Active virological surveillance in backyard ducks in Bangladesh: detection of avian influenza and gammacoronaviruses

Abstract

Domestic waterfowl play an important role in the perpetuation and transmission of avian pathogens including avian influenza viruses (AIV) of low and high pathogenicity, which pose severe economic and public health concerns in Bangladesh. This study focused on active surveillance of several avian viral pathogens with a special reference to AIV in selected backyard duck populations in Bangladesh. A total of 500 pooled oropharyngeal and cloacal samples from individual ducks of four districts were tested by real time PCRs for the presence of AIV, avian avulavirus-1, anatid herpesvirus-1, avian parvovirus, avian bornavirus and avian coronavirus. The investigation identified 27 (5.4%) ducks positive for AIV and 12 (2.4%) positive for avian coronavirus. In 13 samples, RNA specific for AIV H4N6 was detected. Phylogenetic analysis of the AIV haemagglutinin H4 and neuraminidase N6 genes suggested a clustering of Bangladeshi AIV H4N6 in Eurasian lineage group 2. Other AIV positive samples had very low virus loads (Cq > 36) and were not subtyped. Coronaviral sequences of a fragment of the polymerase gene were related to Eurasian-Australian duck gammacoronaviruses. Our current active surveillance in free-range domestic backyard ducks in Bangladesh failed to detect highly pathogenic (HP) AIV in contrast to our previous passive monitoring study. Nevertheless, active monitoring of domestic duck populations may be important to highlight presence and transmission dynamics of economically less important AIV that still may serve as reassortment partners for the generation of new HP and zoonotic AIV. RESEARCH HIGHLIGHTS. Active surveillance for viral pathogens in domestic free-range backyard ducks.. Detection of avian influenza virus subtype H4N6.. First identification of avian gammacoronavirus in ducks in Bangladesh.

Circulation of three genotypes and identification of unique mutations in neutralizing epitopes of infectious bronchitis virus in chickens in Bangladesh

“…Single-step RT-qPCR assays were performed with previously designed unique oligonucleotide primers for the detection of the untranslated regions (5′-UTR) and a fragment of the polymerase gene of avian gammacoronaviruses (AvCoV) in a single assay [ 13 ]. The assay was carried out using a Luna Universal One-Step RT-qPCR Kit (New England Biolabs Inc., USA) containing SYBR Green reagents following a slightly modified previous protocol [ 28 ]. The final reaction volume was 12.5 μL, including 2.5 μL of RNA template, 5 μL of 2x RT-PCR SYBR reaction mix, 0.5 μL of Luna WarmStart RT Enzyme Mix, 2.5 μL of nuclease-free water, and 2 μL of IBV primer mix (10 pmol each).…”

“…Positive samples were further screened for IBV using probe-based (TaqMan) single-step RT-qPCR assays, using a Luna Universal Probe One-Step RT-qPCR Kit (New England Biolabs Inc., USA) and IBV-specific oligonucleotides [ 8 ]. All samples were screened for other respiratory viral pathogens, including avian influenza virus (AIV) and Newcastle disease virus (NDV) following a previously described protocol [ 28 ].…”

“…Infectious bronchitis (IB) is an acute, highly contagious disease caused by IBV that mainly infects the respiratory system but also affects other organs such as kidneys and the reproductive system of layer and breeder chickens of all ages worldwide [ 11 ]. AvCoVs also infect other domestic birds, such as turkeys, guinea fowl, quail, ducks, and migratory birds [ 7 , 8 , 13 , 28 ]. IB in chickens is characterized predominantly by tracheal rales, coughing, sneezing, and thickened air sacs.…”

Controlling Avian Influenza Virus in Bangladesh: Challenges and Recommendations

“…Apart from the endemic LPAI H9N2 viruses, other LPAI virus subtypes identified in domestic birds from LBM samples in Bangladesh include H4N6 and H11N3. Subtypes H1N1, H1N3, H1N5, H2N4, H2N5, H3N1, H3N2, H4N2, H5N2, H6N1, H7N1, H7N5, and H7N9 ( Supplemental Table S1 ) have been detected sporadically and mostly in domestic birds, especially backyard ducks or ducks sold in LBMs, but seldom in wild birds [ 22 , 29 , 36 ].…”

“…Both viruses cause significant economic damage in poultry production and threaten public health by their zoonotic propensity [ 27 ]. AIV surveillance studies in Bangladesh [ 22 , 26 , 28 , 29 ] have shown that domestic ducks play an important role in the transmission and emergence of new AIV sub- and genotypes.…”