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Abstract Avian influenza viruses undergo frequent genetic reassortment, which can coincide with phenotypic changes in transmission, pathogenicity, and host species niche . Since 2020, clade 2.3.4.4b H5 high pathogenicity avian influenza viruses (HPAIVs) have driven a global panzootic , causing mass mortality in wild birds, poultry , and, for the first time, repeated spillover infections in a variety of mammalian species . This resurgence of H5 HPAIV has coincided with a dramatic increase in the number of circulating reassortant strains ; however, the scale, impact and drivers of these reassortants remain unknown. Here, we combined statistical and phylodynamic modelling to reconstruct the global evolutionary dynamics of H5Nx viruses across four epizootic seasons (2020-2024). We identified 209 genetically distinct reassortants , stratified into three transmission categories based on their phylogenetic and epidemiological profiles. Accounting for sampling depth and HPAIV incidence, we est...

ABSTRACT Newly emerging or “re-emerging” influenza viruses have been regarded as a huge global threat to human public health . However, there are few reports of human deaths caused by newly emerging influenza viruses derived from pigs and poultry . Here, we described the clinical and virological features of a fatal encephalitis caused by a novel H3N2 reassortant virus generated from swine H3N2 and human H7N9 viruses. A 7-year-old boy was diagnosed with acute encephalitis in Yixing, China, in August 2022. Chest computed tomography (CT) showed mild pneumonia . Brain CT indicated acute encephalitis companied brain parenchyma swelling. Haematological examinations revealed a markedly elevation of lactate dehydrogenase, alanine aminotransferase, aspartate aminotransferase, creatine kinase and cytokines . Pathogenic analysis confirmed that a novel H3N2 virus (A/Yixing/805/2022, YX805) was responsible for this case. Phylogenetic analysis showed that the surface protein-coding genes were origin...

Abstract The November 2021 introduction of highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b into North America triggered a devastating outbreak , affecting more than 180 million domestic birds and spreading to more than 80 wildlife species across Canada and the US . From this outbreak, we have sequenced 2955 complete A( H5N1 ) viral genomes from samples collected in Canada and, in conjunction with previously published data, performed multifaceted phylodynamic analyses. These analyses reveal extensive diversification of A(H5N1) viruses via reassortment with low-pathogenic avian influenza viruses. We find evidence of repeated ancestral strain replacement by direct descendants, indicative of compounding viral fitness increases . Spatiotemporal modeling identified critical geographic areas facilitating transcontinental spread and demonstrated genotype-specific host dynamics, offering essential data for ongoing control and prevention strategies. Source: Science Advances,  https:...

ABSTRACT Influenza A (H3N2) viruses are historically responsible for the 1968 Hong Kong flu pandemic. Since then, H3N2 has continued to circulate as a seasonal influenza virus in humans. Public health concerns were raised in 2022 when human infections with novel reassortant H3N8 influenza viruses originating from chickens were first reported in China . Here, we conducted a systematic surveillance of H3 avian influenza viruses (AIVs) circulating in poultry and assessed the public health risk of emergent H3 reassortants. We found that H3 AIVs were prevalent in both ducks and chickens . Notably, in December 2022, a novel chicken-derived H3N3 subtype virus was identified, which gradually replaced the previously predominant H3N8 virus and became prevalent in chickens. Genetic analysis demonstrated that the novel H3N3 virus is a triple-reassortment strain with the H3 gene segment from chicken H3N8 virus, the N3 gene segment from the H10N3 virus , and internal gene segments derived from H9N2 ...

{Excerpt} A novel reassortant Oropouche virus (OROV) lineage (with medium [M], large [L], and small [S] RNA segments : M1L2S2) has driven Brazil's largest and most geographically widespread OROV epidemic , expanding beyond the endemic Amazon basin to establish local transmission across multiple Brazilian states and other previously unaffected Latin American countries . The rapid spread of this lineage underscores its evolutionary potential and reinforces its significance as a public health threat .1 Similar to chikungunya and Zika viruses, expanding arboviruses can exhibit unexpected clinical and epidemiological shifts , including vertical transmissions , neuroinvasive effects, and potentially fatal outcomes.2–4 Although OROV typically causes self-limited febrile illness, accumulating clinical and experimental evidence suggests neurotropic potential .5 This Correspondence describes the first confirmed case of neuroinvasive OROV infection caused by the emergent M1L2S2 lineage in ext...

Abstract Avian influenza H9N2 viruses cause significant economic losses to the poultry industry and pose a public health risk due to their potential to reassort with other avian influenza viruses, generating strains with zoonotic and pandemic potential . Two major H9N2 lineages dominate globally: the G1 lineage (genotype G1-B), prevalent in the Middle East, Africa and the Indian subcontinent , and the BJ/94 lineage (predominantly genotype G57), dominant in China, Vietnam, South Korea, Indonesia, and the Far East . We investigated replication, transmission, and pathogenicity of representatives of these two lineages, linking genotype to phenotype. The G57 strain A/Ck/Vietnam/H7F-14-BN4-315/2014 (Vietnam/315) was more lethal to chicken embryos than the G1-B strain A/chicken/Pakistan/UDL-01/2008 (Pakistan/UDL-01). Vietnam/315 exhibited higher replication in both directly infected and contact chickens, with increased virus shedding from the oropharynx and cloaca. In contrast, Pakistan/UDL-0...

Abstract Genomic sequencing of re-emerging highly pathogenic avian influenza A(H5N1) virus detected in Argentina in February 2025 revealed novel triple-reassortant viruses containing gene segments from Eurasian H5N1 and low pathogenic viruses from South and North American lineages . These findings underscore continued evolution and diversification of clade 2.3.4.4b H5N1 in the Americas. Source: BioRxIV,  https://www.biorxiv.org/content/10.1101/2025.05.23.655175v1 ____

Abstract Avian influenza viruses continue to challenge poultry and human health ; therefore, careful surveillance and evaluation of emerging viruses are important for animal disease control and human influenza pandemic preparedness . In this study, we detected a series of H3N3 subtype avian influenza viruses in chickens , pigeons, and ducks during our routine surveillance and diagnosis between September 2022 and May 2023. We performed extensive analyses to fully understand the origins of these viruses and their risk to animals and humans. We found that the viruses were complex reassortants ; the viruses from chickens and pigeons carry genes mainly derived from H3N8 viruses and H10N3 viruses , whereas the two duck viruses were reassortants of duck and wild bird viruses. The chicken and pigeon , but not duck, viruses replicated in multiple organs of chickens and were shed for up to 13 days, but none caused disease or death. Six of the viruses tested all bound to both avian- and human-typ...

Abstract The interspecies transmission of avian influenza viruses remains a significant public health concern. H6 viruses have gained attention following the first human infection by a chicken-origin H6N1 virus (A/Taiwan/02/2013, Hu/13), highlighting their zoonotic potential . To understand the evolutionary trajectory and mammalian adaptation of this Taiwan lineage , we compared two avian isolates (A/Chicken/Taiwan/CF19/2009, Ck/09; A/Chicken/Taiwan/2267/2012, Ck/12) and Hu/13 in vitro and in vivo. Hu/13 exhibited enhanced replication in MDCK cells , producing larger plaques and higher viral titers than Ck/09 and Ck/12. In BALB/c mice , Hu/13 demonstrated the highest pathogenicity and mortality , followed by Ck/12, while Ck/09 induced minimal morbidity. Hu/13 and Ck/12 replicated efficiently in respiratory tissues , eliciting robust cytokine responses and severe pulmonary lesions . In ferrets , Hu/13 showed relatively efficient transmission , infecting all direct physical-contact and t...

Abstract Thousands of outbreaks of the highly pathogenic avian influenza A(H5N1) virus in birds and an increasing number of mammal infections are registered annually. In 2023, multiple avian influenza outbreaks were registered among wild birds, poultry and seals in Russia . The genetic characterization of seventy-seven avian viruses and three viruses from seals showed that they belonged to the 2.3.4.4b clade and represented four distinct reassortant genotypes . The majority of viruses represented genotype BB , which was widespread in Europe in 2023. Viruses from seals and four viruses from birds , isolated from outbreaks in the Far East region , belonged to the G1 (A3) genotype and had the amino acid substitution N319K in the NP protein , previously associated with an increased virulence for mammals . In addition, one virus of the G10 genotype and two viruses, representing a previously undescribed genotype (designated as Ru-23-G4) were identified. The viruses analyzed showed normal inh...

Abstract Low pathogenic H9N2 avian influenza viruses have become widespread in wild birds and poultry worldwide, raising concerns about their potential to spark pandemics or their role in enhancing the virulence and infectivity of H5Nx viruses through genetic reassortment . Therefore, influenza monitoring studies, including those of H9N2 viruses, are crucial for understanding, evaluating, and mitigating the risks associated with avian infections, and have broader implications for global public health. Although H9N2 viruses are not considered enzootic in Kazakhstan , they have been repeatedly detected in wild waterfowls and domestic poultry . In this study, all eight gene segments of influenza A/H9N2 viruses isolated in various regions of Kazakhstan between 2014 and 2020 were sequenced and analyzed. Molecular characterization revealed the presence of genetic markers associated with mammalian infectivity and disease potential . Furthermore, their predicted receptor binding site sequences...

Abstract Recently, Clade 2.3.4.4b H5N1 virus has been widely prevalent globally. Although no outbreaks of Avian Influenza have occurred in poultry in China recently, Clade 2.3.4.4b H5 virus can still be isolated from wild birds , live poultry markets and environment , indicating the ongoing co-circulation of H5N1 and H5N6 viruses. In this study, phylogenetic analysis of global Clade 2.3.4.4b viruses and 20 laboratory-isolated H5 strains revealed that Chinese H5N1 and H5N6 viruses since 2021 cluster into two distinct groups , G-I and G-II. Bayesian phylodynamic analysis reveals that G-I H5N6 virus has become an endemic virus in China . In contrast, G-II H5N1 virus, with South China as its main epicentre, has been disseminated in China and its surrounding countries, with its transmission more reliant on the connections of wild birds and waterfowl . Reassortment analysis indicates that since 2023, Clade 2.3.4.4b H5 viruses isolated in China have formed seven genotypes . The genome of H5 v...

Abstract In Europe, highly pathogenic avian influenza (HPAI) virus circulates in avian wildlife, undergoing frequent reassortment , sporadic introductions in domestic birds , and spillover to mammals . An H5N1 clade 2.3.4.4b reassortant, EA-2023-DG, affecting wild and domestic birds was detected in western Europe in November 2023. Six of its RNA segments came from the EA-2021-AB genotype, but the polymerase basic 2 and polymerase acidic segments originated from low pathogenicity avian influenza viruses . Discrete phylogeographic analyses of concatenated genomes and single polymerase basic 2 and polymerase acidic segments suggested reassortment in summer 2023 near the southwestern Baltic Sea . Subsequent continuous phylogeographic analysis of all concatenated EA-2023-DG genomes highlighted circulation in northwestern Europe until June 2024 and long-distance dispersal toward France, Norway, England, Slovakia, Switzerland, and Austria . Those results illustrate the value of phylodynamic a...

Editor’s summary High-pathogenicity avian influenza subtype H5N1 is now present throughout the US , and possibly beyond. More cattle infections elevate the risk of the virus evolving the capacity to transmit between humans , potentially with high fatality rates . Nguyen et al. show that from a single transmission event from a wild bird to dairy cattle in December 2023, there has been cattle-to-poultry, cattle-to-peridomestic bird , and cattle-to-other mammal transmission. The movement of asymptomatic dairy cattle has facilitated the rapid dissemination of H5N1 from Texas across the US . Evolution within cattle, assessed using deep-sequencing data, has detected low-frequency sequence variants that had previously been associated with mammalian adaptation and transmission efficiency. —Caroline Ash Structured Abstract INTRODUCTION Highly pathogenic avian influenza (HPAI) viruses have critical consequences for animal health and the agricultural economy—and may have pandemic potential. HPAI ...

Abstract In November 2022, we reported a fatal case of human infection caused by a highly pathogenic avian influenza A(H5N6) virus bearing a clade 2.3.4.4b HA gene in Changsha City . We investigated the transmission route and distribution of the H5N6 virus in the largest live-poultry market (LPM), which is linked to the human infection. A total of 1357 samples from the LPM were collected for avian influenza A virus detection from 2020 to 2023. The proportion of LPM samples positive for H5 subtype avian influenza virus was 14.30% (194/1357). Sequences of H5N6 (n = 10) and H5N1 (n = 4) avian influenza viruses were obtained from the LPM samples using next-generation sequencing. The complete genome sequence of the H5N6 virus from the human infection case, A/Changsha/1/2022(EPI_ISL_16466440), was determined and analyzed. The PB1 and PB2 segments shared 99.65% and 99.23% sequence identity with A/duck/Hunan/S40199/2021(H5N6) and A/Whooper swan/Sanmenxia/H615/2020(H5N8), respectively. The othe...

Context and significance Wang et al. provided valuable insights into the epidemiological patterns of avian influenza virus (AIV) spillover and the role of H9N2 in the process. Their analysis highlighted the significant contribution of the internal genes (INGEs) from 12 key strains of H9N2 in facilitating human adaptability by reducing the species barrier between poultry and humans , essentially acting as internal genetic donors for AIV spillover . Due to its low pathogenicity, H9N2 has been neglected in poultry vaccination programs , leading to a lack of vaccines specifically targeting the INGEs of these 12 key strains. Their findings suggest that reducing the prevalence of H9N2 is fundamental to mitigating AIV spillover risks. Highlights •  H9N2 exerts a promoting effect on the spillover of avian influenza viruses (AIVs) •  Expansion of AIV spatial and host ranges reveals an emerging risk of its spillover •  Prevalence of AIVs in human -contacted hosts reveals a re-emerg...

Highlights •  This is the first report of clade 2.3.4.4b H5N1 virus from India. •  Evidence of novel reassortment between H5N1 and low pathogenic H3N8 viruses. •  Absence of H5N1 infection among people with probable exposure. Abstract H5N1 viruses belonging to clade 2.3.4.4b have caused unprecedented outbreaks globally. Outbreaks of H5N1 virus were reported in poultry and wild birds from Kerala (India) in the year 2024. Samples from birds and the environment were collected . Real-time RT-PCR and virus isolation using embryonated chicken eggs were carried out. Eight out of 20 samples were positive for virus isolation. The virus showed avian type receptor specificity using sialidase assay. Full genome sequencing revealed markers associated with high pathogenicity and mammalian adaptation . All the viruses belonged to a single genotype with multiple reassortments , including internal gene segments from an avian influenza (AI) H3N8 virus reported from Kerala . Surveillance am...

Abstract Background In late 2023, the first human case caused by an H10N5 avian influenza virus (AIV) was diagnosed in China . H10Ny AIVs have been identified in various poultry and wild birds in Eurasia, the Americas, and Oceania. Methods We analyzed the clinical data of the H10N5 AIV-infected patient, isolated the virus, and evaluated the virus receptor-binding properties together with the H10N8 and H10N3 AIVs identified in humans and poultry. The genomic data of the human-infecting H10N5 strain and avian H10Ny AIVs (n = 48, including 16 strains of H10N3 and 2 strains of H10N8) from live poultry markets in China , during 2019–2021, were sequenced. We inferred the genetic origin and spread pattern of the H10N5 AIV using the phylodynamic methods. In addition, given all available nucleotide sequences, the spatial-temporal dynamics, host distribution, and the maximum-likelihood phylogenies of global H10 AIVs were reconstructed. Findings The first H10N5 AIV-infected human case co-infected...

Abstract Recombination plays a central role in the evolution of the RNA virus genome , as it allows the exchange of genetic material between different viral lineages . Reassortment is a form of recombination specific to viruses with segmented genomes that involves the exchange of entire segments between lineages. This process has played a significant role in the adaptation and spread of influenza viruses, where novel combinations of genomic segments are produced from divergent lineages (i.e., antigenic shift). In this study, we investigated reassortment events in a representative sample of n = 11, 765 complete genomes of H5Nx influenza A viruses from avian hosts . Using tanglegrams and subtree-prune-regraft (SPR) methods to quantify discordance between segment trees, we found evidence of widespread reassortment among these genomes that is consistent with previous studies. However, we obtained the comparable numbers of reassortment events when applying the same methods to sequence data ...

ABSTRACT Recent avian-origin H3N8 influenza A virus (IAV) that have infected humans pose a potential public health concern . Alterations in the viral surface glycoprotein, hemagglutinin (HA), are typically required for IAVs to cross the species barrier for adaptation to a new host, but whether H3N8 has adapted to infect humans remains elusive. The observation of a degenerative codon in position 228 of HA in human H3N8 A/Henan/4-10/2022 protein sequence , which could be residue G or S, suggests a dynamic viral adaptation for human infection. Previously, we found this human-isolated virus has shown the ability to transmit between ferrets via respiratory droplets , with the HA-G228S substitution mutation emerging as a critical determinant for the airborne transmission of the virus in ferrets. Here, we investigated the receptor-binding properties of these two H3N8 HAs. Our results showed H3N8 HAs have dual receptor-binding properties with a preference for avian receptor binding , and G228S...