Evolutionary and Ecological Dynamics of Transboundary Disease Caused by H5N1 Virus in Southeast Asia

Abstract

Southeast Asia has been the breeding ground for many emerging diseases in the past decade, and it is in this region that new genetic variants of HPAI H5N1 viruses have been emerging. Cross-border movement of animals accelerates the spread of H5N1, and the changing environmental conditions also exert strong selective pressure on the viruses. The transboundary zoonotic diseases caused by H5N1 pose a serious and continual threat to global economy and public health. Here, we divided the H5N1 viruses isolated in Southeast Asia during 2003-2009 into four groups according to their phylogenetic relationships among HA gene sequences. Molecular evolution analysis suggests populations in expansion rather than a positive selection for group 2 and group 3, yet group 4 is under strong positive selection. Site 193 was found to be a potential glycosylation site and located in receptor-binding domain. Note that site 193 tends to appear in avian isolates instead of human strains. Population dynamics analysis reveals that the effective population size of infections in Southeast Asia has undergone three obvious increases, and the results are consistent with the epidemiological analysis. Ecological and phylogeographical analyses show that agro-ecological environments, migratory birds, domestic waterfowl, especially free-ranging ducks, are crucial in the occurrence, maintenance and spread of H5N1 virus. The epidemiological links between Indonesia and Suphanburi observed suggest that viruses in Indonesia were originated from multiple introductions.

Tracking the Evolution in Phylogeny, Structure and Function of H5N1 Influenza Virus PA Gene

“…In addition, all Indonesian viruses ( n = 44), including clades 2.1.1, 2.1.2, 2.1.3 and its subclades, formed an independent branch with a high bootstrap value. All Vietnamese viruses (clades 1, 2.3.2, 2.3.4 and their subclades) had evolved into two distinct branches as previously reported (Wei et al., ). One is composed of clades 1 and 1.1 viruses, and the other consists of clades 2.3.3, 2.3.4 and their subclades viruses.…”

“…Successful culling of all poultry in Hong Kong seemed to have controlled the outbreaks, but additional H5N1 viruses in 1999 and 2001 revealed that variants of the virus continuously circulate in this region (Cauthen et al., ; Wei et al., ). In late 2003 and early 2004, HPAI H5N1 outbreaks recurred with unexplained reasons and the viruses spread persistently to poultry species in China and many South‐East Asian countries, such as Vietnam, Cambodia, Thailand and Indonesia, causing sporadic transmission to humans and catastrophic damage to the poultry industry (Wei et al., ). The movements of wild birds and trade in domestic poultry and wild birds may serve as potential agents for the global dispersion of HPAI H5N1 viruses (Fang et al., ), and other factors such as environment also play a vital role in the occurrence and spread of HPAI H5N1 viruses (Fang et al., ).…”

Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia

“…Cases of human infection with swine‐origin A(H3N2) and variant A(H3N2)v are a public health concern in North America, and human A(H3N2)v infection has been suggested to be associated with agricultural fairs where people get in close contact with infected pigs (Lindstrom et al., ; Jhung et al., ). Other parts of the world, such as South‐East Asia, are regarded priority areas for influenza surveillance, due to the high density and the complex interactions between humans, pigs, poultry and agricultural land (Wei et al., ). Since 2003, South‐East Asia has experienced high pressure from the HP H5N1 virus, resulting in the death or destruction of more than 175 million birds and in 463 human cases, including 318 deaths (Pfeiffer et al., ; World Health Organization, ,b).…”

Climate change and multiple emerging infectious diseases

“…Alternatively, early in the H5N1 highly pathogenic avian influenza (HPAI) panzootic, wild bird migration was offered as a key amplifier. Latterly, the illegal global trade in poultry was found to be a more potent factor in spread (Wei et al, 2013).…”