Highly Pathogenic Avian Influenza Virus Research Articles

Avian influenza A (H5N1) virus in dairy cattle: origin, evolution, and cross-species transmission.

Since the emergence of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.3.4.4b as a novel reassortant virus from subtype H5N8, the virus has led to a massive number of outbreaks worldwide in wild and domestic birds. Compared to the parental HPAIV H5N8 clade 2.3.4.4b, the novel reassortant HPAIV H5N1 displayed an increased ability to escape species barriers and infect multiple mammalian species, including humans. The virus host range has been recently expanded to include ruminants, particularly dairy cattle in the United States, where cattle-to-cattle transmission was reported. As with the avian 2.3.4.4.b H5N1 viruses, the cattle-infecting virus was found to transmit from cattle to other contact animals including cats, raccoons, rodents, opossums, and poultry. Although replication of the virus in cows appears to be mainly confined to the mammary tissue, with high levels of viral loads detected in milk, infected cats and poultry showed severe respiratory disease, neurologic signs, and eventually died. Furthermore, several human infections with HPAIV H5N1 have also been reported in dairy farm workers and were attributed to exposures to infected dairy cattle. This is believed to represent the first mammalian-to-human transmission report of the HPAIV H5N1. Fortunately, infection in humans and cows, as opposed to other animals, appears to be mild in most cases. Nevertheless, the H5N1 bovine outbreak represents the largest outbreak of the H5N1 in a domestic mammal close to humans, increasing the risk that this already mammalian adapted H5N1 further adapts to human-to-human transmission and starts a pandemic. Herein, we discuss the epidemiology, evolution, pathogenesis, and potential impact of the recently identified HPAIV H5N1 clade 2.3.4.4b in dairy cattle in the United States. Eventually, interdisciplinary cooperation under a One Health framework is required to be able to control this ongoing HPAIV H5N1 outbreak to stop it before further expansion of its host range and geographical distribution.

The Thermal Stability of Influenza Viruses in Milk

Highly pathogenic avian influenza viruses (HPAIVs) of the H5N1 subtype (clade 2.3.4.4b) have been detected in raw milk from infected cows. Several studies have examined the time and temperature parameters to ascertain whether influenza viruses in milk can be inactivated completely under commercial pasteurization conditions, yielding conflicting results. This study aimed to investigate whether milk could help protect influenza viruses from heat treatment. After heat treatment at 49 °C for one hour, the titer reduction of the influenza A/WSN/1933 (A/H1) virus in milk was approximately 1.6 log10TCID50/mL, which was significantly lower than that (3 log10TCID50/mL) observed in the Dulbecco’s Modified Eagle Medium (DMEM) control media. The influenza D/bovine/CHN/JY3002/2022 (D/Yama2019) virus in milk retained a high residual infectivity (4.68 × 103 log10TCID50/mL) after treatment at 53 °C; however, the virus in DMEM completely lost its infectivity under the same conditions. Moreover, the influenza A/chicken/CHN/Cangzhou03/2023 (A/H5) virus in DMEM could be inactivated completely using any of the three heat treatment methods: 63 °C for 30 min, 72 °C for 15 s, or 80 °C for 15 s. For the virus present in milk, only heat treatment at 80 °C for 15 s completely inactivated it. These results suggest that milk prevents influenza viruses from pasteurization inactivation.

Epidemiological data of an influenza A/H5N1 outbreak in elephant seals in Argentina indicates mammal-to-mammal transmission.

H5N1 high pathogenicity avian influenza virus has killed thousands of marine mammals in South America since 2022. Here we report epidemiological data and full genome characterization of clade 2.3.4.4b H5N1 HPAI viruses associated with a massive outbreak in southern elephant seals (Mirounga leonina) at Península Valdés, Argentina, in October 2023. We also report on H5N1 viruses in concurrently dead terns. Our genomic analysis shows that viruses from pinnipeds and terns in Argentina form a distinct clade with marine mammal viruses from Peru, Chile, Brazil and Uruguay. Additionally, these marine mammal clade viruses share an identical set of mammalian adaptation mutations which were also present in tern viruses. Our combined ecological and phylogenetic data support mammal-to-mammal transmission and occasional mammal-to-bird spillover and suggest multinational transmission of H5N1 viruses in mammals. We reflect that H5N1 viruses becoming more evolutionary flexible and adapting to mammals in new ways could have global consequences for wildlife, humans, and/or livestock.

The highly pathogenic avian influenza H5N8 sublineage 2.3.4.4b virus: A critical analysis of genetic steadiness based on full HA gene sequencing in Egypt

The highly pathogenic avian influenza virus (HPAIV) continues to be a significant threat to the poultry industry despite the implementation of vaccination programs. The main goal of this study was to explore the incidence of avian influenza viruses (AIVs) and the stability of the hemagglutinating (HA) gene sequence. For this drive, oropharyngeal swabs (n=425) were collected from various wild and domesticated bird species from 13 provinces in Egypt from 2019 to 2021. Viral isolation in specific pathogen-free chicken embryos revealed positive HA activity in 9.88% (n=32) of the wild and 36.37% (n=64) of domesticated species. Only eight H5N8 avian influenza viruses were delivered (4/each category) in mixed infection with Newcastle disease virus (NDV). Clinically, domesticated examined birds exhibited clinical findings suggesting avian influenza, but AIVs were delivered from both apparently healthy and sick wild birds. A/chicken-cobb/Egypt/55/2019(H5N8) sequence generated in this study has been submitted to GenBank under the accession number ON724339, and its in vivo pathogenicity was evaluated in four-week-old chickens, which revealed 90% mortality and typical clinical findings of HPAIV. Based on the full HA gene sequence, the strain has a Furin-sensitive cleavage site in the HA protein, which is an HPAIV. It has been clustered in clade 2.3.4.4b within AIVs from 2016 to 2023 and coexistence of genetically stable viruses 2016-2019 with 99.8-100% similarity. The existing strain is fully identical to three strains: A/green-winged teal/Egypt/877/2016(H5N8), A/northern shoveler/Egypt/MB-D-816OP/2016(H5N8), and A/duck/Egypt/N13736E/2017 (H5N8), with the only point of mutation at position 284 (G284E). In our analysis, the majority of H5NX AIV strains detected in Egypt since 2016 possessed 156T. As a result, there is evidence suggesting that H5N8 has been introduced sequentially through the migration of European wild birds along the Black Sea–Mediterranean and East Asia–West Africa flyways. This raises the possibility of future adaptation to mammals due to spillover from avian-origin strains, especially in native aquatic birds such as geese and ducks.

Dominant HPAIV H5N1 genotypes of Germany 2021/2022 are linked to high virulence in Pekin ducklings

Highly pathogenic avian influenza viruses (HPAIV) of H5 clade 2.3.4.4b pose an ongoing threat worldwide. It remains unclear whether this panzootic situation would favor low virulent phenotypes expected by the ‘avirulence hypothesis’ of viral evolution. Assessing virulence in Pekin ducklings in an intramuscular infection model revealed that the two genotypes that dominated the epidemiological situation in Germany during the period 2021 and 2022 (EU-RL:CH and EU-RL:AB) were of high virulence. In contrast, rare genotypes were of intermediate virulence. The genetic constellation of these reassortants pointed to an important role of the viral polymerase complex (RdRP), particularly the PB1 genome segment, in shaping virulence in ducklings. Occulo-nasal infection of ducklings confirmed the phenotypes for two representative viruses and indicated a more efficient replication for the high virulence strain. These observations would be in line with the ‘virulence-transmission trade-off’ model for describing HPAIV epidemiology in wild birds in Germany.

Highly Pathogenic Avian Influenza A(H5N1) Virus Infection in Cats, South Korea, 2023.

In July 2023, cases of highly pathogenic avian influenza (HPAI) were reported at 2 shelters for stray cats in Seoul, South Korea. The cause of infection was suspected to be improperly sterilized raw food made from domestic duck meat, which was manufactured in South Korea. All viruses isolated from cats at the shelters and from the raw food belonged to HPAI A(H5N1) clade 2.3.4.4b. The gene constellation of all viruses was most similar to that of viruses isolated in Korea in November 2022. Of note, the viruses isolated from infected cats harbored mutations E627K or D701N in polymerase basic 2, which are indicative of adaptation to mammals. Postmortem examination revealed systemic pathologic lesions and the presence of widespread virus in different tissues. Thus, consumption of raw duck meat contaminated with HPAI virus likely caused systemic symptoms and death in cats, indicating the introduction of mammal-adapted mutations of the virus.

A comprehensive epidemiological approach documenting an outbreak of H5N1 highly pathogenic avian influenza virus clade 2.3.4.4b among gulls, terns, and harbor seals in the Northeastern Pacific

Highly pathogenic avian influenza viruses (HPAIV) H5N1 clade 2.3.4.4b continue to have unprecedented global impacts on wild birds and mammals, with especially significant mortality observed in colonial surface-nesting seabirds and in some marine mammal species. In July of 2023 H5N1 HPAIV 2.3.4.4b was detected in Caspian terns nesting on Rat Island, Washington USA. An estimated 1,800–1,900 adult terns populated the breeding colony, based on aerial photographs taken at the start of the outbreak. On a near-weekly basis throughout July and August, we counted and removed carcasses, euthanized moribund birds, and collected swab and tissue samples for diagnostic testing and next-generation sequencing. We directly counted 1,101 dead Caspian tern adults and 520 dead chicks, indicating a minimum 56% loss of the adult colony population and potential impacts to reproductive success. Combining the observed mortality on Rat Island with HPAI-related Caspian tern deaths recorded elsewhere in Washington and Oregon, we estimate that 10–14% of the Pacific Flyway population was lost in the summer of 2023. Comparatively few adult Glaucous-winged gulls (hybrids) nesting on Rat Island died (~3% of the local population), although gull chick mortality was high. Sixteen harbor seals in the immediate or nearby area stranded during the outbreak, and H5N1 HPAIV was detected in brain and/or lung tissue of five seals. These cases are the first known detections of HPAIV in a marine mammal on the Pacific coast of North America. Phylogenetic analyses support the occurrence of at least three independent avian-mammalian virus spillover events (tern or gull to harbor seal). Whole genome sequencing indicated that H5N1 HPAIV may have been introduced to Washington from Caspian terns in Oregon. Ongoing monitoring and surveillance for H5N1 HPAIV in the marine environment is necessary to understand the epidemiology of this virus, assess conservation impacts to susceptible species, and provide support for data-driven management and response actions.

Transmission dynamics of highly pathogenic avian influenza virus at the wildlife-poultry-environmental interface: A case study

Avian influenza viruses (AIVs) regularly circulate between wild and domestic bird populations. Following several high-profile outbreaks, highly pathogenic AIVs (HPAIV) with zoonotic potential have been the subject of increasing attention. While we know that HPAIV is transmitted between domestic birds, wildlife, and the environment, little is known about persistence and spillover/back at these interfaces. We integrated the test results of samples collected on and around an infected domestic poultry premise (IP) where H5N1 HPAIV was confirmed in a flock of poultry in 2022 in Southern Ontario, Canada to explore the transmission cycle of AIVs in wildlife and the environment. We sampled a captive flock of Mallards (Anas platyrhynchos) that resided on site, sediment samples collected from water bodies on site, and examined samples collected through surveillance within a 100 km radius of the IP from live wild ducks and sick and dead wildlife. We found serologic evidence of H5 exposure in the captive mallards that resided on site despite no evidence of morbidity or mortality in these birds and no PCR positive detections from samples collected at two different timepoints. Genetic material from the same H5N1 HPAIV subtype circulating in the domestic birds and from low pathogenicity avian influenza viruses were detected in wetlands on site. The results of live and sick and dead surveillance conducted within a 100 km radius confirmed that the virus was circulating in wildlife before and after IP confirmation. These results suggest that biosecurity remains the most critical aspect of minimising spillover/back risk in a virus that has been shown to circulate in asymptomatic wild birds and persist in the surrounding environment.

Emergence of highly pathogenic avian influenza viruses H5N1 and H5N5 in white-tailed eagles, 2021-2023.

Highly pathogenic avian influenza (HPAI) poses a substantial threat to several raptors. Between 2021 and 2023, HPAI viruses (HPAIVs) of the Goose/Guangdong lineage H5 clade 2.3.4.4b became widespread in wild birds in Norway, and H5N1 and H5N5 viruses were detected in 31 white-tailed eagles (Haliaeetus albicilla, WTEs). Post-mortem examinations of four WTEs revealed no macroscopic pathological findings. Microscopic examinations showed the presence of myocardial and splenic necroses and a few lesions in the brain. In situ hybridization revealed the presence of the virus in several organs, suggesting a multisystemic infection. The detection of HPAIV H5N5 in a WTE in February 2022 marked the first recorded occurrence of this subtype in Norway. Since then, the virus has persisted, sporadically being detected in WTEs and other wild bird species. Phylogenetic analyses reveal that at least two distinct incursions of HPAIV H5N1 Eurasian (EA) genotype C affected WTEs, likely introduced by migratory birds from Eurasia and seabirds entering from Western and Central Europe. Some WTE isolates from 2021 to 2022 clustered with those from Canada and Ireland, aligning with the transatlantic spread of H5N1. Others were related to the 2021 mass mortality of great skuas in the UK or outbreaks in seabird populations, including gannets, gulls and terns, during 2022 in the North Sea region. This suggests that the WTEs were likely preying on the affected birds. Our study highlights that WTEs can act as sentinels for some HPAIV strains, but the absence of several known circulating genotypes in WTEs suggests varying pathogenic effects on this species.

Genetic and pathogenic potential of highly pathogenic avian influenza H5N8 viruses from live bird markets in Egypt in avian and mammalian models

Since its first isolation from migratory birds in Egypt in 2016, highly pathogenic avian influenza (HPAI) H5N8 has caused several outbreaks among domestic poultry in various areas of the country affecting poultry health and production systems. However, the genetic and biological properties of the H5N8 HPAI viruses have not been fully elucidated yet. In this study, we aimed to monitor the evolution of circulating H5N8 viruses and identify the pathogenicity and mammalian adaptation in vitro and in vivo. Three H5N8 HPAI viruses were used in this study and were isolated in 2021–2022 from poultry and wild birds during our routine surveillance. RNA extracts were subjected to full genome sequencing. Genetic, phylogenetic, and antigenic analyses were performed to assess viral characteristics and similarities to previously isolated viruses. Phylogenetic analysis showed that the hemagglutinin genes of the three isolates belonged to clade 2.3.4.4b and grouped with the 2019 viruses from G3 with high similarity to Russian and European lineages. Multiple basic amino acids were observed at cleavage sites in the hemagglutinin proteins of the H5N8 isolates, indicating high pathogenicity. In addition, several mutations associated with increased virulence and polymerase activity in mammals were observed. Growth kinetics assays showed that the H5N8 isolate is capable of replicating efficiently in mammalian cells lines. In vivo studies were conducted in SPF chickens (White Leghorn), mice, and hamsters to compare the virological characteristics of the 2022 H5N8 isolates with previous H5N8 viruses isolated in 2016 from the first introduction. The H5N8 viruses caused lethal infection in all tested chickens and transmitted by direct contact. However, we showed that the 2016 H5N8 virus causes a higher mortality in chickens compared to 2022 H5N8 virus. Moreover, the 2022 virus can replicate efficiently in hamsters and mice without preadaptation causing systemic infection. These findings underscore the need for continued surveillance of H5 viruses to identify circulating strains, determine the commercial vaccine’s effectiveness, and identify zoonotic potential.

Genetic characterization and receptor binding analysis of a novel H5N1 HPAI virus with a H6Nx-derived PA gene in Guangdong, China

Genetic characterization and receptor binding analysis of a novel H5N1 HPAI virus with a H6Nx-derived PA gene in Guangdong, China

High pathogenicity avian influenza virus emergence: Blame it on chickens or on humans raising chickens?

High pathogenicity avian influenza virus emergence: Blame it on chickens or on humans raising chickens?

Dairy cows inoculated with highly pathogenic avian influenza virus H5N1.

Highly pathogenic avian influenza (HPAI) H5N1 hemagglutinin clade 2.3.4.4b was detected in the United States in 2021. These HPAI viruses caused mortality events in poultry, wild birds, and wild mammals. On March 25, 2024, HPAI H5N1 clade 2.3.4.4b was confirmed in a dairy cow in Texas in response to a multi-state investigation into milk production losses.1 Over 200 positive herds were identified in 14 U.S. states. The case description included reduced feed intake and rumen motility in lactating cows, decreased milk production, and thick yellow milk.2,3 The diagnostic investigation revealed viral RNA in milk and mammary tissue with alveolar epithelial degeneration and necrosis and positive immunoreactivity of glandular epithelium. A single transmission event, likely from birds, was followed by limited local transmission and onward horizontal transmission of H5N1 clade 2.3.4.4b genotype B3.13.4 We sought to experimentally reproduce infection with genotype B3.13 in Holstein yearling heifers and lactating cows. Heifers were inoculated by aerosol respiratory route and cows by intramammary route. Clinical disease was mild in heifers, but infection was confirmed by virus detection, lesions, and seroconversion. Clinical disease in lactating cows included decreased rumen motility, changes to milk appearance, and production losses. Infection was confirmed by high levels of viral RNA detected in milk, virus isolation, lesions in mammary tissue, and seroconversion. This study provides the foundation to investigate additional routes of infection, pathogenesis, transmission, and intervention strategies.

An mRNA vaccine candidate encoding H5HA clade 2.3.4.4b protects mice from clade 2.3.2.1a virus infection

Highly pathogenic avian influenza (HPAI) H5 viruses from different clades have been circulating globally, threatening wild/domestic birds and mammals. Given frequent spillovers and high mortality among mammals, coupled with our inability to predict which clade of H5 virus has pandemic potential, cross-clade protective HPAI H5 vaccines are urgently needed. Here, we demonstrate the applicability of a lipid nanoparticle-based mRNA vaccine modality to induce cross-protective immunity against lethal HPAI virus infection.

Continuing evolution of H5N1 highly pathogenic avian influenza viruses of clade 2.3.2.1a G2 genotype in domestic poultry of Bangladesh during 2018–2021

ABSTRACT We characterized 15 H5N1 HPAI viruses from different small- and medium-scale poultry flocks across Bangladesh during 2018–2021 based on their complete genome sequences. The antigenic relatedness of H5N1 HPAI viruses from different timepoints was analysed. During 2020–2021, 42.11% of the flocks tested positive for at least one of the respiratory infections, with 15.79% showing influenza A virus, of which 8.77% tested positive for HPAIV H5N1. Co-infections with two to four pathogens were detected in 15.8% of flocks. Phylogeny and gene constellation analyses based on complete genome sequences of 15 HPAI viruses revealed the continuing circulation of H5 clade 2.3.2.1a genotype G2 viruses. In the HA protein of the study isolates, functionally meaningful mutations caused the loss of an N-linked glycosylation site (T156A), a modified antigenic site A (S141P), and a mutation in the receptor binding pocket (E193R/K). Consequently, antigenic analysis revealed a significant loss of cross-reactivity between viruses from different host species and periods. Most viruses displayed oseltamivir resistance markers at positions V96, I97, S227, and N275 (N1 numbering) of the NA protein. In addition, for the PB2, M1, and NS1 proteins, significant mutations were noticed that have been associated with polymerase activity and increased virulence for mammals in all study isolates. These results highlight the need for intensified genomic surveillance of HPAI circulating in poultry in Bangladesh and for establishing appropriate control measures to decrease the circulation of these viruses in poultry in the country.

Detection of airborne wild waterbird-derived DNA demonstrates potential for transmission of avian influenza virus via air inlets into poultry houses, the Netherlands, 2021 to 2022.

BackgroundOutbreaks of highly pathogenic avian influenza (HPAI) on poultry farms and in wild birds worldwide persists despite intensified control measures. It causes unprecedented mortality in bird populations and is increasingly affecting mammalian species. Better understanding of HPAI introduction pathways into farms are needed for targeted disease prevention and control. The relevance of airborne transmission has been suggested but research involving air sampling is limited and unequivocal evidence on transmission routes is lacking.AimWe aimed to investigate whether HPAI virus from wild birds can enter poultry houses through air inlets by characterising host materials through eukaryote DNA sequencing.MethodsWe collected particulate matter samples in and around three HPAI-affected poultry farms which were cleared and decontaminated before sampling. Indoor measurements (n = 61) were taken directly in the airflow entering through air inlets, while outdoor air samples (n = 60) were collected around the poultry house. Positive controls were obtained from a bird rehabilitation shelter. We performed metabarcoding on environmental DNA by deep sequencing 18S rRNA gene amplicons.ResultsWe detected waterbird DNA in air inside all three, and outside of two, poultry farms. Sequences annotated at species level included swans and tufted ducks. Waterbird DNA was present in all indoor and outdoor air samples from the bird shelter.ConclusionAirborne matter derived from contaminated wild birds can potentially introduce HPAI virus to poultry houses through air inlets. The eDNA metabarcoding could assess breaches in biosecurity for HPAI virus and other pathogens potentially transmitted through air via detection of their hosts.

Avian influenza overview June-September 2024.

Between 15 June and 20 September 2024, 75 highly pathogenic avian influenza (HPAI) A(H5) and A(H7) virus detections were reported in domestic (16) and wild (59) birds across 11 countries in Europe. Although the overall number of detections in Europe continued to be low compared to previous epidemiological years, an increase in cases along the Atlantic, North Sea and Baltic coasts was notable, particularly an increase in the detection of HPAI viruses in colony-breeding seabirds. Besides EA-2022-BB and other circulating genotypes, these detections also included EA-2023-DT, a new genotype that may transmit more efficiently among gulls. In Germany, HPAI A(H7N5) virus emerged in a poultry establishment near the border with the Netherlands. No new HPAI virus detections in mammals were reported in Europe during this period, but the number of reportedly affected dairy cattle establishments in the United States of America (USA) rose to >230 in 14 states, and HPAI virus was identified in three new mammal species. Between 21 June and 20 September 2024, 19 new human cases with avian influenza virus infection were reported from the USA (six A(H5N1) cases and five A(H5) cases), Cambodia (five A(H5N1) cases, including one fatal), China (one fatal A(H5N6) case and one A(H9N2) case), and Ghana (one A(H9N2) case). Most of the human cases (90%, n = 17/19) had reported exposure to poultry, live poultry markets, or dairy cattle prior to avian influenza virus detection or onset of illness. Human infections with avian influenza viruses remain rare and no evidence of human-to-human transmission has been documented in the reporting period. The risk of infection with currently circulating avian A(H5) influenza viruses of clade 2.3.4.4b in Europe remains low for the general public in the European Union/European Economic Area (EU/EEA). The risk of infection remains low-to-moderate for those occupationally or otherwise exposed to infected animals or contaminated environments.

Survivability of low pathogenic avian influenza virus in aqueous poultry manure fertilizer

Avian influenza has been a growing problem in the United States for decades. Low pathogenic avian influenza (LPAI) virus causes low morbidity, while highly pathogenic avian influenza (HPAI) has a devastating effect on the poultry industry causing high morbidity and mortality worldwide. Manure from large and small poultry operations is spread on crop fields as a fertilizer. During an outbreak of avian influenza in a farm it is critical to adequately process the manure to kill the virus before its use in agriculture. Aqueous extraction of poultry manure at high temperature (55-65°C) is an attractive method for treatment of poultry manure, which extracts the nutrients and kills harmful microbes from the manure. The end product is a nutrient rich liquid that can be safely applied to fields or used in hydroponic operations, with nutrients that are more bioavailable to the plant compared to dry litter. However, we do not know whether aqueous high temperature extraction processes completely kill avian influenza virus present in the manure. Our aim in this study was to determine the competence of the aqueous extraction of poultry manure on avian influenza virus inactivation. We optimized the procedure using a LPAI virus isolate in a biosafety level 2 cabinet. Our data indicated that LPAI virus including the hemagglutinin protein of the virus were completely destroyed when the poultry manure was processed by aqueous extraction at temperatures ≥ 55°C for one hour. Future research will identify the conditions required for inactivating HPAI virus using this optimized procedure by performing the study in a BSL3 facility.

The Resurgent Threat of Highly Pathogenic Avian Influenza HPAI A (H5N1) Virus: A Zoonotic Infectious Disease and Public Health Concern

The highly pathogenic avian influenza (HPAI) A (H5N1) virus of clade 2.3.4.4b was identified among waterfowl (wild birds and geese) and domestic poultry across Southeast Asia, Europe, and Africa in 2021. By 2022, the HPAI virus was detected in North America, signifying further global dissemination. There is no human immunity to clade 2.3.4.4b A (H5N1). With the spread of the A (H5N1) virus throughout the United States and increasing viral infection in humans, resurgence of the A (H5N1) virus is of great public health concern that it could lead to the next infectious zoonotic pandemic after Covid-19. This paper describes the characteristics of HPAI A (H5N1) virus of clade 2.3.4.4b and recommendations for clinical treatment and prevention.

Molecular Characterization of a Clade 2.3.4.4b H5N1 High Pathogenicity Avian Influenza Virus from a 2022 Outbreak in Layer Chickens in the Philippines.

H5 subtype high-pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, H5 HPAI outbreaks have been reported in 2020, 2022, and 2023. Here, we report the first publicly available complete whole-genome sequence of an H5N1 high-pathogenicity avian influenza virus from a case in Central Luzon. Samples were collected from a flock of layer chickens exhibiting signs of lethargy, droopy wings, and ecchymotic hemorrhages in trachea with excessive mucus exudates. A high mortality rate of 96-100% was observed within the week. Days prior to the high mortality event, migratory birds were observed around the chicken farm. Lungs, spleen, cloacal swabs, and oropharyngeal-tracheal swabs were taken from two chickens from this flock. These samples were positive in quantitative RT-PCR assays for influenza matrix and H5 hemagglutinin (HA) genes. To further characterize the virus, the same samples were subjected to whole-virus-genome amplification and sequencing using the Oxford Nanopore method with mean coverages of 19,190 and 2984, respectively. A phylogenetic analysis of the HA genes revealed that the H5N1 HPAI virus from Central Luzon belongs to the Goose/Guangdong lineage clade 2.3.4.4b viruses. Other segments also have high sequence identity and the same genetic lineages as other clade 2.3.4.4b viruses from Asia. Collectively, these data indicate that wild migratory birds are the likely source of H5N1 viruses from the 2022 outbreaks in the Philippines. Thus, biosecurity practices and surveillance for HPAI viruses in both domestic and wild birds should be increased to prevent and mitigate HPAI outbreaks.