Phylogenetic analysis revealed genetic similarity of the H5N1 avian influenza viruses isolated from HPAI outbreaks in chickens in Maharashtra, India with those isolated from swan in Italy and Iran in 2006

Abstract

India was free from highly pathogenic avian influenza (HPAI) virus H5N1 till January 2006. In February 2006, our laboratory diagnosed two H5N1 outbreaks in chickens in the neighbouring districts of Nandurbar (first outbreak) and Jalgaon (second outbreak) of Maharashtra, India. Both the outbreaks occurred in a span of 12 days with heavy mortality in affected chicken populations. From the first outbreak, AIV H5N1 was isolated from cloacal swab of chickens and in case of second outbreak the virus was isolated from dead chickens in embryonated chicken eggs. Both the H5N1 viruses met all the criteria of highly pathogenic avian influenza virus. In the present investigation an attempt has been made to trace the origin of both the Indian H5N1 viruses by comparing their partial nucleotide sequences in the HA1 and HA2 regions of the HA gene with 30 other H5N1 viruses that were isolated in different countries of Asia, Europe and Africa during the years 1997 (02), 2003 (02) and 2004-2006 (26). From the study it is clear that the H5N1 virus that caused outbreak in chickens in Jalgaon did not originate from the neighbouring district of Nandurbar where the first outbreak occurred; instead both the HPAI outbreaks in Maharashtra were due to two different populations of the virus introduced at two different times. Genetic heterogeneity was observed between the H5N1 viruses isolated in 2006 in different countries; the two viruses of Malaysia and Laos formed a sublineage different from the one consisting of the viruses of India, Iran, Iraq, Italy, Nigeria and Egypt.