Highly pathogenic H5N1 avian influenza viruses exhibit few barriers to gene flow in Vietnam

Abstract

Locating areas where genetic change is inhibited can illuminate underlying processes that drive evolution of pathogens. The persistence of highly pathogenic H5N1 avian influenza in Vietnam since 2003, and the continuous molecular evolution of Vietnamese avian influenza viruses, indicates that local environmental factors are supportive not only of incidence but also of viral adaptation. This article explores whether gene flow is constant across Vietnam, or whether there exist boundary areas where gene flow exhibits discontinuity. Using a dataset of 125 highly pathogenic H5N1 avian influenza viruses, principal components analysis and wombling analysis are used to indicate the location, magnitude, and statistical significance of genetic boundaries. Results show that a small number of geographically minor boundaries to gene flow in highly pathogenic H5N1 avian influenza viruses exist in Vietnam, but that overall there is little division in genetic exchange. This suggests that differences in genetic characteristics of viruses from one region to another are not the result of barriers to H5N1 viral exchange in Vietnam, and that H5N1 avian influenza is able to spread relatively unimpeded across the country.

Figure 1

Two criteria for boundary element connections. In drawing 1, two boundary elements (represented by circles) may be connected into a boundary because the directions of their associated slopes are <90° different. The third boundary element in drawing 1 has an opposing direction and will not be combined into a boundary. Two boundary elements in drawing 2 will be connected into a boundary because the bearing of the connection is >30° different than the direction of the slope. The third boundary element in drawing 2 has similar bearing for both the boundary connection and the direction of change, so connecting this would not accurately reflect the presence of a boundary. Adapted from Rosenberg and Anderson (2010).

Figure 2

PCA scores for the first two factors, plotted according to region of viral incidence.

Figure 3

Interpolated factor scores for the first and second principal components. Average factor scores were created for provinces with more than one H5N1 influenza virus.

Figure 4

PCA factor scores according to year of viral isolation.

Figure 5

Statistically significant boundaries detected in the overall 2003–2007 dataset. Black circles indicate province centroids. Boundary elements are represented in light gray, thickness indicates degree of magnitude and arrows indicate the direction of the gradient. Boundary connections are represented in dark gray.

Figure 6

Statistically significant barriers detected in 2003–2004 viruses. Province centroids are shown in black circles, individual boundary elements in light gray, and connected boundaries in dark gray. Magnitude is indicated by thickness, while direction of genetic gradient is indicated by an arrow.