Avian influenza (H5N1) virus of clade 2.3.2 in domestic poultry in India

Abstract

South Asia has experienced regular outbreaks of H5N1 avian influenza virus since its first detection in India and Pakistan in February, 2006. Till 2009, the outbreaks in this region were due to clade 2.2 H5N1 virus. In 2010, Nepal reported the first outbreak of clade 2.3.2 virus in South Asia. In February 2011, two outbreaks of H5N1 virus were reported in the State of Tripura in India. The antigenic and genetic analyses of seven H5N1 viruses isolated during these outbreaks were carried out. Antigenic analysis confirmed 64 to 256-fold reduction in cross reactivity compared with clade 2.2 viruses. The intravenous pathogenicity index of the isolates ranged from 2.80-2.95 indicating high pathogenicity to chickens. Sequencing of all the eight gene-segments of seven H5N1 viruses isolated in these outbreaks was carried out. The predicted amino acid sequence analysis revealed high pathogenicity to chickens and susceptibility to the antivirals, amantadine and oseltamivir. Phylogenetic analyses indicated that these viruses belong to clade 2.3.2.1 and were distinct to the clade 2.3.2.1 viruses isolated in Nepal. Identification of new clade 2.3.2 H5N1 viruses in South Asia is reminiscent of the introduction of clade 2.2 viruses in this region in 2006/7. It is now important to monitor whether the clade 2.3.2.1 is replacing clade 2.2 in this region or co-circulating with it. Continued co-circulation of various subclades of the H5N1 virus which are more adapted to land based poultry in a highly populated region such as South Asia increases the risk of evolution of pandemic H5N1 strains.

Figure 1. Phylogenetic relationships of the coding sequences of hemagglutinin (HA) genes of representative influenza A viruses.

Analysis was based on full length or near full length sequences. The numbers next to the branch nodes indicate bootstrap values/posterior probabilities expressed as percentages from, respectively, 500 bootstrap replicates of a maximum likelihood tree and posterior probabilities from a MrBayes 3.2 analysis (see methods). Not all support valuess are shown due to space constraints. Numbers labeled on the HA tree refer to the WHO H5N1 clade designations (http://www.who.int/csr/disease/avian_influenza/guidelines/nomenclature/en). Viruses isolated in this work are in green and other recent Indian, Bangladesh and Bhutan viruses are in red. Scale bar, indicates nucleotide substitutions per site.

Figure 2. Phylogenetic relationships of neuraminidase (NA) genes of representative influenza A viruses.

Details are as in the legend to Figure 1. The presence of deletions in the stalk region are indicated by Δ20aa. Genotype designations are from references 14 and 15.

Figure 3. Phylogenetic relationships of polymerase acidic (PA) genes of representative influenza A viruses.

Details are as in the legends to Figures 1 and 2.

Figure 4. Circulation of H5N1 viruses in South Asia till 2009.

Figure 5. Circulation of H5N1 viruses in South Asia since 2010.