Genome Analysis Linking Recent European and African Influenza Viruses
Genome Analysis Linking Recent European and African Influenza Viruses
To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.
The first cases of human infection with highly pathogenic avian influenza (HPAI) strain H5N1 occurred in Hong Kong in 1997; it was brought under control by massive culling of the chicken population. An antigenically distinct strain emerged in 2002, in the same location, and has since spread to hundreds of millions of birds. More alarming has been the growing number of human influenza (H5N1) infections; by September 2006, 251 human cases had been reported, resulting in 148 deaths. From late 2005 to early 2006, HPAI (H5N1) was detected for the first time in birds in eastern Europe, the Middle East, and northern Africa, indications that the virus was spreading, possibly aided by wild bird migration. Human cases were reported beginning in January 2006 in Egypt, Iraq, Turkey, Djibouti, and Azerbaijan.
Abstract and Introduction
Abstract
To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.
Introduction
The first cases of human infection with highly pathogenic avian influenza (HPAI) strain H5N1 occurred in Hong Kong in 1997; it was brought under control by massive culling of the chicken population. An antigenically distinct strain emerged in 2002, in the same location, and has since spread to hundreds of millions of birds. More alarming has been the growing number of human influenza (H5N1) infections; by September 2006, 251 human cases had been reported, resulting in 148 deaths. From late 2005 to early 2006, HPAI (H5N1) was detected for the first time in birds in eastern Europe, the Middle East, and northern Africa, indications that the virus was spreading, possibly aided by wild bird migration. Human cases were reported beginning in January 2006 in Egypt, Iraq, Turkey, Djibouti, and Azerbaijan.
