Archives of Virology最新文献

Mycoviruses have been classified into 35 virus families so far. In addition to numerous mycoviruses with proven fungal or oomycetes hosts, many newly discovered viruses from environmental water and soil samples and various animal or plant specimens exhibit significant similarity to classified mycoviruses, thereby expanding the known sequence space of fungal and related viruses. In this study, we searched for mycoviruses in two environmental water samples that had been collected from the Teltow Canal and the Havel River in Berlin, Germany. Viral sequences with similarity to members of 16 virus families were identified. The most common viruses in our samples were botourmia-like viruses with moderate similarity to members of the genus Ourmiavirus. Notably, 58 of the ourmia-like sequences from the Teltow Canal and Havel River and 10 ourmia-like sequences from other sources exhibited a dicistronic genome layout. The second open reading frame (ORF) of these viruses encoded a putative capsid protein with an S domain that showed little similarity to the structural proteins of the classified ourmiaviruses. The second-largest virus group (59 sequences) was assigned to the order Ghabrivirales, and 13 of these sequences exhibited similarity to members of the suborder Alphatotivirineae (families Orthototiviridae, Pseudototiviridae, Botybirnaviridae, and Chrysoviridae). Thirty-three sequences clustered with members of the suborder Betatotivirineae – three of them with members of the family Artiviridae. Fifteen highly divergent toti-like sequences suggest the need to establish a new higher-order taxon within the order Ghabrivirales. Other virus sequences were assigned to the families Mitoviridae (three unuamitoviruses and 10 highly divergent mitovirus-like sequences), Narnaviridae (five "alphanarnavirus"-like sequences), Amalgaviridae (two zybavirus-like sequences), Hypoviridae (one partial RdRP sequence), and Mymonaviridae (one partial RdRP sequence), and one was not classified (Sclerophthora macrospora B-like virus). Notable results include a clade of highly divergent mitovirus-like sequences with a standard translation code, three narnavirus-like sequences with a reverse-frame ORF, and a clade of four Ghabrivirales-like replicase sequences that were found to have numerous termination codons regardless of which translation table was used.

Typification, the linkage of a name-bearing “type” to a taxon and the description and deposition of a corresponding type specimen, has been a principle of biological taxonomy for over two centuries. It was introduced to promote nomenclatural uniformity and stability. Until recently, a modified form of typification was also written in the rules governing the taxonomy of viruses. However, in 2021, the International Committee on Taxonomy of Viruses abolished all type species and removed the requirement to designate a type species when a new genus is created. In this article, I briefly review the history of typification, explain its purpose and evaluate its relevance to current virological practice.

Here, we report the isolation of a novel mycovirus from Phomopsis asparagi strain XJ5. The viral genome consists of a positive-sense, single-stranded RNA (+ ssRNA) molecule that is 2,657 nucleotides (nt) in length and has a GC content of 42%. It contains a single open reading frame (ORF) encoding a putative protein of 731 amino acids, with a predicted molecular mass of 83.0 kDa. A BLASTp search showed that the putative protein shared the highest sequence similarity with Fusarium pseudograminearum mitovirus 5 (FpgMV5), exhibiting 55.84% sequence identity. Phylogenetic analysis revealed that this mycovirus clusters with members of the genus Unuamitovirus, belonging to the family Mitoviridae. Based on these findings, we propose to designate this virus as "Phomopsis asparagi mitovirus 1" (PhaMV1).

Alphabaculoviruses rel, in combination with natural putrefaction, on the auxiliary genes v-cath and chiA for host liquefaction, a process that is critical for virus release and horizontal transmission. Here, we describe DijuNPV-DF/23, a natural isolate infecting the passion fruit caterpillar Dione juno that fails to induce liquefaction. PCR amplification of the v-cath/chiA locus revealed a shorter amplicon compared to a previously reported virus, DijuNPV-Araguarina, suggesting gene disruption. Genome sequencing confirmed a 122,265-bp genome with 152 ORFs and a major structural alteration: v-cath was fragmented into two truncated ORFs due to a 76-nt deletion, while chiA remained intact. This provides a direct molecular explanation for the observed non-liquefying phenotype.

Here, we describe a novel ourmia-like virus, Botryosphaeria dothidea ourmia-like virus 3 (BdOLV3), obtained from the phytopathogenic fungus Botryosphaeria dothidea strain ZM211299-2 infecting apple shoots in Shandong province of China. The genome of BdOLV3 is a positive-sense single-stranded RNA with a length of 2,650 nucleotides (nt), containing a large open reading frame (ORF) that encodes a putative RNA-dependent RNA polymerase (RdRp) consisting of 673 amino acids (aa) with a molecular mass of 75.53 kDa. This RdRp protein contains eight typical conserved motifs associated with ourmia-like viruses. BLASTp analysis revealed that the RdRp protein of BdOLV3 had the highest similarity (61.98%, 61.83%, and 51.47% identity, respectively) to viruses previously identified as Plasmopara viticola lesion associated ourmia-like virus 45, Erysiphe necator associated ourmia-like virus 130, and Magnaporthe oryzae botourmiavirus 7. Phylogenetic analysis based on RdRp sequences indicated that BdOLV3 is a new member of the genus Epsilonscleroulivirus in the family Botourmiaviridae. This is the first report of the complete genomic sequence of a member of the genus Epsilonscleroulivirus found in B. dothidea.

Aeromonas veronii is a mesophilic bacterium that is widely distributed in terrestrial and aquatic environments and is able to cause disease in various species of fish and other animals. In humans, pathogenic A. veronii causes mainly foodborne infections due to increased consumption of chilled seafood. In this study, the novel lytic Aeromonas veronii phage AerV_348 was isolated and characterized. The phage and its bacterial host, A. veronii CEMTC 9558, were isolated from Lake Pestroe, North Kazakhstan. AerV_348 is a dsDNA virus with a genome size of 43,779 bp. The phage is lytic and has a very narrow host range, reproducing only in its host strain. The latent time was determined to be 50 minutes, and the burst size was 55 plaque-forming units per cell. The AerV_348 genome content corresponds to a lytic phage with myovirus morphology that does not contain genetic signs of being a temperate phage. Comparative analysis revealed that AerV_348 belongs to a large group of unclassified tailed phages that infect aquatic bacteria such as Vibrio, Shewanella, and Oceanospirillum. All of these phages have similar genome sizes and structures and share a conserved cluster of genes that encode structural proteins. However, these phages demonstrate high variability in a cluster of genes responsible for DNA metabolism and translation. Currently, the classification of this phage group is not clear, and new phage genomic data may help to separate this group as a new taxonomic unit within the class Caudoviricetes.

Here, we report the identification of a positive-sense single-stranded RNA virus from Ceratobasidium AG-Bo strain LC-JK-2, designated as "Rhizoctonia cerealis alphaendornavirus 2" (RcAEV-2). The complete genome sequence of this virus was determined and found to be 15,244 nt in length with a GC content of 39%. The genome contains a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp) of 4974 amino acids (aa) with a predicted molecular weight of 547.14 kDa. BLASTp results showed that the RdRp of RcAEV-2 had the highest amino acid sequence similarity to that of Ceratobasidium endornavirus A (YP_009310113.1). Phylogenetic analysis revealed that RcAEV-2 exhibited the closest evolutionary relationship to Ceratobasidium endornavirus A within the genus Alphaendornavirus, forming a distinct clade separate from other virus families. Thus, RcAEV-2 has been identified as a new member of the genus Alphaendornavirus within the family Endornaviridae.

A novel partitivirus was detected in quinoa (Chenopodium quinoa) plants growing in China. The complete genome sequence of quinoa cryptic virus (QCV) was determined using a combination of next-generation sequencing, RT-PCR, and RACE. Phylogenetic analysis based on amino acid (aa) sequences of the RdRP revealed that QCV belongs to the genus Deltapartitivirus within the family Partitiviridae. The aa sequence identity values obtained when comparing RdRP and CP of QCV with those of the most closely related virus, pistacia cryptic virus, were significantly below the threshold for species demarcation within the genus (≤ 90% aa sequence identity for RdRP and ≤ 80% for CP), suggesting that QCV represents a new species.

The COVID-19 pandemic caused by SARS-CoV-2 has had a significant impact on global social and economic activities. The continuous emergence of new SARS-CoV-2 variants has made the global pandemic of COVID-19 difficult to predict. Therefore, it is of great significance to closely monitor the SARS-CoV-2 epidemic and understand the evolution and transmission characteristics of SARS-CoV-2. In this study, we examined 36 cases of SARS-CoV-2 infection in Wuhan in June 2023. Genomic surveillance revealed that this outbreak was caused by Omicron XBB variants, among which FY.3 and its descendants FY.3.1 and FY.3.2 dominated, and this trend was consistent with the prevalence of SARS-CoV-2 nationwide in June and July. Analysis of sequence variations within hosts and between populations suggested that the S and ORF8 genes had undergone positive selection, possibly due to their important role in host adaptation, suggesting that some of these variations might be harmful mutations that reduce vaccine effectiveness. These findings may provide insights that will aid in predicting the evolutionary direction of SARS-CoV-2 in terms of variant competition, informing the design of next-generation multivalent vaccines and therapeutic strategies targeting conserved or rapidly evolving regions such as the S and ORF8 genes and supporting the evaluation and adjustment of surveillance, prevention, and control strategies in the Wuhan region.

Senecavirus A (SVA) infection causes vesicular disease in pigs, resulting in significant economic losses for swine producers and trade restrictions on pork exports. Due to its clinical similarity to other vesicular diseases, implementing control measures, such as vaccination, is essential to mitigate the impact of the disease. In this study, we assessed the immunogenicity of an inactivated SVA vaccine derived from a representative strain circulating in Brazil and the duration of vaccine-induced immunity in swine. Vaccinated 6- to 8-week-old pigs exhibited a robust humoral response, evidenced by significant increases in SVA-specific IgG and virus-neutralizing antibody titers. These humoral responses were detectable as early as seven days after primary vaccination and persisted for at least 11 weeks. Regarding cellular immunity, vaccinated pigs exhibited significantly higher proliferation of B lymphocyte subpopulations (CD19⁺CD79α⁺) and T lymphocyte subpopulations (CD3e⁺CD4⁺, CD3e⁺CD8α⁺, CD3e⁺CD8α⁺CD25⁺, CD3e⁺CD4⁺CD8α⁺), compared to controls (p ≤ 0.05) in splenocytes collected in the fifth-week post-vaccination. A significant increase in T lymphocyte proliferation (CD3e⁺CD4⁺, CD3e⁺CD8α⁺, CD3e⁺CD8α⁺CD25⁺, CD8α⁺CD27⁺) was also observed in splenocytes collected in the eleventh-week post-vaccination. These findings demonstrate that the inactivated SVA vaccine induces a robust and long-lasting humoral and cellular immune response, extending through the market age of slaughter (~ 130 days) and potentially contributing to the effective control of SVA infections in swine herds.