Search Results (404)

Avian orthoreovirus (ARV) has re-emerged as one of the most important viral pathogens affecting modern poultry production worldwide. In China, the epidemiological landscape of ARV has undergone a substantial transformation over the past decade, characterized by increasing genotypic diversity, frequent genome reassortment, an expanding host range, and recurrent vaccine-breakthrough outbreaks. Growing evidence indicates that contemporary ARV populations evolve within a dynamic multispecies transmission network shaped by intensive poultry production, host adaptation, and vaccine-associated selective pressures. Recent molecular studies have revealed extensive genetic heterogeneity among circulating strains and highlighted the limitations of conventional σC-based classification systems for accurately describing viral evolution, pathogenicity, and antigenic diversity. Whole-genome analyses further demonstrate that reassortment among chicken-origin, duck-origin, and goose-origin orthoreoviruses plays a pivotal role in generating novel viral variants with altered biological properties. In parallel, accumulating evidence suggests that ARV exerts broad immunomodulatory effects through the disruption of innate antiviral signaling, impairment of lymphoid organ function, interference with vaccine responsiveness, and the enhancement of susceptibility to secondary infections. These findings indicate that ARV should be regarded not only as an arthrotropic pathogen but also as an important immunopathological agent influencing flock health and productivity. This review summarizes current knowledge of ARV in China, with an emphasis on molecular epidemiology, genomic evolution, reassortment mechanisms, transmission ecology, immune interference, vaccine escape, and integrated prevention strategies. Particular attention is given to the increasing importance of whole-genome surveillance, phylodynamic analysis, and multispecies epidemiological monitoring for understanding contemporary ARV evolution. Future perspectives involving structural vaccinology, precision immunization, metagenomics-assisted surveillance, and predictive evolutionary modeling are also discussed. Collectively, sustainable ARV control will likely require genome-informed and adaptive prevention frameworks integrating virology, immunology, epidemiology, and precision poultry management. Full article

Porcine rotavirus (PoRV) has emerged as a primary pathogen causing viral diarrhea in pigs, resulting in significant economic losses. This study was conducted to systematically characterize the epidemiology and genotypic characteristics of PoRV in Guangxi, China. A total of 870 diarrheic pig samples were collected from Guangxi during 2020–2025. The qRT-PCR results indicated an overall PoRV-positive rate of 41.38% (360/870), and the annual positivity rate showed an overall upward trend. The genetic evolutionary analysis of the VP4, VP6, and VP7 genes indicated that PoRV predominantly belonged to the A group and the predominant P genotype observed was P[13] (76.83%), while the G genotypes were G5 (36.56%) and G9 (33.33%). The most prevalent genotype combinations were G9P[13]I5 and G5P[13]I5. CH-GXGL-PoRV-3151-2021, a PoRV strain isolated from positive samples, was identified via RT-PCR, qRT-PCR, whole-genome sequencing, and IFA. This strain was assigned the 11-segment genotype constellation G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 based on whole-genome sequencing. NSP1 and NSP2 showed high similarity to human rotavirus strains, whereas VP1–VP4, VP6, VP7, and NSP3–NSP5 showed high similarity to porcine rotavirus strains. This study indicates the widespread circulation of PoRV in Guangxi, with multiple G genotypes, including G9, G5, G4, G3, G2, and G26, being detected. The isolated G9P[23]I5 strain exhibits the same genotype as the strains that have become increasingly prevalent in recent years. This strain may represent a possible reassortant between porcine and human rotaviruses. This study offers significant insights into the epidemiology of PoRV and the prevalent genotypes in Guangxi, thereby supporting the development of targeted prevention strategies and novel vaccines. Full article

Highly pathogenic avian influenza (HPAI) A(H5N1) viruses of clade 2.3.4.4b have recently spread across the Americas, prompting intensified surveillance efforts in Brazil aimed at early detection in wild birds. As part of these efforts, we identified a low pathogenic avian influenza A(H11N2) virus in a white-rumped sandpiper (Calidris fuscicollis) sampled at Lagoa do Peixe National Park (PNLP) in southern Brazil. Whole-genome sequencing revealed that seven of the eight gene segments shared high nucleotide similarity (approximately 98.8%) with viruses previously detected in shorebirds from Delaware Bay, North America. In contrast, the PB1 segment showed high nucleotide similarity (approximately 99%) to the PB1 lineage associated with clade 2.3.4.4b A(H5N1) genotype B3.2 viruses circulating in the Americas. Phylogenetic, nucleotide identity, and molecular clock analyses indicated that this lineage shares a recent common ancestor with North American LPAI viruses and was subsequently detected in distinct viral genetic backgrounds. Although no HPAI virus was identified in this study, the presence of a PB1 segment related to H5N1-associated lineages suggests that genetic components linked to these viruses were circulating among low pathogenic avian influenza viruses in South America. These findings highlight the importance of continued surveillance in migratory bird populations to improve understanding of avian influenza virus diversity and support epidemiological monitoring. Full article

H3N2 subtype avian influenza virus (AIV) is prevalent in poultry and wild birds and typically causes asymptomatic or mild respiratory infections. However, genetic reassortment between H3N2 and other AIV subtypes generates novel strains capable of crossing the species barrier, posing a threat to both poultry and public health. In this study, nine H3N2 AIVs were isolated from ducks in live poultry markets (LPMs) in Guangxi, southern China, during 2022–2024. Phylogenetic analysis revealed that all eight gene segments of the nine isolates were clustered within the Eurasian lineage, with internal genes derived from multiple subtypes, including H1, H2, H3, H4, H5, H6, H7, and H9. These findings indicate complex gene reassortment of H3N2 AIVs in Guangxi. Importantly, the PB2 genes of certain isolates were closely related to those of highly pathogenic H5 subtype viruses, suggesting that H3N2 AIVs may contribute internal genes to H5 viruses. Three representative isolates (LZD44, NND98, and NND100) were assessed for pathogenicity in SPF chickens and mice. All three strains successfully replicated in the respiratory tissues of both species. Notably, the LZD44 virus, which harbored the mammalian-adaptive mutations PB2-MVV and NP-I353V, presented significantly higher virulence in chickens and mice than the other two strains. These results demonstrate that H3N2 subtype AIVs are capable of replicating in certain tissues of chickens and mice without prior adaptation, underscoring a potential risk for cross-species transmission. Consequently, sustained surveillance of H3N2 subtype AIVs is essential to prevent the spillover of novel recombinants into the human population. Full article

Rotavirus A (RVA) G3P[3] genotype is widely reported in dogs and less frequently in cats, with only sporadic human cases worldwide. All reported human infections have occurred in children, suggesting increased susceptibility likely linked to close contact with pets and age-related hygiene practices. The identification of a novel genotype constellation in Brazilian canine G3P[3] strains in 2017 prompted full-genotype characterization of the historical RVA/Human-wt/BRA/IAL-R451/2011/G3P[3] strain, previously sequenced only for VP7 and VP4, to define its genomic constellation and relatedness to canine strains. All 11 segments were analyzed by RT-PCR, sequencing and phylogenetics. The rare genotype–lineage constellation G3.III-P[3]-I2.XX-R3.II-C2.V-M3.II-A9-N2.XXIV-T3.II-E3.II-H6.I, shared with Brazilian canine strains, was identified, supporting a potential common origin. RVA/Human-wt/BRA/IAL-R451/2011/G3P[3] strain showed high genetic similarity (93.2–99%) with canine, feline and canine/feline-like human strains worldwide, with six genes (VP1, VP6 and NSP2–NSP5) closely related to Brazilian dog isolates (97.6–99%), indicating its canine origin. NSP2 clustered with strains from domestic (bovine), synanthropic (rat) and human hosts, while VP7 and VP4 were associated with wildlife (bat; raccoon dog) and environmental (sewage; river water) strains, supporting interhost reassortment and highlighting aquatic environments as reservoirs for interspecies transmission. Identification of new lineages (VP1, VP3 and NSP2) within the AU-1-like backbone reflects its underexplored diversity. This novel constellation likely circulated in dogs and may spill over to humans via close contact, reinforcing a One Health approach to understand RVA zoonotic risk, especially in hotspot regions like Brazil. Full article

During 2022–2024, a highly pathogenic avian influenza virus (HPAIV) H5N1 strain, designated A/Seagull/Hebei/qhd6/2024 (H5N1), was isolated from migratory birds in Beidaihe National Wetland Park, North China. Phylogenetic analyses revealed that its hemagglutinin (HA) gene belongs to the 2.3.4.4b clade, while the neuraminidase (NA) gene and internal genes clustered with strains originating from multiple continents, consistent with a transcontinental reassortment event. The virus also exhibited 90.1–98.1% nucleotide homology with human-derived H5N1 isolates. Molecular characterization identified key virulence-associated mutations, including the classic HPAIV HA cleavage site, HA-T160A (associated with enhanced human receptor-binding capacity), and NA-I117T (potentially linked to drug resistance). BALB/c mouse infection experiments confirmed systemic replication and high pathogenicity of strain qhd6, with a 50% lethal dose (LD50) of 0.95 log₁₀EID₅₀/mL. Antigenic analysis revealed good cross-reactivity with the widely used H5-Re14 vaccine strain. This study reports the identification, in Beidaihe National Wetland Park, of an HPAIV H5N1 strain whose genetic characteristics suggest intercontinental reassortment and indicate cross-species transmission risk. It clarifies the genetic characteristics and pathogenicity of this strain, providing an important theoretical and practical basis for precise surveillance, risk early warning, and comprehensive prevention and control of AIV at migratory bird stopover sites in North China. Full article

Pigs play a key role in the ecology of influenza A viruses (IAVs), particularly in avian influenza (AI)-endemic regions where co-circulation of viruses from different hosts increases reassortment risk. Between September 2023 and August 2024, we surveyed pigs from Lebanon and Egypt to study IAV ecology in AI-endemic countries. Nasal swabs and sera were collected and tested using real-time RT-PCR and hemagglutination inhibition assays against avian, swine, and human seasonal IAVs. Molecular analyses identified IAV-infections in both countries, including human H1 and avian H5 subtypes, which may reflect potential cross-species transmission from humans and birds. Serologic analyses revealed prior exposure to avian, swine, and human IAVs. Avian virus seropositivity reached 4.6% (H5N1) and 15.2% (H9N2) in Egypt and 8.6% (H5N1) and 4.3% (H9N2) in Lebanon. Antibodies against human H1N1 and H3N2 were prevalent in both countries. Serologic evidence exceeded molecular detection, indicating frequent past or transient infections not captured by PCR alone. Antibody responses were significantly associated with host-level factors such as housing type, age, shaping exposure risk. These findings demonstrate repeated multisource exposure of pigs to genetically distinct IAVs in AI–endemic countries, supporting the need for integrated virologic and serologic surveillance within a One Health framework. Full article

Highly pathogenic avian influenza (HPAI) H5N1 viruses of the goose/Guangdong (Gs/GD) lineage have driven a global panzootic since 2020, with clade 2.3.4.4b establishing sustained transmission in wild birds. In South America, early outbreaks were largely associated with the North American-derived B3.2 genotype, which showed limited diversification after its introduction. Here, we report the genomic characterization of eight H5N1 viruses detected in Uruguay during the reemergence of avian influenza in February–March 2026. Complete genomes were obtained from wild birds exhibiting neurological signs, predominantly Coscoroba coscoroba. All viruses belong to clade 2.3.4.4b but exhibit a reassortant genomic constellation distinct from B3.2. The HA, NA, and MP segments retain the Eurasian backbone, whereas internal genes derive from both South American and North American low-pathogenicity avian influenza lineages. PB2 variation distinguishes two closely related viral groups differing in PB2 origin, whereas the remaining genomic segments retain a shared background. Sequence variation in the neuraminidase gene reduced the sensitivity of a widely used N1-specific RT-qPCR assay, highlighting limitations of existing diagnostic tools during viral evolution. These findings confirm the presence of reassortant H5N1 viruses in Uruguay and, together with recent reports from Argentina and Brazil, support an emerging pattern of genomic diversification in southern South America. Full article

The H5N1 subtype of highly pathogenic avian influenza (HPAI) poses a major zoonotic threat due to its high fatality rate and capacity for cross species transmission. In early 2025, Argentina detected a novel triple reassortant A(H5N1) virus in Chaco Province, combining Eurasian, North American, and South American lineage segments. Genomic analyses of subsequent outbreaks in Buenos Aires and Entre Ríos confirmed persistence of this reassortant and additional HA substitutions (T204K, P251S) potentially linked to increased mammalian receptor affinity. Although PB2 sequences lacked canonical mammalian-adaptive markers (E627K, Q591K, D701N), all contained I292M, a mutation associated with human adaptation. Phylogenetic analyses revealed distinct genotypes and increasing divergence. These findings indicate ongoing viral evolution and adaptation within Argentina, emphasizing the urgent need for sustained genomic surveillance, timely data sharing, and integrated One Health strategies to mitigate zoonotic and socioeconomic risks associated with H5N1 spread in South America. Full article

The 2022 highly pathogenic avian influenza (HPAI) outbreak of H5N1 clade 2.3.4.4b was one of the major avian influenza outbreaks, leading to multiple spillover events infecting domestic and wild bird flocks, as well as mammals. The sustained spread was a result of viral circulation in wild birds across migratory flyways in North America. Pennsylvania has a significant poultry population that supports both retail and live bird markets. The state also features migratory bird stopovers on the Atlantic flyway, increasing exposure to HPAI infections. This study investigates clinical presentation and sequence data from H5N1 clade 2.3.4.4b viruses during the 2022 outbreak in Pennsylvania. Eight different H5N1 clade 2.3.4.4b genotypes were detected (A1, B1.1, B1.2, B1.3, B2.2, B3.3, B3.5, and one minor genotype) during the first year. The earliest detection was genotype A1, a fully Eurasian virus, in commercial poultry in April 2022. All other genotypes identified were reassortants of A1 with North American avian influenza gene segments (denoted with “B”). Genotype B3.3 was a rare genotype prior to the initial spillover into the live bird market system, but remained predominant among backyard flocks in Pennsylvania and surrounding states until September 2023. Genotype B3.3 has not been detected in migratory waterfowl since, suggesting the genotype has waned and is no longer in circulation. This study sheds light on the genotype diversity of H5N1 during the 2022 outbreak in Pennsylvania poultry, contributing to the understanding of virus evolution and its potential impacts. Full article

Bluetongue (BT) is an infectious, non-contagious, arthropod-borne viral disease of ruminants, and has a severe impact on livestock. It is caused by Bluetongue virus (BTV), a double-stranded (ds) RNA virus with a segmented genome (10 segments), belonging to the Seoreoviridae family, Orbivirus genus. Over the last 25 years, Europe has suffered multiple incursions of different BTV serotypes with serious consequences, which have mainly been controlled thanks to vaccination. In the case of Spain, from 2000 to 2023, BTV serotypes 1, 2, 4 and 8 have caused epidemics, and, sporadically, BTV-1 and -4 were detected in the same area and period. In 2024, BTV serotypes 1, 3 and 8 circulated simultaneously in the southwest of the country, causing a severe clinical impact in sheep but also in cattle and a multitude of outbreaks. Additionally, despite vaccination, serotype 4 also circulated that year, especially in areas where the other serotypes were already circulating. Whole-genome sequencing and phylogenetic analyses allowed us to confirm that serotypes 1 and 4 were homologous to viruses circulating in the country since 2000s, while serotypes 3 and 8 were homologous to BTVs recently notified in neighboring countries. In this context, many BTV co-infections of two or more different serotypes were confirmed by serotype-specific RT-PCRs, both in farms and individual animals. An epidemic caused by four serotypes coinciding in space and time had never occurred before in Spain, being a challenge for the diagnosis and control of this disease. Moreover, it could have favored the appearance of reassortant viruses with an unknown virulence, posing an additional risk. The data presented here raise the question of whether the co-circulation of different BTV strains, an exceptional situation, could become the new normal in certain areas of Europe. Full article

Infectious bursal disease virus (IBDV) is an immunosuppressive pathogen posing a major threat to poultry health worldwide. Its marked phenotypic variability is driven by the rapid evolution of its double-stranded RNA genome, primarily achieved through mutation and reassortment. Although extensive evidence has been generated on molecular determinants of antigenicity and pathogenicity, interpretation is often hindered by heterogeneity and lack of systematicity. This scoping review synthesizes over 35 years of research on amino acid positions influencing IBDV phenotype. A total of 62 studies reporting 107 functionally relevant sites were identified and critically appraised based on evidence type, methodological approach, and ability to infer causality. The results confirmed the central role of VP2, particularly its hypervariable region, while also highlighting the increasingly recognized contribution of other viral proteins. Despite good agreement, comparability across studies was limited by substantial heterogeneity in experimental design and the frequent focus on partial genomic regions. Notably, some molecular markers were context-dependent or inconsistently associated with phenotypic outcomes, underscoring the need for proper interpretation of molecular determinants and for more standardized and comprehensive approaches, including full-genome analyses and reverse genetics. Overall, these findings provide a valuable framework for enhancing molecular diagnostics and supporting the rational design of next-generation vaccines. Full article

Bovine rotavirus (BRV) poses a major threat to the global cattle industry, driving significant morbidity and mortality in young calves. In Yunnan Province, China, BRV is the primary cause of neonatal calf diarrhea (NCD), yet the molecular epidemiology of circulating strains remains poorly understood. This study aimed to investigate the molecular characteristics of bovine rotavirus strains associated with a severe outbreak of the NCD on a local farm. Fecal samples were collected from 396 calves and screened for BRV by RT-PCR targeting the VP6 gene. Positive samples were subjected to virus isolation in MA104 cells, followed by whole-genome sequencing, phylogenetic analysis, and pathogenicity assessment in suckling mice. Of 396 samples, 85 tested positive for BRV, corresponding to an animal-level prevalence of 21.5% (95% CI: 17.5–25.8%), with four fatalities recorded. A strain designated as BRV-YN1-2021 was successfully isolated, exhibiting characteristic cytopathic effects, specific immunofluorescence, and typical rotavirus morphology by electron microscopy. Genomic analysis revealed the constellation G8-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, identified as genotype G8P[1]. BLAST analysis showed that four genomic segments shared the highest identity with deer rotavirus strains, five with human rotavirus strains, and two with bovine rotavirus strains. Phylogenetic analysis demonstrated close relationships with US deer strains, Japanese bovine strains, and human strains circulating in China. Experimental infection in suckling mice induced diarrhea and significant intestinal histopathology, degeneration of villous epithelial cells, goblet cell hyperplasia, and inflammatory infiltration. This study reports the first isolation of a G8P[1] bovine rotavirus from a diarrhea outbreak in Chinese cattle. The multi-host genetic composition provides evidence of interspecies reassortment events, highlighting the zoonotic potential of BRV and emphasizing the need for continuous molecular surveillance to inform effective control strategies. Full article

Birds serve as the primary natural reservoirs for avian influenza viruses (AIVs), harboring nearly all known AIV subtypes. The seasonal migratory movements of wild birds play a significant role in the transmission and dissemination of AIVs. Jianhu Lake in Dali, Yunnan Province, serves as a vital congregation point along avian migratory routes, providing an ideal habitat for birds. In this study, a total of 619 avian samples were collected from the Jianhu area, from which four H6N2 subtype AIV strains were successfully isolated. Among these, A/grey heron/Jianhu/JH-89/2024 (hereafter referred to as JH-89) and A/grey heron/Jianhu/JH-91/2024 (JH-91) were isolated from grey herons (Ardea cinerea); A/mareca penelope/Jianhu/JH-2-11/2025 (JH-2-11) from a Eurasian wigeon (Mareca penelope); and A/duck/Jianhu/JH-1-1/2025 (JH-1-1) from a domestic duck (Anas platyrhynchos domesticus). Genomic analyses revealed that these four H6N2 isolates belong to the Eurasian lineage, with all eight gene segments originating from complex reassortment events among diverse Asian isolates. In vitro assays demonstrated that the representative strain JH-2-11 replicated efficiently in various human- and animal-derived cell lines. In vivo infection models revealed that, without prior adaptation, the JH-2-11 strain successfully infected BALB/c mice, resulting in suppressed body weight gain and severe pathological lesions in the respiratory tract (nasal turbinates, trachea, and lungs), without causing mortality or extrapulmonary dissemination. Collectively, although these H6N2 viruses evolve primarily within avian hosts, they exhibit potential for mammalian adaptation and require continuous epidemiological monitoring. Full article

Influenza viruses are significant causes of acute respiratory infections, often leading to severe health issues and mortality. These viruses undergo continuous mutations and genetic reassortments, resulting in annual epidemics and potential pandemics. The A(H3N2) strains exhibit high genetic and antigenic variability, that influence vaccine efficacy. This study aimed to assess the prevalence of influenza viruses, including A(H3N2) strains, in Kazakhstan during 2020–2025. The study used nasopharyngeal swab and serum samples obtained from patients. The presence of influenza virus antigens in nasopharyngeal swabs was analyzed using real-time polymerase chain reaction. The level of specific antibodies in the blood serum was determined using the hemagglutination inhibition reaction and enzyme-linked immunosorbent assay methods. Influenza A/H1N1, A/H3N2 and B viruses were diagnosed using real-time PCR. Antibodies to A/H1N1pdm09, A/H3N2 and B were detected in serological studies. Our studies revealed a trend toward seasonal patterns in influenza A viruses circulation. Therefore, it was established that the A/H3N2 strains dominated in Kazakhstan during the 2021–2022 and 2023–2024 epidemic seasons. The 2023–2024 strains belong to the specific genetic clade J.2 or 3C.2a1b.2a.2a.3a.1. These studies confirmed the role of influenza viruses in the etiology of respiratory infections and emphasized the need to continue monitoring their spread in Kazakhstan. Full article