaf samples was confirmed by PCR and Sanger sequencing. It has a circular genome of 1,321 nucleotides with typical features of alphasatellites belonging to the subfamily Geminialphasatellitinae, including a replication-associated hairpin sequence (TAGTATTAC) and an open reading frame encoding a replication-associated protein. Pairwise sequence comparisons and phylogenetic analysis indicated that this alphasatellite represents a new species, with 69–77% sequence identity to other members of the genus Clecrusatellite. Tomato golden vein virus (TGVV) was the only begomovirus present in all six positive samples. However, it was not possible to determine which of these viruses can function as a helper virus for the alphasatellite. The species name "Clecrusatellite solanumbrasiliensis" is proposed to classify this alphasatellite associated with endemic Brazilian begomoviruses. To our knowledge, this is the first report of a tomato-associated alphasatellite in the New World.

The genus Begomovirus (family Geminiviridae) includes plant viruses that have a negative impact on the production of several economically important crops worldwide. Begomoviruses infect a wide range of non-cultivated plants, which may serve as alternative hosts or inoculum sources for epidemics in crops. In this study, we evaluated the genetic variability and population structure of Macroptilium yellow vein virus (MacYVV; Begomovirus macroptilivenae), associated with non-cultivated Macroptilium spp. in the state of Alagoas (AL), northeastern Brazil. Complete DNA-A sequences (n = 29) were obtained from symptomatic plants collected in different municipalities of AL during 2019 and 2020. Pairwise sequence comparisons indicated a low degree of genetic variability, with 93.9–100% identity to 18 previously characterized sequences. To better understand the population structuring of MacYVV in AL, the complete DNA-A data set (n = 47) was analyzed. Although the DAPC and STRUCTURE approaches yielded slightly divergent numbers of putative MacYVV subpopulations, the results are consistent with the phylogenetic relationships among MacYVV isolates, where five well-supported subgroups correlated with geographic location were observed. The low variability of the MacYVV population could be related to the small number of recombination events detected and be reflective of a long-term virus-host relationship in which the virus is very well adapted to the host.

Human non-polio enteroviruses (NPEVs) cause a wide range of illnesses such as hand, foot, and mouth disease (HFMD), herpangina, and aseptic meningitis. In this study, we investigated the incidence of NPEV infections in the Ural Federal District and Western Siberia, Russia, from 2019 to 2023 in patients with various NPEV-associated diseases, identified the main circulating genotypes in 2023, and analyzed their epidemiological characteristics. A total of 384 samples that tested positive by polymerase chain reaction (PCR) for NPEVs were genotyped by semi-nested PCR specific for the VP1 gene. A total of 20 genotypes were identified among the patients in this study, with enterovirus A accounting for 57.2% of all typed samples, enterovirus B accounting for 41%, and enterovirus C accounting for 1.8%. Coxsackievirus A6 (CVA6) was the most common genotype in HFMD cases. Echovirus 30 (E30) was predominant in aseptic meningitis patients, and coxsackievirus A2 was primarily associated with herpangina. Phylogenetic analysis showed that most of the CVA6 strains identified in this study displayed a close genetic relationship to strains that circulated in China, while E30 genotypes circulating in the studied region belonged to subgenotype V. Laboratory-based monitoring and epidemiological surveillance for genetic changes and evolutionary studies are necessary for improving prevention and clinical care.

Knowledge about the genetic diversity of enteroviruses in sub-Saharan Africa remains biased by the fact that it has mainly been described through the characterization of specimens isolated in cell cultures. The aim of this study was to characterize enteroviruses that circulate among humans in Cameroon by focusing more specifically on respiratory enteroviruses and on enteroviruses that are non-cultivable or non-cytopathogenic in standard cell lines. For this purpose, RNA was extracted from nasopharyngeal swabs, stool suspensions, and sewage concentrates collected in Cameroon from January 2018 to December 2019, and the RNA extracts were subjected to molecular screening to detect enterovirus genomes, which were subsequently sequenced using Illumina technology. Overall, 81 strains of 32 virus types were identified. Most of the strains (61.7%) belonged to the species Enterovirus coxsackiepol, followed by members of the species Enterovirus betacoxsackie (21%), Enterovirus alphacoxsackie (14.8%), and Enterovirus deconjuncti (2.5%). Almost all of the strains were found in sewage concentrates (79%) and stool suspensions (18.5%). Only two EV-D68 strains were identified in nasopharyngeal swabs. Interestingly, several virus types that have rarely been reported were detected, including non-cultivable/non-cytopathogenic EV-C strains, among which was a new virus type assigned as EV-C119. These results highlight the fact that virus isolation and unbiased cell-culture-free approaches complement each other to provide a more complete view of the enterovirus landscape in humans.

The escalating challenges of antibiotic resistance in bacterial pathogens have necessitated the exploration of alternative therapeutic strategies. Among these, bacteriophage therapy has regained attention as a promising approach to combat multidrug-resistant bacteria. Bacteriophages are viruses that infect and lyse specific bacterial strains, making them attractive candidates for targeted antimicrobial treatment. Burkholderia multivorans, a Gram-negative bacterium, is known to cause opportunistic infections, particularly in individuals with a compromised immune system or with cystic fibrosis. The prevalence of antibiotic-resistant Burkholderia strains has raised concerns about treatment options. In this study, we characterized the Burkholderia phage Bm1, a virulent bacteriophage isolated from an environmental source. Electron microscopy revealed that Bm1 phage particles have myovirus morphology, with an icosahedral head of 72 nm in diameter and a contractile tail of 100 nm in length and 18 nm in width. The genome of phage Bm1 consists of a double-stranded DNA of 67,539 bp with a terminal repeat region at each end. Comparative analysis indicated that the closest relative of phage Bm1 is Burkholderia phage BCSR129, with a calculated VIRIDIC identity of 57.7%. The apparent absence of an integrase gene suggests that the Burkholderia phage Bm1 has a strictly lytic life cycle.

A new polerovirus, designated as "ageratum virus 3" (AgV3), was detected in an Ageratum conyzoides plant in China. The complete genome sequence of AgV3 was determined using high-throughput sequencing, rapid amplification of cDNA ends, and Sanger sequencing of RT-PCR fragments. The organization of its single-stranded RNA genome of 5,652 nucleotides is typical of members of the genus Polerovirus in the family Solemoviridae, with seven putative open reading frames (ORFs 0–5 and ORF3a). The AgV3 genome shares the highest nucleotide sequence identity (65.7%) with that of cucurbit aphid-borne yellows virus (genus Polerovirus). Sequence comparisons of the gene products of AgV3 to those of its closest relatives revealed that all of them, with the exception of the ORF3a protein, had amino acid sequence identity values that were below the threshold for demarcation for species within the genus Polerovirus established by the International Committee of Taxonomy of Viruses (ICTV), suggesting that AgV3 is a new member of the genus Polerovirus. Phylogenetic analysis based on P1-P2 and coat protein amino acid sequences also indicated that AgV3 is a novel polerovirus.

Human adenovirus (HAdV) is a leading cause of respiratory infections, with clinical manifestations and disease severity varying by type. In this study, we analyzed HAdV types in South Korea over a 12-year period before the COVID-19 pandemic. From January 2008 to December 2019, HAdV isolates were prospectively collected from children with suspected respiratory infections at a single tertiary center. HAdV typing was performed through sequence analysis of hexon gene hypervariable regions (HVRs) 1–6. Among 350 HAdV isolates, members of four species (A, B, C, and E) and 10 types (1–6, 31, 34, 35, and 55) were identified. Overall, HAdV-3 was most prevalent (49.4%), followed by HAdV-2 (19.1%), HAdV-1 (14.6%), and HAdV-4 (6.6%). HAdV-3 caused four recurrent outbreaks at intervals of 3 to 4 years without significant genetic changes in the hexon HVRs. HAdV species C (types 1, 2, 5, and 6) was detected endemically throughout the study period. Notably, HAdV-55, which was associated with fatal cases in military recruits in South Korea during 2017–2018, appeared in pediatric cases. HAdV epidemiology studies are important for providing clinical data on circulating HAdVs in children, and there is a need for ongoing surveillance and research.

The relationship between hosts and viruses is influenced by various factors. One potential factor is sociality. In social organisms such as ants, the interaction between hosts and viruses might differ from those of solitary organisms due to their unique ecology. We previously isolated a double-stranded RNA toti-like virus, Camponotus yamaokai virus (CYV), from the arboreal ant Camponotus yamaokai. The ant exhibits a polygynous colony structure with multiple queens and within-nest mating behaviors. Such unique ecological traits may have driven the evolution of a distinctive relationship with the virus. However, the biological characteristics of CYV have not been sufficiently studied. In this study, we investigated the biological characteristics of CYV through rearing experiments and field surveys. No horizontal transmission between workers and broods was detected, and there were no significant differences in prevalence between castes. CYV was detected at all seven locations surveyed, with prevalence ranging from 60–95%. The high CYV prevalence across the host's distribution range indicates that the geographical distribution of CYV aligns with that of its host. These results suggest that CYV has spread throughout the host population, primarily through vertical transmission.

In this study, we isolated a novel double-stranded RNA (dsRNA) mycovirus from the phytopathogenic fungus Colletotrichum cliviicola, designated as "Colletotrichum cliviicola partitivirus 1" (CcPV1). The complete genome of CcPV1 comprises two dsRNA fragments, referred to as dsRNA1 and dsRNA2, which are 1,756 bp and 1,485 bp in length, respectively. Each dsRNA segment contains an open reading frame (ORF), with the larger ORF1 in dsRNA 1 encoding the viral RNA-dependent RNA polymerase (RdRp) and the smaller ORF2 in dsRNA 2 encoding the capsid protein (CP). Sequence comparisons revealed that the RdRp of CcPV1 shares the highest amino acid sequence identity (76.35%) with the RdRp of Nigrospora sphaerica partitivirus 1 (NsPV1). Phylogenetic analysis based on both RdRp and CP sequences indicated that CcPV1 is a member of the genus Gammapartitivirus of the family Partitiviridae. This is the first report of a gammapartitivirus in C. cliviicola.