Highly Pathogenic Avian Influenza A(H5N6) Virus Clade 2.3.4.4h in Wild Birds and Live Poultry Markets, Bangladesh

Reassortment of newly emergent clade 2.3.4.4b A(H5N1) highly pathogenic avian influenza A viruses in Bangladesh

ABSTRACTAvian influenza active surveillance was conducted in Bangladesh from January 2022 to November 2023 in live-poultry markets (LPMs) and Tanguar Haor wetlands. The predominant viruses circulating in LPMs were low pathogenic avian influenza (LPAI) A(H9N2) and clade 2.3.2.1a highly pathogenic avian influenza (HPAI) A(H5N1) viruses. Non-H9N2 LPAIs were found at Tanguar Haor and at a lower prevalence in LPMs. Starting from June 2023, we detected novel genotypes of clade 2.3.4.4b A(H5N1) viruses from ducks in LPMs. The HA, NA, and M genes of these viruses are related to those of 2020 European clade 2.3.4.4b H5N1 viruses such as A/Eurasian Wigeon/Netherlands/1/2020 (Netherlands/1). However, analyses of the other five gene segments' sequences identified three distinct genotypes (BD-G2, BD-G3, and BD-G4). BD-G2 viruses were closely related to the clade 2.3.4.4b H5N1 viruses that have been detected in Japan and nearby regions since November 2022. BD-G3 viruses were reassortants, with gene segments from other Eurasian LPAI viruses. BD-G4 viruses were similar to BD-G2 viruses, but their NS gene was accrued from contemporary Bangladeshi clade 2.3.2.1a A(H5N1) viruses. The ability of any of the clade 2.3.4.4b viruses to displace the long-entrenched 2.3.2.1a A(H5N1) viruses in Bangladesh is unknown.

Avian influenza overview March-June 2024

Between 16 March and 14 June 2024, 42 highly pathogenic avian influenza (HPAI) A(H5) virus detections were reported in domestic (15) and wild (27) birds across 13 countries in Europe. Although the overall number of detections in Europe has not been this low since the 2019-2020 epidemiological year, HPAI viruses continue to circulate at a very low level. Most detections in poultry were due to indirect contact with wild birds, but there was also secondary spread. Outside Europe, the HPAI situation intensified particularly in the USA, where a new A(H5N1) virus genotype (B3.13) has been identified in >130 dairy herds in 12 states. Infection in cattle appears to be centred on the udder, with milk from infected animals showing high viral loads and representing a new vehicle of transmission. Apart from cattle, HPAI viruses were identified in two other mammal species (alpaca and walrus) for the first time. Between 13 March and 20 June 2024, 14 new human cases with avian influenza virus infection were reported from Vietnam (one A(H5N1), one A(H9N2)), Australia (with travel history to India, one A(H5N1)), USA (three A(H5N1)), China (two A(H5N6), three A(H9N2), one A(H10N3)), India (one A(H9N2)), and Mexico (one fatal A(H5N2) case). The latter case was the first laboratory-confirmed human infection with avian influenza virus subtype A(H5N2). Most of the human cases 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 human-to-human transmission has been observed. 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 EU/EEA. The risk of infection remains low-to-moderate for those occupationally or otherwise exposed to infected animals or contaminated environments.

Development and evaluation of a multiplex real-time RT-PCR assay for simultaneous detection of H5, H7, and H9 subtype avian influenza viruses

H5, H7 and H9 are the major subtypes of avian influenza virus (AIV) that cause economic losses in the poultry industry and sporadic zoonotic infection. Early detection of AIV is essential for preventing disease spread. Therefore, molecular diagnosis and subtyping of AIV via real-time RT-PCR (rRT-PCR) is preferred over other classical diagnostic methods, such as egg inoculation, RT-PCR and HI test, due to its high sensitivity, specificity and convenience. The singleplex rRT-PCRs for the Matrix, H5 and H7 gene used for the national surveillance program in Korea have been developed in 2017; however, these methods were not designed for multiplexing, and does not reflect the sequences of currently circulating strains completely. In this study, the multiplex H5/7/9 rRT-PCR assay was developed with sets of primers and probe updated or newly designed to simultaneously detect the H5, H7 and H9 genes. Multiplex H5/7/9 rRT-PCR showed 100% specificity without cross-reactivity with other subtypes of AIVs and avian disease-causing viruses or bacteria, and the limit of detection was 1-10 EID50/0.1 ml (50% egg infectious dose). Artificial mixed infections with the three different subtypes could be detected accurately with high analytical sensitivity even under highly biased relative molecular ratios by balancing the reactivities of each subtype by modifying the concentration of the primers and probes. The multiplex H5/7/9 rRT-PCR assay developed in this study could be a useful tool for large-scale surveillance programs for viral detection as well as subtyping due to its high specificity, sensitivity and robustness in discriminating viruses in mixed infections, and this approach would greatly decrease the time, cost, effort and chance of cross-contamination compared to the conventional method of testing three subtypes by different singleplex rRT-PCR methods in parallel or in series.

Virulence and transmission characteristics of clade 2.3.4.4b H5N6 subtype avian influenza viruses possessing different internal gene constellations

Clade 2.3.4.4 H5N6 avian influenza virus (AIV) has been predominant in poultry in China, and the circulating haemagglutinin (HA) gene has changed from clade 2.3.4.4h to clade 2.3.4.4b in recent years. In 2021, we isolated four H5N6 viruses from ducks during the routine surveillance of AIV in China. The whole-genome sequencing results demonstrated that the four isolates all belonged to the currently prevalent clade 2.3.4.4b but had different internal gene constellations, which could be divided into G1 and G2 genotypes. Specifically, G1 possessed H9-like PB2 and PB1 genes on the H5-like genetic backbone while G2 owned an H3-like PB1 gene and the H5-like remaining internal genes. By determining the characteristics of H5N6 viruses, including growth performance on different cells, plaque-formation ability, virus attachment ability, and pathogenicity and transmission in different animal models, we found that G1 strains were more conducive to replication in mammalian cells (MDCK and A549) and BALB/c mice than G2 strains. However, G2 strains were more advantageously replicated in avian cells (CEF and DF-1) and slightly more transmissible in waterfowls (mallards) than G1 strains. This study enriched the epidemiological data of H5 subtype AIV to further understand its dynamic evolution, and laid the foundation for further research on the mechanism of low pathogenic AIV internal genes in generating novel H5 subtype reassortants.

Emergence of a new genotype of clade 2.3.4.4b H5N1 highly pathogenic avian influenza A viruses in Bangladesh

Influenza virological surveillance was conducted in Bangladesh from January to December 2021 in live poultry markets (LPMs) and in Tanguar Haor, a wetland region where domestic ducks have frequent contact with migratory birds. The predominant viruses circulating in LPMs were low pathogenic avian influenza (LPAI) H9N2 and clade 2.3.2.1a highly pathogenic avian influenza (HPAI) H5N1 viruses. Additional LPAIs were found in both LPM (H4N6) and Tanguar Haor wetlands (H7N7). Genetic analyses of these LPAIs strongly suggested long-distance movement of viruses along the Central Asian migratory bird flyway. We also detected a novel clade 2.3.4.4b H5N1 virus from ducks in free-range farms in Tanguar Haor that was similar to viruses first detected in October 2020 in The Netherlands but with a different PB2. Identification of clade 2.3.4.4b HPAI H5N1 viruses in Tanguar Haor provides continued support of the role of migratory birds in transboundary movement of influenza A viruses (IAV), including HPAI viruses. Domestic ducks in free range farm in wetland areas, like Tangua Haor, serve as a conduit for the introduction of LPAI and HPAI viruses into Bangladesh. Clade 2.3.4.4b viruses have dominated in many regions of the world since mid-2021, and it remains to be seen if these viruses will replace the endemic clade 2.3.2.1a H5N1 viruses in Bangladesh.

Assessing potential pathogenicity of novel highly pathogenic avian influenza (H5N6) viruses isolated from Mongolian wild duck feces using a mouse model

Several novel highly pathogenic avian influenza (HPAIVs) A(H5N6) viruses were reported in Mongolia in 2020, some of which included host-specific markers associated with mammalian infection. However, their pathogenicity has not yet been investigated. Here, we isolated and evaluate two novel genotypes of A(H5N6) subtype in Mongolia during 2018–2019 (A/wildDuck/MN/H5N6/2018-19). Their evolution pattern and molecular characteristics were evaluated using gene sequencing and their pathogenicity was determined using a mouse model. We also compared their antigenicity with previous H5 Clade 2.3.4.4 human isolates by cross-hemagglutination inhibition (HI). Our data suggests that A/wildDuck/MN/H5N6/2018-19 belongs to clade 2.3.4.4h, and maintains several residues associated with mammal adaptation. In addition, our evaluations revealed that their isolates are less virulent in mice than the previously identified H5 human isolates. However, their antigenicity is distinct from other HPAIVs H5 clade 2.3.4.4, thus supporting their continued evaluation as potential infection risks and the preparation of novel candidate vaccines for their neutralization.

Avian influenza overview September - December 2021

Between 16 September and 8 December 2021, 867 highly pathogenic avian influenza (HPAI) virus detections were reported in 27 EU/EEA countries and the UK in poultry (316), in wild (523) and in captive birds (28). The detections in poultry were mainly reported by Italy (167) followed by Hungary and Poland (35 each). Tha majority of the detections in wild birds were reported by Germany (280), Netherlands (65) and United Kingdom (53). The observed persistence and continuous circulation of HPAI viruses in migratory and resident wild birds will continue to pose a risk for the poultry industry in Europe for the coming months. The frequent occurrence of HPAI A(H5) incursions in commercial farms (including poultry production types considered at low avian influenza risk) raises concern about the capacity of the applied biosecurity measures to prevent virus introduction. Short-term preparedness and medium- and long-term prevention strategies, including revising and reinforcing biosecurity measures, reduction of the density of commercial poultry farms and possible appropriate vaccination strategies, should be implemented. The results of the genetic analysis indicate that the viruses characterised during this reporting period belong to clade 2.3.4.4b. Some of the characterized HPAI A(H5N1) viruses detected in Sweden, Germany, Poland and United Kingdom are related to the viruses which have been circulating in Europe since October 2020; in North, Central, South and East Europe novel reassortant A(H5N1) virus has been introduced starting from October 2021. HPAI A(H5N1) was also detected in wild mammal species in Sweden, Estonia and Finland; some of these strains characterised so far present an adaptive marker that is associated with increased virulence and replication in mammals. Since the last report, 13 human infections due to HPAI A(H5N6) and two human cases due to LPAI A(H9N2) virus have been reported from China. Some of these A(H5N6) cases were caused by a reassortant virus of clade 2.3.4.4b, which possessed an HA gene closely related to the A(H5) viruses circulating in Europe. The risk of infection for the general population in the EU/EEA is assessed as low, and for occupationally exposed people, low to medium, with large uncertainty due to the high diversity of circulating viruses in the bird populations.