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In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Drought and soil salinity reduce agricultural output worldwide. Plant-growth-promoting rhizobacteria (PGPR) can enhance plant growth and augment plant tolerance to biotic and abiotic stresses. Haloxylon ammodendron, a C4 perennial succulent xerohalophyte shrub with excellent drought and salt tolerance, is naturally distributed in the desert area of northwest China. In our previous work, a bacterium strain numbered as M30-35 was isolated from the rhizosphere of H. ammodendron in Tengger desert, Gansu province, northwest China. In current work, the effects of M30-35 inoculation on salt tolerance of perennial ryegrass were evaluated and its genome was sequenced to identify genes associated with plant growth promotion. Results showed that M30-35 significantly enhanced growth and salt tolerance of perennial ryegrass by increasing shoot fresh and dry weights, chlorophyll content, root volume, root activity, leaf catalase activity, soluble sugar and proline contents that contributed to reduced osmotic potential, tissue K+ content and K+/Na+ ratio, while decreasing malondialdehyde (MDA) content and relative electric conductivity (REC), especially under higher salinity. The genome of M30-35 contains 4421 protein encoding genes, 12 rRNA, 63 tRNA-encoding genes and four rRNA operons. M30-35 was initially classified as a new species in Pseudomonas and named as Pseudomonas sp. M30-35. Thirty-four genes showing homology to genes associated with PGPR traits and abiotic stress tolerance were identified in Pseudomonas sp. M30-35 genome, including 12 related to insoluble phosphorus solubilization, four to auxin biosynthesis, four to other process of growth promotion, seven to oxidative stress alleviation, four to salt and drought tolerance and three to cold and heat tolerance. Further study is needed to clarify the correlation between these genes from M30-35 and the salt stress alleviation of inoculated plants under salt stress. Overall, our research indicated that desert shrubs appear rich in PGPRs that can help important crops tolerate abiotic stress.

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.

Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.

Infectious bronchitis virus (IBV) infection in chickens can lead to an economically important disease, namely, infectious bronchitis (IB). New IBV variants are continuously emerging, which complicates vaccination-based IB control. In this study, five IBVs were isolated from clinical samples submitted to a diagnostic laboratory in Ontario, Canada, and subjected to detailed molecular characterization. Analysis of the spike (S)1 gene showed that these five IBVs were highly related to the Delmarva (DMV/1639) strain (~97.0% nucleotide sequence similarity) that was firstly isolated from an IB outbreak in the Delmarva peninsula, United States of America (USA), in 2011. However, the complete genomic sequence analysis showed a 93.5–93.7% similarity with the Connecticut (Conn) vaccine strain, suggesting that Conn-like viruses contributed to the evolution of the five Canadian IBV/DMV isolates. A SimPlot analysis of the complete genomic sequence showed evidence of recombination for at least three different IBV strains, including a Conn vaccine-like strain, a 4/91 vaccine-like strain, and one strain that is yet-unidentified. The unidentified strain may have contributed the genomic regions of the S, 3, and membrane (M) genes of the five Canadian IBV/DMV isolates. The study outcomes add to the existing knowledge about involvement of recombination in IBV evolution.

Mobile genetic elements (MGEs) or mobilomes promote the mobilization and dissemination of antimicrobial resistance genes (ARGs), serving as critical drivers for antimicrobial resistance (AMR) accumulation, interaction, and persistence. However, systematic and quantitative evaluations of the role of mobilome in spreading resistome in a bacterial pathogen remain unaddressed, partially due to the lack of closed genomes. Here, we examined MGEs across 1,817 Salmonella isolates with complete genomic sequences from 58 countries between 1911 and 2022. We found the plasmid harboring 69.8% ARGs to be the largest ARG reservoir, correlated with serovar-based evolution in most Salmonella lineages. Prophages, specifically RCS47 and SJ46, play a crucial role in the plasmids’ plasticity and the acquisition of ARGs. Furthermore, distinct ARG accumulation, including resistance toward last-resort antibiotics, exhibited an MGE-favored manner. Certain socioeconomic and ecological factors, as additional layers of mediators, are associated with the preferential distribution of MGE-mediated ARGs in Salmonella . Collectively, this study demonstrated an uncharted knowledge of the segmentation of Salmonella resistome driven by mobilome, elucidating dynamic drivers and distinct mediators for resistome development that are of immediate relevance for targeted interventions. Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella , a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes ( n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.

Salmonellosis occurs frequently worldwide, causing serious threats to public health. The abuse of antibiotics is increasing antibiotic resistance in bacteria, thereby making the prevention and control of Salmonella more difficult. A phage can help control the spread of bacteria. In this study, the lytic phage S55, whose host bacterium is Salmonella Pullorum, was isolated from fecal samples obtained from poultry farms. This phage belongs to the Siphoviridae and has a polyhedral head and a retraction-free tail. S55 lysed most cells of Salmonella Pullorum (58 of 60 strains, 96.67%) and Salmonella Enteritidis (97 of 104 strains, 93.27%). One-step growth kinetics revealed that the latent period was 10 min, the burst period was 80 min, and the burst size was 40 PFU per cell. The optimal multiplicity of infection was 0.01, and the phage was able to survive at pH values of 4 to 11 and temperatures of 40 to 60°C for 60 min. Complete genome sequence analysis revealed that the S55 genome consists of 42,781 bp (50.28% GC content) and 58 open reading frames, including 25 frames with known or assumed functions without tRNA genes. S55 does not carry genes that encode virulence or resistance factors. At 4 and 25°C, S55 reduced the populations of Salmonella Pullorum and Salmonella Enteritidis on chicken skin surfaces. S55 may be useful as a biological agent for the prevention and control of Salmonella infections.

Objective To conduct an epidemiological investigation on a case of severe fever with thrombocytopenia syndrome (SFTS) reported in Longyou County, Zhejiang Province in April 2025, and to perform nucleic acid detection and genetic characterization of Dabie bandavirus (DBV) in the patient’s serum sample, aiming to provide scientific evidence and technical support for local SFTS prevention and control. Methods An epidemiological investigation was conducted on the case. Serum samples from the confirmed case and close contacts, as well as related vector host specimens, were collected. DBV-specific nucleic acid was detected using real-time fluorescent quantitative PCR. The viral genome was amplified by RT-PCR and subjected to whole-genome sequencing. Professional computer software (SeqMan Ultra 17.2, Clustal X 2.1, BioEdit V7.2.6.1, and MEGA V7.0.26, etc.) was used for nucleotide and amino acid sequence alignment, phylogenetic tree construction, and calculation of genetic distances and homology percentages. Results The case had a history of tick bite and no history of travel outside the area. Fluorescence quantitative PCR detection showed that only the case’s serum sample was positive for DBV nucleic acid, while serum samples from close contacts and related vector host specimens were all negative for DBV nucleic acid. After amplification and sequencing, the three fragments L, M, and S were successfully obtained. Genetic evolution analysis showed that they belonged to genotypes L (C), M (C), and S (A), respectively. Compared with the closest reference strain HZ2023-16 in the phylogenetic tree, the nucleotide homologies of the L, M, NS, and NP genes were 99.74%, 99.53%, 99.66%, and 99.19%, respectively, and the amino acid homologies were 100%, 99.72%, 99.66%, and 99.59%, respectively. Compared with the type C reference strain AHL/China/2011 (L(C)/M(C)/S(D)), the nucleotide homologies of the L, M, NS, and NP genes were 96.87%, 96%, 93.76%, and 95.66%, respectively, and the amino acid homologies were 99.42%, 98.51%, 98.29%, and 99.18%, respectively. Compared with the type A reference strain JX23XSH (L(A)/M(A)/S(A)), the nucleotide homologies of the L, M, NS, and NP genes were 96.24%, 95.97%, 95.35%, and 97.02%, respectively, and the amino acid homologies were 99.52%, 98.14%, 99.32%, and 99.18%, respectively. The average genetic distances of the L, M, and S genes compared with the HZ2023-16 reference strain were 0.003, 0.005, and 0.005, respectively; compared with the type C reference strain AHL/China/2011 (L(C)/M(C)/S(D)), they were 0.031, 0.04, and 0.053, respectively; compared with the type A reference strain JX23XSH (L(A)/M(A)/S(A)), they were 0.038, 0.04, and 0.038, respectively. Amino acid variation analysis showed that compared with the reference strains, this strain had 0–12 amino acid substitutions in the L protein (e.g., V68I, A140V), 3–20 substitutions in the M protein (e.g., D151E, G863S), 1–5 substitutions in the NS protein, and 1–2 substitutions in the NP protein. Conclusion Combining the clinical manifestations, epidemiological history, and laboratory test results of the case, this outbreak can be determined as a local case of severe fever with thrombocytopenia syndrome. The strain is genetically closely related to human-derived reference strains and possesses specific genomic characteristics.

Here, we present the whole genome sequence of Bt S2160-1, a potential alternative to the mosquitocidal model strain, Bti . One chromosome genome and four mega-plasmids were contained in Bt S2160-1, and 13 predicted genes encoding predicted insecticidal crystal proteins were identified clustered on one plasmid pS2160-1p2 containing two pathogenic islands (PAIs) designed as PAI-1 (Cry54Ba, Cry30Ea4, Cry69Aa-like, Cry50Ba2-like, Cry4Ca1-like, Cry30Ga2, Cry71Aa-like, Cry72Aa-like, Cry70Aa-like, Cyt1Da2-like and Vpb4C1-like) and PAI-2 (Cyt1Aa-like, and Tpp80Aa1-like). The clusters appear to represent mosquitocidal toxin islands similar to pathogenicity islands. Transcription/translation of 10 of the 13 predicted genes was confirmed by whole-proteome analysis using LTQ-Orbitrap LC–MS/MS. In summary, the present study identified the existence of a mosquitocidal toxin island in Bacillus thuringiensis , and provides important genomic information for understanding the insecticidal mechanism of B. thuringiensis .