ETIDIOH - NEW

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...

Abstract In January 2025, the highly pathogenic avian influenza A(H5N1) virus clade 2.3.2.1a infection was detected in domestic cats and whole-genome sequencing of two cat H5N1 isolates was performed using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis revealed the circulation of triple reassortant viruses in cats. Although cat viruses lacked classic mammalian adaptation markers they carried mutations associated with enhanced polymerase activity in mammalian cells and increased affinity for α2-6 sialic acid receptor suggesting their potential role in facilitating infection in cats. The identification of reassortant HPAI H5N1 clade 2.3.2.1a viruses in domestic cats in India highlights the urgent need for enhanced surveillance in domestic poultry, wild birds, and mammals, including humans, to track genomic diversity and molecular evolution of circulating strains. Source: BioRxIV,  https://www.biorxiv.org/content/10.1101/2025.02.23.638954v1 ____

Abstract Influenza viruses are highly capable of mutating and adapting in mammalian hosts . While these viruses have been extensively studied in birds, research on their presence in bats has been limited. However, influenza viruses circulating in bats have shown notable molecular divergence . The present study aimed to characterize the phylogenetic, evolutionary, and antigenic relationships of an influenza A virus detected in the fishing bat Noctilio albiventris . As part of a pathogen surveillance study of public health interest, 159 rectal samples were collected from bats in the Colombian Caribbean . The samples were sequenced using RNA-Seq. A genome (eight viral contigs) associated with the Orthomyxoviridae family was identified in a pool. Most segments showed approximately 90% similarity with H18N11, except for the neuraminidase. Analysis of the N protein shows that occupies a basal position relative to the N11 subtype, with its divergence date estimated to be approximately 50 year...

Abstract We report the detection of a clade 2.3.4.4b A(H5N1) reassortant virus with a neuraminidase surface protein derived from a North American lineage low-pathogenic avian influenza virus. This virus caused a widespread and ongoing outbreak across 45 poultry farms in British Columbia, Canada . Isolates from 8 farms reveal a mutation in the neuraminidase protein (H275Y) that is exceptionally rare among clade 2.3.4.4b viruses (present in 0.045% of publicly available clade 2.3.4.4b isolates). NA-H275Y is a well-known marker of resistance to the neuraminidase inhibitor oseltamivir . We demonstrate that this substitution maintains its resistance phenotype on the genetic background of H5N1 clade 2.3.4.4b viruses. Source: Emerging Microbes and Infections,  https://www.tandfonline.com/doi/full/10.1080/22221751.2025.2469643 ____

Abstract The H9N2 subtype of avian influenza virus poses significant challenges to global poultry and human health . During the active surveillance of avian influenza virus in wild birds in Shanghai from 2020 to 2023, a total of nine H9N2 viruses were identified. To better understand the genetic characteristics of these H9N2 viruses in Shanghai, the whole genome sequences were analyzed. Phylogenetical analysis showed that the nine H9N2 viruses have undergone complicated reassortment with waterfowl viruses along the East Asian-Australasian flyways . The nine H9N2 viruses were classified into seven genotypes , and some of them could contribute internal genes to recently circulating HPAI A( H5N8 ) and A( H5N1 ) viruses of clade 2.3.4.4b. These results highlight the importance of active surveillance of AIVs in wild birds to comprehend viral ecology and evaluate potential transmission risk in poultry and humans. Source: Poultry Sciences,  https://www.sciencedirect.com/science/article/pi...

Abstract In 2018, a single detection of a novel reassortant swine influenza A virus (swIAV) was made in Denmark . The hemagglutinin (HA) of the virus was from the H1N1 pandemic 2009 (H1N1pdm09) lineage and the neuraminidase (NA) from the H1N1 Eurasian avian-like swine lineage (H1N1av). By 2022, the novel reassortant virus (H1pdm09N1av) constituted 27% of swIAVs identified through the Danish passive swIAV surveillance program . Sequencing detected two H1pdm09N1av genotypes; Genotype 1 contained an entire internal gene cassette of H1N1pdm09 origin, Genotype 2 differed by carrying an NS gene segment of H1N1av origin . The internal gene cassette of Genotype 2 became increasingly dominant, not only in the H1pdm09N1av population, but also in other Danish enzootic swIAV subtypes. Phylogenetic analysis of the HA genes from H1pdm09N1av viruses revealed a monophyletic source , a higher substitution rate compared to other H1N1pdm09 viruses and genetic differences with human seasonal and other swi...

Abstract As a rare subtype of avian influenza virus, H16 viruses are predominant in gulls but rarely found in domestic birds . The low prevalence of H16 viruses has limited our understanding of their epidemiology and evolutionary dynamics . In this study, we isolated three novel H16N3 viruses from migratory gulls in East Asian–Australasian Flyway in eastern China in 2023, which are significantly different from previously identified isolates. To fully understand the epidemiology and genetics characteristics of the global H16 viruses, we compared the host divergence of several rare subtypes and determined that the H13 and H16 subtypes were predominantly pooled into different species of gulls by sharing their internal genes, whereas the waterfowl of Anatidae served as the primary natural reservoirs of the H8, H11, H12, H14, and H15 subtypes. Detailed phylogenetic analysis revealed the evolutionary divergence of globally circulating H16 viruses and their frequent gene reassortment . Furthe...

Background    In March 2024, the USDA confirmed the first case of highly pathogenic avian influenza (HPAI) spreading between dairy cattle herds in the United States.  This followed reports from dairy producers of an unusual illness in their lactating cows over the preceding 2-3 months.  Virus whole genome sequencing and modeling performed by USDA suggested a single spillover of HPAI H5N1, clade 2.3.4.4b, genotype B3.13 from wild birds into dairy cattle likely occurred between October 2023 and January 2024 (1).  Since then, federal, state, and industry partners have collaborated to address the HPAI threat in dairy cattle, resulting in two federal orders and the implementation of the National Milk Testing Strategy (NMTS).  States began enrolling in the NMTS in December 2024, in which they are continuing to conduct or now implementing state-wide bulk tank surveillance and/or milk processing plant silo monitoring.  Nevada was among the first to participate...

Abstract After nearly a decade without reported human A/H5N1 infections , Cambodia faced a sudden resurgence with 16 cases between February 2023 and August 2024, all caused by A/H5 clade 2.3.2.1c viruses . Fourteen cases involved a novel reassortant A/H5N1 virus with gene segments from both clade 2.3.2.1c and clade 2.3.4.4b viruses. The emergence of this novel genotype underscores the persistent and ongoing threat of avian influenza in Southeast Asia . This study details the timeline and genomic epidemiology of these infections and related poultry outbreaks in Cambodia. Source: MedRxIV,  https://www.medrxiv.org/content/10.1101/2024.11.04.24313747v2 _____

ABSTRACT Reassortant highly pathogenic avian influenza A(H5N2) clade 2.3.4.4.b viruses were detected from ducks and environmental samples in Egypt , June 2024. Genomic and phylogenetic analyses revealed a novel genotype produced by the reassortment of an A( H5N1 ) clade 2.3.3.4b virus with an A( H9N2 ) G1-like virus. Monitoring the spread of this virus is important. Source: Emerging Microbes and Infections,  https://www.tandfonline.com/doi/full/10.1080/22221751.2025.2455601#abstract _____

Abstract Pigs serve as a mixing vessel for influenza viruses and can independently promote the emergence of pandemic strains in humans. During our surveillance of pig populations from 2021 to 2023 in China , 11 H1 subtype swine influenza viruses (SIVs) were isolated. All viruses were reassortants , possessing internal genes of identical origins ( PB2, PB1, PA, NP, M : pdm09/H1N1 origin, NS : North American triple reassortant origin). The H1N1 isolates were all the dominant G4 EA H1N1 viruses in China. Two H1N2 isolates carried early human pdm09/H1N1 HA genes, suggesting a possible pig-to-human transmission route. Mutations that dictate host range specificity were identified in all isolates, a phenomenon which may enhance the affinity to human receptors. These H1 subtype viruses effectively replicated both in vivo and in vitro without prior adaptation and exhibited different pathogenicity and growth characteristics. Some of the H1 viruses were even found to cause lethal infections in mi...

Abstract Influenza A virus (IAV) continuously threatens animal and public health globally , with swine serving as a crucial reservoir for viral reassortment and evolution . In Chile , H1N2 and H3N2 subtypes were introduced in the swine population before the H1N1 2009 pandemic, and the H1N1 was introduced from the H1N1pdm09 by successive reverse zoonotic events . Here, we report two novel introductions of IAV H3N2 human-origin in Chilean swine during 2023. Our study reveals a closer relationship between recent human seasonal H3N2 and novel swine strains. Interestingly, one strain maintains all the genes from the original human virus , but the other strain is already a reassortment of human H3N2 and an H1N2 previously observed on the farm. Observing global IAV sequences, a similar pattern was identified in the USA confirming the reverse zoonotic potential of current seasonal human H3N2 strains. These results highlight the importance of ongoing surveillance and reinforcing biosecurity in ...

Abstract Wild birds and waterfowl serve as the natural reservoirs of avian influenza viruses (AIVs). When AIVs originating from wild birds cross species barriers to infect mammals or humans , they pose a significant threat to public health . The H12 subtype of AIVs primarily circulates in wild birds, with relatively few isolates reported worldwide , and the evolutionary and biological characteristics of H12 subtype AIVs remain largely unknown. In this study, we analyzed the spatiotemporal distribution of H12 subtype AIVs worldwide and conducted a comprehensive investigation into the evolutionary and biological characteristics of an H12N2 virus isolated from a whooper swan in Central China . Phylogenetic analysis revealed that the H12N2 isolate belongs to the Eurasian lineage , with its HA gene likely originating from a duck-derived H12N5 virus and its NA gene potentially derived from an H9N2 virus , indicating that it is a complex reassorted virus. Animal experiments in domestic ducks ...

{Excerpt} Dear Editor, The highly pathogenic avian influenza viruses (HPAIVs) are important epizootic and zoonotic pathogens that cause significant economic losses to the poultry industry and pose a serious risk to veterinary and public health . Wild birds have been recognized as the primary reservoirs for influenza A virus, and some species show little sign of clinical disease or even can be asymptomatic during long distance carriers of the virus (Lycett et al., 2019). Since it was first discovered in 1959, the H5Nx HPAIVs have spread globally and cause outbreaks in wild birds, poultry and sporadic human and other mammalian infections (Lycett et al., 2019). Due to the reassortant events of diverse strains facilitated by migratory waterfowl, the clade 2.3.4.4 of H5Nx viruses acquiring neuraminidase (NA) gene from other low pathogenicity avian influenza viruses (LPAIVs) emerged in 2014 and gradually became the dominant sub-clade (Lee et al., 2017). The genetic diversity of clade 2.3.4.4...

Abstract H4Nx avian influenza viruses (AIVs) have been isolated from wild birds and poultry and can also cross the species barrier to infect mammals ( pigs and muskrats ). The widespread presence of these viruses in wild birds and poultry and their ability to be transmitted interspecies make them an undeniable hazard to the poultry farming industry. In the present study, we collected fecal and swab samples from wild birds and poultry in Guangdong Province from January 2019 to March 2024, and various subtypes of AIVs were isolated, including 19 strains of H4 subtype AIVs . Further analysis was conducted on the internal genes of the 19 strains . These strains clustered together with high homology to highly pathogenic avian influenza virus (HPAIV), suggesting that H4Nx AIV may be reassorted from HPAIV . Two H4N8 strains are phylogenetically related to the porcine H4N8 AIV. Molecular characterization revealed that all viruses in this study were less pathogenic but had potential mammalian-a...