Abstract
The outbreak of highly pathogenic avian influenza (HPAI) H5N1 disease has led to significant loss of poultry and wild life and case fatality rates in humans of 60%. Wild birds are natural hosts for all avian influenza virus subtypes and over120 bird species have been reported with evidence of H5N1 infection. Influenza A viruses possess a segmented RNA genome and are characterized by frequently occurring genetic reassortment events, which play a very important role in virus evolution and the spread of novel gene constellations in immunologically naïve human and animal populations. Phylogenetic analysis of whole genome or sub-genomic sequences is a standard means for delineating genetic variation, novel reassortment events, and surveillance to trace the global transmission pathways. In this paper, special emphasis is given to the transmission and circulation of H5N1 among wild life populations, and to the reassortment events that are associated with inter-host transmission of the H5N1 viruses when they infect different hosts, such as birds, pigs and humans. In addition, we review the inter-subtype reassortment of the viral segments encoding inner proteins between the H5N1 viruses and viruses of other subtypes, such as H9N2 and H6N1. Finally, we highlight the usefulness of genomic sequences in molecular epidemiological analysis of HPAI H5N1 and the technical limitations in existing analytical methods that hinder them from playing a greater role in virological research.
Highlights
A highly pathogenic avian influenza (HPAI) H5N1 virus was firstly isolated from Guangdong, China in 1996 [1]
This review of the H5N1 viruses in wild birds described to date at Qinghai Lake suggests that they were mostly circulated by wild birds through the Central Asian flyway, and that HPAI pathotypes still exist at the lake and are still undergoing evolution
Transmission of HPAI H5N1 to Humans In May 1997, an H5N1 virus was isolated from a 3-yearold boy from Hong Kong Special Autonomous Region (SAR) for the first time [46,47,48]
Summary
A highly pathogenic avian influenza (HPAI) H5N1 virus was firstly isolated from Guangdong, China in 1996 [1]. In 2006, more European countries reported HPAI H5N1 outbreaks in poultries and wild birds and in February 2006, the first outbreak of HPAI H5N1 virus in Africa was reported in Nigeria (http://www.who.int/csr/disease/avian_influenza/ ai_timeline/en/index.html). HPAI H5N1 virus has caused outbreaks in more than 63 countries of Eurasia and Africa since 2003 and circulation is ongoing in 2011 (http://www.who.int/csr/disease/avian_ influenza/ai_timeline/en/index.html). Phylogenetic analysis of the viral genome sequences has provided a lot of evidence that wild birds are implicated in the spread of HPAI H5N1 viruses from southern China to Africa along the migratory flyways. The introduction of the HPAI H5N1 virus from Qinghai Lake to western Siberia was suggested to be caused by migratory birds revealed by the viral genomic sequencing analysis [35]. The barheaded goose isolates from this outbreak were found sharing PB2 genes common to HPAI H5N1 circulating in live bird markets in Tibet [39]
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