Novel Reassortant Highly Pathogenic Avian Influenza A(H5N2) Virus in Broiler Chickens, Egypt

Abstract

We detected a novel reassortant highly pathogenic avian influenza A(H5N2) virus in 3 poultry farms in Egypt. The virus carried genome segments of a pigeon H9N2 influenza virus detected in 2014, a nucleoprotein segment of contemporary chicken H9N2 viruses from Egypt, and hemagglutinin derived from the 2.3.4.4b H5N8 virus clade.

Keywords: Egypt; H5N2; avian influenza virus; broiler chickens; highly pathogenic avian influenza; influenza; poultry; reassortant; respiratory infections; viruses; zoonoses.

Figure 1

Genotype and reassortment analyses based on full-length genome sequences of avian influenza viruses in Egypt previously detected and those identified in this study. Colors indicate grouping of segment origin according to phylogenetic analyses (Appendix 1 Figure): highly pathogenic avian influenza (HPAI) H5N1 2.2.1.2 virus from Egypt (black); H9N2 subtype from Egypt circulating in chickens since 2010 (gray); H9N2 subtype from Egypt first detected in pigeons in 2014 (red); HPAI H5N8 viruses previously detected and circulating in Egypt (brown; different genotypes); Polymerase basic (PB) 2 segment most closely related to an H3N6 virus from Bangladesh (purple); PB1 segment most closely related to an H7N7 virus from Georgia (yellow); segments most closely related to H5N8 viruses from China (blue) or Russia (green).

Figure 2

Phylogenetic analysis of the hemagglutinin segments of reassortant highly pathogenic avian influenza H5N2 and H5N8 viruses belonging to clade 2.3.3.4b from Egypt and reference viruses. Sequence analysis was based on alignment analyses by MAFFT version 7.450 embedded in the Geneious software suite, version 11.1.7 (https://www.geneious.com) with manual editing. We performed maximum-likelihood calculations using PhyML version 3.0 (http://www.atgc-montpellier.fr/phyml); we chose the best-fit model according to the Bayesian selection criterion using Model Finder embedded in Geneious. Colors indicate grouping of segment origin and match those shown in Figure 1: blue, most closely related to H5N8 viruses from China; green, most closely related to H5N8 viruses from Russia and Europe. GenBank or GISAID accession numbers (http://www.gisaid.org) are provided for reference sequences.