A(H5N1) Virus Evolution in South East Asia

Abstract

Highly Pathogenic Avian Influenza (HPAI) H5N1 virus is an ongoing public health and socio-economic challenge, particularly in South East Asia. H5N1 is now endemic in poultry in many countries, and represents a major pandemic threat. Here, we describe the evolution of H5N1 virus in South East Asia, the reassortment events leading to high genetic diversity in the region, and factors responsible for virus spread. The virus has evolved with genetic variations affecting virulence, drug-resistance, and adaptation to new host species. The constant surveillance of these changes is of primary importance in the global efforts of the scientific community.

Keywords: H5N1 virus; South East Asia; avian influenza; evolution.

Figure 1.

Diagram representing the emergence and persistence of major H5N1 reassortant viruses. Gene segments are ordered PB2, PB1, PA, HA, NP, NA, M, NS from top to bottom within the virus particle diagram. NS1 deletion (position 80–84) and NA-stalk deletion (position 49–68) are represented by discontinuous gene segments. Virus particles outlined in simple black represent potential donor viruses and those outlined in bold black represent characterized H5N1 genotypes placed at the year of first detection. Particles named “HxNy” represent potential donor viruses of which HA and NA subtypes were not identified. Arrows in dotted lines represent possible reassortment pathways of genotype development. Persistence of each genotype since first year of detection is represented by red lines, under the timeline.

Figure 2.

Phylogenetic tree of the HA gene of representative South East Asian H5N1 viruses. Analysis of HA gene based on full length gene sequences. The tree was generated by Bayesian analysis using MrBayes v3.1.2 [57]. Numbers on branches indicate Bayesian posterior probability values. The tree was rooted to A/Goose/Guangdong/1/1996. Scale bar: 0.01 substitutions per site. Colors used for the different countries are: Cambodia = light green; Indonesia = dark green; Lao PDR = pink; Malaysia = purple; Myanmar = maroon; Thailand = red; Vietnam = blue.

Figure 3.

Phylogenetic tree of the NA gene of representative South East Asian H5N1 viruses. Analysis of NA gene based on full length gene sequences. The tree was generated by Bayesian analysis using MrBayes v3.1.2 [57]. Numbers on branches indicate Bayesian posterior probability values. The tree was rooted to A/Goose/Guangdong/1/1996. Scale bar: 0.1 substitutions per site. Colors used for the different countries are: Cambodia = light green; Indonesia = dark green; Lao PDR = pink; Malaysia = purple; Myanmar = maroon; Thailand = red; Vietnam = blue.

Figure 4.

Map of major H5N1 migration events in South East Asia, based on epidemiological evidence. Arrows represent probable transmission routes. Arrows in dotted lines represent migrations for which the exact origin or the direction has not been elucidated.