Archives of Virology最新文献

Hepatitis B is a health threat with regional variations in prevalence. Our aim was to conduct a systematic review and meta-analysis of available data on the prevalence of hepatitis B virus (HBV) in Latin America and the Caribbean (LAC). A literature search was conducted from 2000 to 2024 using the databases Medline, Embase, LILACS and Web of Science, following PRISMA guideline. Search terms included: “hepatitis B virus”, “HBsAg”, “HBV”, “prevalence”, and “Latin America and the Caribbean”. Random-effects meta-analysis was performed to estimate the prevalence of HBV (HBsAg), and the I² statistic was used to assess heterogeneity between studies. Subgroup and meta-regression analyses were performed to investigate possible sources of heterogeneity. In total, 190 studies were included in the analysis and the estimated global prevalence of HBV was 1.0% (95% CI: 1.0%-1.0%). In population subgroup analyses, the prevalence in general population was 1.0%, indigenous people was 6.0%, HIV-infected individuals was 5.0%, and inmates was 1.0%. The prevalence found was 2.0% in the period of 2000–2008, 1.0% in 2009–2016, and 1.0% in 2017–2024. The prevalence trends over time in the general population, indigenous people, HIV-infected individuals and inmate subgroups were 1.0%, 11.0%, 6.0% and 12.0% in the period of 2000–2008, 1.0%, 4.0%, 3.0% and 0.0% in 2009–2016, and 1.0%, 5.0%, 8.0% and 0.1% in 2017–2024, respectively. In LAC, HBV prevalence decreases over time, but risk subgroups stand out with elevated prevalence, such as indigenous people and HIV-infected individuals. Strategies to expand testing, treatment and vaccination with a focus on these subgroups may be relevant to reduce the prevalence of HBV.

The family Closteroviridae comprises filamentous, RNA genome-containing viruses that infect plants. In the present study, public domain SRA libraries derived from plants were mined for novel closteroviral sequences, resulting in the identification of twenty-two putative novel closterovirids across twenty-two plant genera. The identified viruses were represented by nineteen coding-complete and three partial genomes. Based on genome organization, pairwise sequence identity and phylogenetic analysis, the viruses were classified in the following genera: Ampelovirus (6), Bluvavirus (1), Closterovirus (7), Olivavirus (2) and Velarivirus (2), while four other viruses may represent four novel genera within the family. Other significant findings of the study include: (i) the identification of a 3’→5’ exonuclease-like protein in ampeloviruses and olivaviruses, (ii) the identification of an ampelovirus that encodes a polyprotein containing an RNA-dependent RNA polymerase motif without employing a + 1 ribosomal frameshift, (iii) the identification of a virus with the largest known genome among closterovirids, and (iv) the identification of a monopartite crini-like virus in Musa hosts potentially representing a novel genus. Besides, expanding the known closterovirid diversity by 0.25-fold, this study provides a base for future research aimed at understanding the biology and distribution of the identified novel viruses.

Influenza A virus (IAV) remains a persistent threat to global pandemics. Although previous studies have profiled circular RNA (circRNA) expressions following IAV infection, none have been conducted in human primary cells. Here, we used CIRIquant to analyse circRNA expression in RNA-seq datasets from H1N1 IAV-infected human tracheobronchial epithelial (HTBE) cells and validated selected circRNAs in A549-PB1 cells. We identified 10, 6, 73, 20, and 41 differentially expressed (DE) circRNAs at 3, 6, 12, 18, and 24 hours post infection (hpi), respectively. Notably, nine circRNAs were commonly upregulated at 12, 18 and 24 hpi timepoints. Functional enrichment analysis revealed that the parental genes of DE-circRNAs and the circRNA-targeted genes were associated with antiviral immune response and viral infection. In A549-PB1 cells infected with H1N1, we validated the circular nature and full-length of two circRNAs from DDX58 (circDDX58/9 and /11) and one from PML (circPML) using RNase R digestion, and circRNA-rolling circle amplification. RT-qPCR confirm their upregulation upon H1N1 infection, corroborating our bioinformatics results in HTBE cells. Moreover, these circRNAs were also induced by Vesicular Stomatitis Virus and Sendai Virus, suggesting a potential common molecular response mechanism for virus infections. circPML and circDDX58/9 were predicted to regulate mRNA targets in a circRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network. Overall, this study is the first to report circRNA expression profiles in H1N1-infected HTBE cells, with selected circRNAs validated in A549 cells, highlighting DE circRNAs potentially involved in host responses to IAV and warrant further functional investigation.

Kiwifruit (Actinidia spp.) is a widely popular fruit crop worldwide with significant economic value. From kiwifruit leaves exhibiting symptoms of chlorosis and mosaic in Shaanxi Province of China, a novel tymovirus tentatively named “Actinidia tymovirus 1” (AcTmV1) was identified by high-throughput sequencing, and its complete genome sequence was determined by RT-PCR and RACE technologies. The genome of AcTmV1 with a length of 6,155 nucleotides (nt) contains three open reading frames (ORFs) encoding movement protein (MP) of 610 amino acids (aa), replicase polyprotein (RP) of 1,782 aa and coat protein (CP) of 187 aa, exhibiting typical tymovirus-like organization. The AcTmV1 genome shares the highest nt sequence identity of 64.5% to that of Valeriana jatamansi tymovirus 1 (VaJV1) (GenBank No. OQ730267), and CP shares the highest aa sequence identity of 55.1% to that of Kennedya yellow mosaic virus (KYMV) (GenBank No. D00637). Phylogenetic analyses based on both genome nt and CP aa sequences confirmed that AcTmV1 is most closely related to VaJV1. Therefore, it is proposed that AcTmV1 represents a new member of the genus Tymovirus.

A novel ampelovirus, named as “plumeria ampelovirus 1” (PluAV1), was identified in plumeria (Plumeria spp.) through high-throughput sequencing. The PluAV1 genome was Sanger-sequenced independently, revealing a complete genome of 14,044 nucleotides and encoding 10 open reading frames. The amino acid sequences of the taxonomically informative gene products (RdRP, HSP70h, CP) of PluAV1 diverged from those of other ampeloviruses by over 25%, and maximum-likelihood phylogenetic analysis of these proteins revealed that PluAV1 belongs to the ampelovirus subgroup II. Two distinct PluAV1 phylogroups were identified underscoring the divergent nature of its natural populations. The species name Ampelovirus plumeria is proposed for PluAV1.

Avian infectious bronchitis virus (IBV) remains a persistent threat to poultry health and production, particularly in Pakistan, where frequent outbreaks occur despite routine vaccination. To investigate suspected vaccine breakthrough events, one hundred clinical samples (oropharyngeal/tracheal swabs and kidney, lung, and liver tissues) were collected between January and May 2025 from ten commercial chicken farms experiencing IBV-like outbreaks. Postmortem findings revealed classic IBV-associated lesions, including hemorrhagic tracheitis, severe airsacculitis, nephritis with urate deposits, and fluid-filled abdominal cysts in layer birds. Nested RT-PCR confirmed IBV RNA in 26% of samples (26/100), representing 70% of the investigated farms (7/10). Phylogenetic characterization of three representative S1 gene sequences (GenBank PV818074–PV818076) demonstrated clustering within the GI-1 lineage, showing 99.7–100% nucleotide identity with Massachusetts-type vaccine strains (H120, H52, Ma5, M41). The detection of such highly conserved vaccine-like sequences in recently vaccinated flocks suggests that current outbreaks are more likely associated with re-isolation, persistence, or circulation of vaccine-derived strains rather than novel divergent field variants. These findings highlight the potential role of vaccine-related viruses in field outbreaks, emphasize the need for incorporating vaccination history into molecular surveillance, and call for periodic reassessment of vaccination programs to maintain protective efficacy. Overall, this study underscores the importance of continuous genomic monitoring to better understand IBV evolution under vaccine pressure and to support evidence-based strategies for improving disease control and ensuring poultry industry sustainability.

Mycoplasma ovipneumoniae (MO) and Ovine parainfluenza virus type 3 (OPIV3) are significant pathogens implicated in ovine respiratory diseases, which impose substantial threats to extensive sheep farming. However, no commercial bivalent vaccines targeting both pathogens are currently available. In this study, we constructed a recombinant live-attenuated OPIV3 using Red/ET recombination, inserting MO adhesion protein genes (P60, P113) between the N and P genes of the OPIV3 genome. The recombinant candidate rOPIV3-MO was successfully generated and inhibited growth kinetics similar to those of the parental OPIV3 TJ2022 strain. Immunization trials in sheep indicated that rOPIV3-MO displayed a favorable safety profile. Both rOPIV3-MO and OPIV3 TJ2022 inoculation induced specific and neutralizing antibodies, as well as T-cell receptor (TCR) rearrangements.

Respiratory viruses, including influenza, SARS-CoV-2, and RSV, pose significant public health challenges in low-and-middle-income countries like Pakistan. This study, conducted from January-2023 to January-2024, investigated SARS-CoV-2, Influenza virus and RSV infections in individuals with respiratory symptoms and explored the genomic diversity of these viruses in Pakistan. This study analyzed 320 oropharyngeal/nasopharyngeal swabs, of which 57.1% (n = 183) tested positive for respiratory viruses using RT-PCR, including Influenza virus (59%; n = 108), SARS-CoV-2 (30%; n = 54), and RSV (11%; n = 21). Whole-genome sequencing was performed on 100 samples with Ct-value < 30, yielding 85 complete genomes: 48.24% (n = 41) were Influenza A (H3N2: 87.80%, n = 36; H1N1pdm09: 12.20%, n = 5), 45.88% (n = 39) were SARS-CoV-2 Omicron variants, and 5.88% (n = 5) were RSV-B. H3N2 sequences clustered mainly in clade 3 C.2a1b.2a.2a.3a.1 (94.4%, n = 34/36) with 99.32%–99.56% nucleotide identity to 2023 strains from Russia, USA, UK, and Pakistan, and 1.05%–1.87% divergence from the vaccine strain A/Thailand/8/2022. Key NA gene mutations included E50K, T3A in the signal peptide, and R150H, that have implications on antiviral resistance. H1N1 sequences, confined to clade 6B.1 A.5a.2a, showed high similarity (99.41%–100%) with 2022–2023 USA and Pakistan strains but increased divergence (1.44%–1.66%) from vaccine strain A/Wisconsin/588/2019, with significant mutations (K54Q, D94N, E224A) at antigenic sites., that can potentially enhance viral fitness. The SARS-CoV-2 Omicron subvariants included GW.5, XBB.1.22, and FL, closely resembling sequences from England, Singapore, and Canada. All RSV-B sequences belonged to the GB5.0.5a G_clade, with 97.8% to 99.5% similarity to strains from England, Australia, Bangladesh, Senegal, and the USA. Notably, RSV-B exhibited a deletion (L250 to I268) in the G protein and key mutations in the F protein (S190N, S211N, and L173del), which could affect therapeutic and vaccine efficacy. These findings highlight the need for integrated surveillance of these viruses to inform public health responses.

Infectious diseases in birds represent a significant threat to poultry economies, wild bird biodiversity, and public health, underscoring the importance of surveillance within a One Health framework. Synanthropic birds, which live in close proximity to humans and domestic animals, can act as crucial bridge hosts for viral transmission between wild and domestic populations. This study aimed to assess the prevalence and diversity of four key viral families—Orthomyxoviridae, Paramyxoviridae, Coronaviridae, and Astroviridae—in synanthropic birds from the south of Western Siberia, an important convergence zone of major migratory flyways for many bird species. Using molecular detection methods, we identified avian coronaviruses (ACoV) and avastroviruses (AAstV), but found no evidence of avian influenza virus (AIV) or avian paramyxoviruses (APMV). Overall, 3.8% of birds tested positive for at least one of the studied viruses, with ACoV detected in 1.4% and AAstV in 2.4% of samples. Phylogenetic analysis revealed that the detected coronaviruses belong to the genus Deltacoronavirus and form a distinct clade with a previously identified virus from North Siberia, suggesting a stable, regional corvid-associated lineage. The detected astroviruses were highly diverse, falling within a broad group of unclassified passerine-associated avastroviruses with phylogenetic links to viruses from Kazakhstan and China, reflecting the region's role as a migratory crossroads. The absence of AIV and APMV may reflect low prevalence at the time of sampling or host-specific factors like low susceptibility or immunocompetence that suppress viral replication. These findings highlight that synanthropic birds in this key ecological region harbor novel and diverse viruses and represent important, though often overlooked, subjects for expanding our understanding of viral diversity in surveillance programs.

Bacillus subtilis is a key starter culture in food fermentation, but phage contamination threatens production stability. As fermentation processes scale up, the risk of phage contamination rises significantly, driving the need for fundamental research on phage-host interactions to develop targeted mitigation strategies. In this study, we isolated and characterized a novel lytic phage, vB_Bsu_W1188, which efficiently lyses B. subtilis WB800. Transmission electron microscopy revealed a short-tailed morphology, while stability tests demonstrated remarkable tolerance to pH 3-12, temperatures of 4-80℃, and even 90℃ for 30 minutes. Genomic and phylogenetic analysis classified it within the genus Beecentumtrevirus, with no virulence or antibiotic resistance genes detected. Through resistance mutant screening and functional validation, we identified that wall teichoic acid (WTA) glycosylation, mediated by the host tagE and galU genes, serves as the critical receptor for phage recognition. Although phage-resistant mutants exhibited fitness costs (e.g., delayed growth and impaired biofilm formation), their mCherry protein expression capacity remained unaffected. This study not only highlights the potential of vB_Bsu_W1188 as a biocontrol agent but, more importantly, elucidates the molecular basis of phage resistance, providing a theoretical foundation and technical support for engineering industrial phage-resistant strains.