Search Results (185)

Avian influenza A viruses (AIVs) pose a significant pandemic threat due to their cross-species transmission potential. However, AIV surveillance at the critical “migratory birds–poultry-exposed population” interface remains limited. Between 2021 and 2024, we implemented a prospective One Health surveillance program around Nansi Lake, monitoring AIVs in migratory birds, poultry, and environmental samples, as well as serological investigations against representative AIVs among migratory birds or poultry-exposed subjects. AIVs were detected in 2.1% (30/1417) of migratory bird samples and 10.2% (100/978) of poultry samples. Among these, we identified ten highly pathogenic avian influenza (HPAI) H5 subtype viruses, one HPAI H7N9 virus, and five low pathogenic avian influenza (LPAI) H9N2 viruses. Phylogenetic analysis revealed evidence of frequent genomic reassortment events involving H5 subtype viruses among migratory birds, poultry, and humans. Serological investigation also suggested that both migratory birds and the poultry-exposed population had a higher risk of getting AIV infection than the general control population, especially against the H9N2 virus. Our study emphasizes the importance of strengthening continuous prospective surveillance of AIVs among migratory birds, poultry, and their exposed individuals to prevent and control potential outbreaks. Full article

In Brazil, molecular surveillance expanded after Rotarix™ vaccine introduction, alongside G2P[4] dominance. The G2P[6] genotype, despite sharing the same DS-1-like constellation as G2P[4] strains, remains rare. This retrospective study analyzed eight Brazilian G2P[6] strains (2012–2014) through RT-PCR and 11-segments sequencing, followed by phylogenetic analysis. Two distinct groups were identified: 2012–2013 strains (six) carried a DS-1-like backbone with the rare NSP4 E6 genotype, while 2014 strains (two) exhibited the classical DS-1-like constellation with E2. Phylogenetic analysis confirmed the two main clusters: 2012–2013 strains related to classical G2P[4] and uncommon global genotypes, and 2014 strains resembling emerging DS-1-like G1/G3/G8P[8] reassortants. The 2012–2013 strains clustered within G2-VP7 Lineage IVa, while the 2014 strains belonged to Lineage V, reflecting the global distribution of these variants. All VP4 genes were classified within the P[6]-Ia lineage, with phylogenetic analyses suggesting separate introductions from Asia and Africa. The E6 NSP4 gene segment identified in these strains has an undetermined origin and was not previously associated with G2P[6] strains in Brazil. Despite similarities to G2P[4], G2P[6] strains remain rare, with no genomic features explaining their limited spread. Phylogenetic data indicate multiple reassortment events and international viral exchange, highlighting Brazil’s role in RVA diversity. Ongoing full-genome surveillance is crucial to track rare variants and assess their public health relevance. Full article

Group A rotavirus (RVA) is a leading causative agent of diarrhea in both young animals and humans. In China, multiple genotypes are commonly found within the bovine population. In this study, we investigated 1917 fecal samples from calves with diarrhea between 2022 and 2025, with 695 testing positive for RVA, yielding an overall detection rate of 36.25%. The highest positivity rate was observed in Hohhot (38.98%), and annual detection rates ranged from 26.75% in 2022 to 42.22% in 2025. A bovine rotavirus (BRV) strain, designated 0205HG, was successfully isolated from a fecal sample of a newborn calf. Its presence was confirmed through cytopathic effects (CPEs), the indirect immunofluorescence assay (IFA), electron microscopy (EM), and high-throughput sequencing. Genomic characterization identified the strain as having the G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3 genotype constellation. The structural proteins VP2 and VP7, along with nonstructural genes NSP1–NSP4, shared high sequence identity with Chinese bovine strains, whereas VP1, VP4, and NSP5 clustered more closely with human rotaviruses, and VP3 was related to feline strains. These findings highlight the genetic diversity and interspecies reassortment of BRVs in China, underlining the importance of continued surveillance and evolutionary analysis. Full article

While a global downward trend in rotavirus diarrhea cases has been observed following vaccine introduction, reassortment, genetic drift, and vaccine-escaping strains remain a concern, particularly in Sub-Saharan Africa. Here, we provide genomic insights into three equine-like G3P[8] rotavirus strains detected in Benin during the post-vaccine era. Whole-genome sequencing was performed using the Illumina MiSeq platform, and genomic analysis was conducted using bioinformatics tools. The G3 of the study strains clustered within the recently described lineage IX, alongside the human-derived equine-like strain D388. The P[8] is grouped within the lineage III, along with cognate strains from the GenBank database. Both the structural and non-structural gene segments of these study strains exhibited genetic diversity, highlighting the ongoing evolution of circulating strains. Notably, we identified a novel NSP2 lineage, designated NSP2-lineage VI. Amino acid comparisons of the G3 gene showed two conservative substitutions at positions 156 (A156V) and 260 (I260V) and one radical substitution at position 250 (K250E) relative to the prototype equine-like strain D388, the equine strain Erv105, and other non-equine-like strains. In the P[8] gene, three conservative (N195G, N195D, N113D) and one radical (D133N) substitutions were observed when compared with vaccine strains Rotarix and RotaTeq. These findings suggest continuous viral evolution, potentially driven by vaccine pressure. Ongoing genomic surveillance is essential to monitor genotype shifts as part of the efforts to evaluate the impact of emerging strains and to assess vaccine effectiveness in Sub-Saharan Africa. Full article

The Crimean–Congo hemorrhagic fever virus (CCHFV) is a single-stranded, segmented RNA virus belonging to the Nairoviridae family, and it is rapidly expanding across Africa, Asia, and southern Europe, probably favored by climate change and livestock trade. Its fatality rate in humans reaches up to 40%, and there is currently no specific treatment or vaccine available. Therefore, the development of therapies against CCHFV is essential, and their design requires understanding of the molecular evolution and genetic distribution of the virus. Motivated by these concerns, we present a comprehensive review of the molecular evolution, genetic characterization, and phylogeography of CCHFV, and we discuss their potential implications for therapeutic design. Specifically, we describe the virus’s capacity to increase its genetic diversity through numerous mutations, recombination events, and genomic reassortments, which affect fundamental viral functions such as RNA binding, host–virus interactions, viral entry, and polymerase activity. We also assess the presence of temporal heterogeneous rates of evolution and molecular adaptation among CCHFV coding regions, where purifying selection is generally predominant but diversifying selection is observed in molecular regions associated with host adaptation and transmission. We emphasize the importance of understanding the complex molecular evolution of CCHFV for the rational design of therapies and highlight the need for efforts in surveillance, evolutionary prediction, and therapeutic development. Full article

Highly pathogenic avian influenza (HPAI) H5N1, particularly clade 2.3.4.4b, has demonstrated an unprecedented capacity for cross-species transmission, with recent reports confirming its presence in dairy cattle in the United States of America (USA) in 2024. This unexpected spillover challenges traditional understanding of the virus’s host range and raises serious public health and veterinary concerns. Infected cattle presented with clinical signs such as decreased milk production, thickened or discolored milk, respiratory issues, and lethargy. Pathological findings revealed inflammation of the mammary glands and the detection of a virus in nasal secretions and raw milk, suggesting a potential for both intra- and interspecies transmission. While the current risk of human-to-human transmission remains low, the detection of H5N1 in a human exposed to infected cattle highlights the need for heightened surveillance and protective measures. Moreover, the presence of infectious viruses in the food chain, particularly in unpasteurized milk, introduces a new dimension of zoonotic risk. This review synthesizes emerging evidence on the epidemiology, pathology, diagnostic findings, and zoonotic implications of HPAI H5N1 infection in cattle. It also highlights the importance of genomic surveillance, intersectoral collaboration, and One Health approaches in managing this evolving threat. As the virus continues to circulate and adapt across diverse hosts, including wild birds, domestic poultry, and now mammals, the potential for reassortment and emergence of novel strains remains a significant concern. Immediate actions to strengthen biosecurity, monitor viral evolution, and protect both animal and human populations are critical to mitigate the global risk posed by this expanding panzootic. Full article

Influenza A virus (IAV) is a highly diverse pathogen with genetic variability primarily driven by mutation and reassortment. Using next-generation sequencing (NGS), we characterised defective viral genomes (DVGs) generated during the serial passaging of influenza A/Puerto Rico/8/1934 (H1N1) virus in embryonated chicken eggs. Deletions were the most abundant DVG type, predominantly accumulating in the polymerase-encoding segments. Notably, we identified and validated a novel class of multisegment DVGs arising from intersegment recombination events, providing evidence that the IAV RNA polymerase can detach from one genomic template and resume synthesis on another. Multisegment recombination primarily involved segments 1–3 but also occurred between other segment pairings. In specific lineages, certain multisegment DVGs reached high frequencies and persisted through multiple passages, suggesting they are not transient by-products of recombination but may possess features that support stable maintenance. Furthermore, multisegment DVGs were shown to be encapsidated within virions, similar to deletion DVGs. The observation of recombination between segments with limited sequence homology underscores the potential for complex recombination to expand IAV genetic diversity. These findings suggest recombination-driven DVGs represent a previously underappreciated mechanism in influenza virus evolution. Full article

The Oropouche virus (OROV) is an arbovirus (Peribunyaviridae: Orthobunyavirus) that traditionally causes febrile outbreaks in Latin America’s Amazon region. Previously, OROV was not associated with severe pregnancy outcomes. During the 2022–2024 outbreak in Brazil, OROV expanded geographically, revealing links to adverse pregnancy outcomes. This study describes six cases with varied fetal outcomes, including miscarriage, antepartum, intrauterine fetal demise (IFD), and normal development, correlating with maternal symptoms but not symptom severity. Vertical transmission was confirmed by detecting OROV through RT-qPCR, ELISA, and immunohistochemistry in fetal tissues. Genome sequencing from an IFD case identified a novel reassortment pattern reported in the 2022–2024 outbreak. Severe encephalomalacia, meningoencephalitis, vascular compromise, and multi-organ damage were evident, underscoring the significant risk OROV poses to fetal development and emphasizing the need for further investigation. Full article

The H12 subtypes of avian influenza viruses (AIVs) are globally prevalent in wild birds, occasionally spilling over into poultry. In this study, we isolated an H12N8 virus from ducks in a live poultry market. Full genomic analysis revealed that the virus bears a single basic amino acid in the cleavage site of the hemagglutinin gene. Phylogenetic analysis revealed that the eight gene segments of the H12N8 virus belong to the Eurasian lineage and the HA gene was clustered with wild bird-originated H12 viruses, with its NP gene showing the highest nucleotide similarity to 2013-like H7N9 viruses. The H12N8 virus replicated effectively in both mammalian and avian cells without prior adaptation. Moreover, the H12N8 virus could infect and replicate in the upper respiratory tract of BALB/c mice without prior adaptation. The H12N8 virus replicated and transmitted inefficiently in both ducks and chickens and hardly triggered high hemagglutination inhibition (HI) antibody titers in the inoculated and contact animals. These results suggest that the wild bird-origin H12N8 virus has reassorted with viruses circulating in domestic poultry, but it inefficiently replicates and transmits in avian hosts. Our findings demonstrate that H12N8 AIV has emerged in domestic poultry, emphasizing the importance of active surveillance of AIVs in both wild and domestic birds. Full article

Rotavirus alphagastroenteritidis is the leading cause of acute gastroenteritis worldwide in young humans and animals. In 2023–2024, a relatively high rotavirus detection rate (34.5%) was detected in children with diarrhea in Caracas. All rotavirus strains were typed as P[8], using a multiplex RT-PCR assay, while the G-type was not identified. This unusual pattern, not previously observed in Venezuela, prompted the VP7 gene sequencing of nineteen strains, which displayed a high sequence identity (99.3–100%) compatible with the G3 genotype. These strains clustered into a well-supported lineage IX encompassing human reassortants of equine-like G3P[8] strains described elsewhere, showing a very close genetic relationship (99.0–99.9%). Old G3 rotavirus isolates obtained from diarrheic samples in the past were included in the analysis and grouped into lineage I together with ancestral reference G3 strains. The novel G3P[8]s carry amino acid changes in VP7-neutralizing epitopes, compared with the RotaTeq-WI78-8-vaccine strain. Full genome sequencing of a representative strain revealed a genotype constellation including an equine-like G3P[8] in a DS-1-like backbone (I2–R2–C2–M2–A2–N2–T2–E2–H2), confirming the role of animal strains as a source of diversification, and the importance of unceasingly revising molecular typing strategies and vaccine efficacy to guarantee their success. Full article

Rift Valley fever phlebovirus (RVFV) is a zoonotic mosquito-borne pathogen endemic to sub-Saharan Africa and the Arabian Peninsula which causes Rift Valley fever in ruminant livestock and humans. Co-infection with divergent viral strains can produce reassortment among the L, S, and M segments of the RVFV genome. Reassortment events can produce novel genotypes with altered virulence, transmission dynamics, and/or mosquito host range. This can have severe implications in areas where RVFV is endemic and convolutes our ability to anticipate transmission and circulation in novel geographic regions. Previously, we evaluated the frequency of RVFV reassortment in a susceptible ruminant host and observed low rates of reassortment (0–1.7%). Here, we tested the hypothesis that reassortment occurs predominantly in the mosquito using a highly permissive vector, Culex tarsalis. Cells derived from Cx. tarsalis or adult mosquitoes were co-infected with either two virulent (Kenya-128B-15 and SA01-1322) or a virulent and attenuated (Kenya-128B-15 and MP-12) strain of RVFV. Our results showed approximately 2% of virus genotypes isolated from co-infected Cx. tarsalis-derived cells were reassortant. Co-infected mosquitoes infected via infectious bloodmeal resulted in a higher percentage of reassortant virus (2–60%) isolated from midgut and salivary tissues at 14 days post-infection. The percentage of reassortant genotypes isolated from the midguts of mosquitoes co-infected with Kenya-128B-15 and SA01-1322 was similar to that of mosquitoes co-infected with Kenya-128B-15 and MP-12- strains (60 vs. 47%). However, only 2% of virus isolated from the salivary glands of Kenya-128B-15 and SA01-1322 co-infected mosquitoes represented reassortant genotypes. This was contrasted by 54% reassortment in the salivary glands of mosquitoes co-infected with Kenya-128B-15 and MP-12 strains. Furthermore, we observed preferential inclusion of genomic segments from the three parental strains among the reassorted viruses. Replication curves of select reassorted genotypes were significantly higher in Vero cells but not in Culex—derived cells. These data imply that mosquitoes play a crucial role in the reassortment of RVFV and potentially contribute to driving evolution of the virus. Full article

In 2020, severe diarrhea occurred in four-month-old fattening pigs from nine farms in Shandong Province, China. Fecal samples were collected from diseased pigs and tested by PCR for the presence of mammalian orthoreovirus (MRV), porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), porcine rotavirus A (PoRVA), transmissible gastroenteritis virus (TGEV), porcine kobuvirus (PKV), and pseudorabies virus (PRV). The viral RNA of MRV and PEDV was detected in the fecal samples. The genome sequences of MRV and PEDV were successfully amplified from the same fecal sample. Genomic and phylogenetic analysis showed that the MRV isolate named MRV2-SD/2020 belongs to serotype 2 MRV (MRV2) and may originate from the reassortment of human and porcine MRVs. Compared with other MRV2 strains, there were four other unique amino acid mutations (L274I, F302L, V347I, and T440M) in the receptor binding region. For the PEDV isolate named PEDV-SD/2020, the nearly complete genome was amplified from the positive fecal samples. Phylogenetic analysis showed that it was classified into the G2a genotype. Compared with CV777 and other PEDV variant strains, its spike (S) protein exhibited two unique mutations (S663T and L966M). This study first reports the co-infection of PEDV and MRV2 in the pigs and provides a new direction for the prevention and control of the diarrhea diseases. Full article

Increased evidence suggests that cattle are the primary host of Influenza D virus (IDV) and may contribute to respiratory disease in this species. The aim of this study was to detect and characterise IDV in the Swedish cattle population using archived respiratory samples. This retrospective study comprised a collection of a total 1763 samples collected between 1 January 2021 and 30 June 2024. The samples were screened for IDV and other respiratory pathogens using real-time reverse transcription quantitative PCR (rRT-qPCR). Fifty-one IDV-positive samples were identified, with a mean cycle threshold (Ct) value of 27 (range: 15–37). Individual samples with a Ct value of <30 for IDV RNA were further analysed by deep sequencing. Phylogenetic analysis was performed by the maximum likelihood estimation method on the whole IDV genome sequence from 16 samples. The IDV strains collected in 2021 (n = 7) belonged to the D/OK clade, whereas samples from 2023 (n = 4) and 2024 (n = 5) consisted of reassortants between the D/OK and D/660 clades, for the PB2 gene. This study reports the first detection of IDV in Swedish cattle and the circulation of D/OK and reassortant D/OK-D/660 in this population. Full article

Infectious bursal disease (IBD) is among the most impactful immunosuppressive diseases of poultry. Its agent, infectious bursal disease virus (IBDV), is prone to both mutation and reassortment, resulting in a remarkable variability. Traditionally, IBDV characterization relies on antigenicity and pathogenicity assessment, but multiple phylogenetic classifications have been recently proposed, whose implementation in molecular surveys helps generating informative and standardized epidemiological data. In the present study, the Algerian IBDV scenario was assessed based on the novel classification guidelines by sequencing portions of both genome segments. Seventy pools of bursal samples were collected in 2022–2023 in 11 districts of Northern Algeria, mostly from broiler flocks. Out of 55 (78.6%) positive flocks, 40 (57.1%) were infected by field strains, which were characterized as very virulent strains (genotype A3B2) and phylogenetically related to previously reported Algerian strains. Significant differences in the percentage of field infections were observed between vaccinated (25/52, 46.2%) and unvaccinated (14/17, 82.3%) groups, and also between birds immunized with live intermediate (13/20, 65.0%) and intermediate plus (10/28, 35.7%) vaccines. Nonetheless, the number of field strain detections suggests a high infectious pressure and the inadequacy of current vaccination efforts, demanding a reevaluation of control measures coupled with attentive monitoring activities. Full article

Avian influenza subtype H5N1 has caused outbreaks worldwide since 1996, with the emergence of the Guandong lineage in China. The current clade 2.3.4.4b has evolved from this lineage, with increased virulence and mass mortality events in birds and mammals. The objective of this study was the analysis of 17 viral genomes of H5N1 avian influenza isolated in Venezuela during the 2022–2023 outbreak. The eight viral genomic segments were amplified using universal primers and sequenced via next-generation sequencing. The sequences were analyzed to confirm the H5 hemagglutinin clade, identify possible genetic reassortments, and perform a phylogenetic and docking analysis of the viral isolates. The viruses found in Venezuela belonged, as expected, to clade 2.3.4.4b and formed a monophyletic clade with North American influenza viruses, with no evidence of further reassortment. The introduction of the virus in South America is associated with bird migration through the Atlantic (Venezuela), Atlantic/Mississippi (Choco, Colombia), and Pacific migratory flyways, with the emergence of several viral lineages. Several mutations were found in all segments of the genome, although none of the key mutations was involved in mammalian adaptation. Moreover, in silico structural analysis suggests, as expected, that the viral hemagglutinin maintained a predilection for avian α2,3-linked sialic acid. The unprecedented pathogenic outbreak of avian influenza disease in South America was associated with the circulation of three different lineages, which maintain a lower affinity for the mammalian receptor. Full article