A new reassortant clade 2.3.2.1a H5N1 highly pathogenic avian influenza virus causing recent outbreaks in ducks, geese, chickens and turkeys in Bangladesh

Abstract

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. K E Y W O R D S Bangladesh, clade 2.3.2.1a, domestic poultry, H5N1 HPAIV, new reassortant | 2121 NOORUZZAMAN et Al. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Nooruzzaman M, Mumu TT, Hasnat A, et al. A new reassortant clade 2.3.2.1a H5N1 highly pathogenic avian influenza virus causing recent outbreaks in ducks, geese, chickens and turkeys in Bangladesh. Transbound Emerg Dis.

Controlling Avian Influenza Virus in Bangladesh: Challenges and Recommendations

“…The majority of frequently identified AIV subtypes arise from outbreaks in backyard, small to medium commercial farms and from surveillance sampling at LBMs [ 30 , 56 , 73 , 74 , 75 ]. Sampling from wild aquatic birds appears to be more unsteady [ 22 , 36 , 76 ].…”

“…Interestingly, the latter two clades, 2.3.4.2 and 2.3.2.1c, have been detected in chickens at LBM but never in wild birds [ 85 ]. Since 2014, only viruses of the clade 2.3.2.1a prevailed in domestic poultry, wild and migratory birds, and in LBMs of Bangladesh [ 30 , 47 , 70 , 74 , 75 ]. The only fatal human HPAIV infection was detected in Bangladesh in 2013 and was caused by a clade 2.3.2.1a virus [ 86 ].…”

“…In June 2015, a new reassortant genotype of the clade 2.3.2.1a (here designated as clade 2.3.2.1a (new) R1) was detected in apparently healthy free-range ducks in wetland areas and poultry in LBMs [ 22 ]. The reassortment events shaping this genotype started even earlier as four surveillance samples from domestic ducks obtained in 2013 had a similar gene constellation [ 74 ]. These viruses are reassortants between HPAI and LPAI viruses: Their HA , NA , and M genes derived from circulating clade 2.3.2.1a viruses, whereas PB2 , PB1 , PA , NP , and NS genes originated from unknown Eurasian LPAI viruses ( Table 3 ).…”

“…These viruses are reassortants between HPAI and LPAI viruses: Their HA , NA , and M genes derived from circulating clade 2.3.2.1a viruses, whereas PB2 , PB1 , PA , NP , and NS genes originated from unknown Eurasian LPAI viruses ( Table 3 ). Of note, the HA gene of the new clade 2.3.2.1a viruses is about 2.7% divergent from the old clade 2.3.2.1a viruses, but, in only two out of 66 isolates examined, amino acid substitutions in antigenic sites 1 (position 141) and 3 (position 129), respectively, were noticed [ 74 ]. Subsequently, this genotype has been extensively detected in domestic poultry associated with clinical outbreaks [ 74 ].…”

Avian influenza overview February– August 2019

“…The only wild bird case of the Asian lineage HPAI A(H5N1) was a house crow (Corvus splendens) reported by Nepal in the relevant time period (Figure 10). Geographical distribution, based on available geocoordinates, of confirmed HPAI A(H5N1) outbreaks in domestic birds (circles) and wild birds (triangles); grey symbols indicate outbreaks that occurred from 15 February 2018 to 15 February 2019, red symbols indicate outbreaks that occurred from 16 February to 15 August 2019 (n=83) (FAO, online)Information extracted from the scientific literatureNooruzzaman et al (2019) analyzed genomes of A(H5N1) detected in ducks, geese, chickens and turkeys in 2017 in Bangladesh. The viruses were classified in clade 2.3.2.1a, but a number of internal segments originated from LPAI viruses.…”