DNA Barcoding and Avian Flu

Influenza viruses that infect birds are called avian influenza viruses (AIV). Only influenza A viruses infect birds, and all known subtypes of influenza A viruses can infect birds. However, there are substantial genetic differences between the subtypes that typically infect both people and birds. Two subtypes called H5 and H7 each can be separated into low pathogenic and high pathogenic forms on the basis of genetic features of the virus and the severity of the illness they cause in poultry.

The subtype H7 is repeatedly found in wild birds across the world but usually not in a pathogenic form. However, once introduced into domestic birds such as poultry it may become highly pathogenic and cause outbreaks of avian influenza. We know that since 2002, H7 viruses have infected more than 100 humans who as a consequence usually showed mild clinical signs of conjunctivitis, with the exception of one fatal case in the Netherlands.

In South Korea, active surveillance has been applied to wild birds and domestic birds since a first outbreak in 2003–2004. Swab samples are obtained from poultry farms on a regular basis and authorities also scree wild bird habitats by collecting fecal samples. These habitats are located mainly along the western and southern plain regions of South Korea where migratory birds mostly aggregate in overwintering locations for species that migrate from northern Asia, including Russia and Mongolia in the fall. 

Until about 2007 the avian influence subtypes identified in the fecal samples could not be associated with bird species. Only the development of DNA Barcoding and the efforts of the bird barcoding initiative enabled researchers to identify host species, using mitochondrial DNA recovered from fecal samples. The potential of this approach is shown in a new paper that was published in PLoSONE a few days ago. 

The results provide insights into the origin of virus strains. All Korean H7 viruses belong to an Eurasian lineage and they showed substantial genetic variation, in particular in the wild birds. The team could also show that the H7 viruses from poultry were closely related to those of wild birds.

Our results suggest that domestic Korean viruses were transferred directly from wild birds through at least two independent introductions. Our data did not indicate that wild birds carried poultry viruses between Korea and China, but rather, that wild-type H7 viruses were introduced several times into different poultry populations in eastern Asia.

The idea to use DNA Barcoding to help with vector identification is not a new one but so far there haven't been many examples that clearly showed the advantage of this additional layer of information for disease prevention and management. Here is another one.