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Poultry production in Bangladesh has been experiencing H5N1 highly pathogenic avian influenza (HPAI) and H9N2 low pathogenic avian influenza (LPAI) for the last 14 years. Vaccination of chickens against H5 HPAI is in practice since the end of 2012. Subsequently, the official reporting of HPAI outbreaks gradually decreased. However, the true extent of circulation of avian influenza virus (AIV) in commercial poultry production is not clear. To explore this, we conducted active surveillance in 422 small‐scale commercial layer farms in 20 villages of Mymensingh and Tangail districts of Bangladesh during 2017 and 2018 for the presence of diseases with respiratory signs. A total of 88 farms with respiratory disease problems were identified and investigated during the surveillance. In addition, 22 small‐scale commercial layer farms in the neighbouring areas with respiratory disease problem were also investigated on request from the farmers. Pooled samples of oropharyngeal swabs from live birds or respiratory tissues from dead birds of the farm suffering from respiratory disease problem were tested for molecular detection of avian influenza virus (AIV), Newcastle disease virus (NDV), infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), Mycoplasma gallisepticum and Avibacterium paragallinarum. A total of 110 farms (88 in the surveillance site and 22 in the neighbouring region) were investigated, and one or more respiratory pathogens were detected from 89 farms. AIV was detected in 57 farms often concurrently with other pathogens. Among these 57 farms, H5, H9, both H5 and H9 or non‐H5 and non‐H9 AIV were detected in 28, 9, 13 or 7 farms, respectively. Birds of most of the H5 AIV‐positive farms did not present typical clinical signs or high mortality. Twenty such farms were observed longitudinally, which had only 1.05%–5.50% mortality but a marked drop in egg production. This widespread circulation of H5 AIV along with H9 AIV and other pathogens in small‐scale commercial layer farms, often with low mortality, reaffirms the enzootic circulation of AIV in Bangladesh, which may escape syndromic surveillance focused on unusual mortality only. To reduce public health risks, strengthening of the control programme with comprehensive vaccination, enhanced biosecurity, improved surveillance and outbreak response is suggested. [ABSTRACT FROM AUTHOR]

A total of 15 dead or sick birds from 13 clinical outbreaks of avian influenza in ducks, geese, chickens and turkeys in 2017 in Bangladesh were examined. The presence of H5N1 influenza A virus in the affected birds was detected by RT‐PCR. Phylogenetic analysis based on full‐length gene sequences of all eight gene segments revealed that these recent outbreaks were caused by a new reassortant of clade 2.3.2.1a H5N1 virus, which had been detected earlier in 2015 during surveillance in live bird markets (LBMs) and wet lands. This reassortant virus acquired PB2, PB1, PA, NP and NS genes from low pathogenic avian influenza viruses mostly of non‐H9N2 subtypes but retained HA, NA and M genes of the old clade 2.3.2.1a viruses. Nevertheless, the HA gene of these new viruses was 2.7% divergent from that of the old clade 2.3.2.1a viruses circulated in Bangladesh. Interestingly, similar reassortment events could be traced back in four 2.3.2.1a virus isolates of 2013 from backyard ducks. It suggests that this reassortant virus emerged in 2013, which took two years to be detected at a broader scale (i.e. in LBMs), another two years until it became widely spread in poultry and fully replaced the old viruses. Several mutations were detected in the recent Bangladeshi isolates, which are likely to influence possible phenotypic alterations such as increased mammalian adaptation, reduced susceptibility to antiviral agents and reduced host antiviral response. [ABSTRACT FROM AUTHOR]

Here, we performed molecular and pathogenic characterization of a Newcastle disease virus (NDV) isolate from pigeons in Bangladesh. Molecular phylogenetic analysis based on the complete fusion gene sequences classified the three study isolates into genotype XXI (sub-genotype XXI.1.2) together with recent NDV isolates obtained from pigeons in Pakistan (2014–2018). The Bayesian Markov Chain Monte Carlo analysis revealed that the ancestor of Bangladeshi pigeon NDVs and the viruses from sub-genotype XXI.1.2 existed in the late 1990s. Pathogenicity testing using mean embryo death time pathotyped the viruses as mesogenic, while all isolates carried multiple basic amino acid residues at the fusion protein cleavage site. Experimental infection of chickens and pigeons revealed no or minimum clinical signs in chickens, while a relatively high morbidity (70%) and mortality (60%) were observed in pigeons. The infected pigeons showed extensive and systemic lesions including hemorrhagic and/or vascular changes in the conjunctiva, respiratory and digestive system and brain, and atrophy in the spleen, while only mild congestion in the lungs was noticed in the inoculated chickens. Histologically, consolidation in the lungs with collapsed alveoli and edema around the blood vessels, hemorrhages in the trachea, severe hemorrhages and congestion, focal aggregation of mononuclear cells, and single hepatocellular necrosis in the liver, severe congestion, multifocal tubular degeneration, and necrosis, as well as mononuclear cell infiltration in the renal parenchyma, encephalomalacia with severe neuronal necrosis with neuronophagia were noticed in the brain in infected pigeons. In contrast, only slight congestion was found in lungs of the infected chickens. qRT-PCR revealed the replication of the virus in both pigeons and chickens; however, higher viral RNA loads were observed in oropharyngeal and cloacal swabs, respiratory tissues, and spleen of infected pigeons than the chickens. In conclusion, genotype XXI.1.2 NDVs are circulating in the pigeon population of Bangladesh since 1990s, produce high mortality in pigeons with pneumonia, hepatocellular necrosis, renal tubular degeneration, and neuronal necrosis in pigeons, and may infect chickens without overt signs of clinical disease and are likely to shed viruses via the oral or cloacal routes. • The genotype XXI.1.2 NDVs is circulating in pigeons of Bangladesh. • The ancestor of Bangladeshi pigeon NDVs existed in the late 1990s. • The pigeon NDVs belonged to mesogenic pathotype and carry virulent FPCS motif. • Pigeon NDV infection in chickens was asymptomatic but shed viruses via the oral or cloacal routes. • Pigeon NDV infection in pigeons caused high morality, systemic lesions and high viral RNA load in tissues and secretions. [ABSTRACT FROM AUTHOR]

Infectious bursal disease (IBD) is a highly immunosuppressive and often fatal viral disease of young chickens. The causal agent IBD virus (IBDV) is an avian Birnavirus having two genome segments that have evolved independently and contributed to the emergence of many genotypes with different pathogenic profile. The present study aimed at genetic and pathogenic characterization of IBDVs from Bangladesh. We performed phylogenetic analysis of 15 IBDV isolates recovered from field outbreaks in chickens during 2020–2021 and compared the pathogenicity of three selected isolates belonging to different genotypes on experimental infection in chickens. Out of 15 isolates, one was the typical vvIBDV of genotype A3B2, 13 were reassortant vvIBDV of genotype A3B3 having very virulent-like segment A and early Australian-like segment B, and the remaining one isolate was a classical virulent IBDV of A1aB1 genotype. A few amino acid substitutions were observed between the genotypes in four putative antigenic sites on VP2. In a comparative pathogenicity study, the typical vvIBDV isolate BD-25(A3B2) appeared to be the most virulent with 100% morbidity and 90% mortality, followed by the segment-reassortant vvIBDV isolate BD-28(A3B3) with 50% morbidity and 30% mortality. However, the gross and histopathological lesions in the bursa of Fabricius were similar. The classical virulent isolate BD-26(A1aB1) did not cause any clinical disease. In conclusion, three genotypes of IBDV are co-circulating in poultry of Bangladesh and the typical vvIBDV of A3B2 genotype was more virulent than the reassortant vvIBDV of A3B3 genotype. Further studies are required to assess the country-wide distribution of IBDV of different genotypes and the efficacy of the currently available vaccines in protecting chickens against different genotypes of IBDV in Bangladesh. • IBDVs of 3 genotypes, A1aB1, A3B2 and A3B3, were detected in chickens of Bangladesh. • The typical vvIBDV (A3B2) was more pathogenic than the reassortant vvIBDV (A3B3). • The classical virulent IBDV (A1aB1) did not cause any clinical disease. • Amino acid substitutions were observed between genotypes at putative antigenic sites. [ABSTRACT FROM AUTHOR]

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.