Genetic analysis and evaluation of the reassortment of influenza B viruses isolated in Taiwan during the 2004–2005 and 2006–2007 epidemics

Influenza B viruses were predominant in Taiwan during the 2004–2005 epidemic and both Victoria and Yamagata lineage viruses co-circulated. A reassortant influenza B virus that contained a Victoria lineage hemagglutinin (HA) gene and Yamagata lineage neuraminidase (NA) gene appeared first in 2002 and became predominant during the 2004–2005 epidemic. During the 2006–2007 epidemic, an influenza B outbreak occurred in Taiwan and only Victoria lineage viruses circulated. We characterized the viruses isolated in the 2006–2007 epidemic and found that the HA genes of influenza B viruses from that epidemic were highly similar to those from the 2004–2005 epidemic. We also analyzed the NA genes of isolates from the 2006–2007 epidemic and found that they all belonged to the Yamagata lineage and formed a new genetic subclade. Comparison of isolates from the 2004–2005 and 2006–2007 epidemics revealed four substitutions, N220K, E320D, K343R and E404K in NA genes. Although the HA sequences from the 2006–2007 epidemic were similar to those from the 2004–2005 epidemic, the NA sequences differed, suggesting distinct patterns of evolution of the HA and NA genes from 2004–2007 in Taiwan. This study emphasizes that the evolution of the NA genes may contribute to reemergence of influenza B viruses.