Type and subtype distribution of influenza virus and genetic evolution of hemagglutinin in Shanghai area in duration of 2004 - 2008

Abstract

To analyze the type and subtype distribution of influenza virus and the genetic evolution of hemagglutinin (HA) in Shanghai area during 2004 to 2008. All 962 throat swabs were collected from influenza-like patients in 5 influenza sentry hospitals and influenza outbreaks. Influenza viruses were isolated in MDCK cell lines, and then viral types and subtypes were identified. The HA of influenza A isolates selected by outbreak or sporadic patients in different areas and epidemic seasons were sequenced and analyzed by phylogenetic trees. A/H3N2, accounting for 54.9% (162/295), was the dominate subtype in recent years, but less popular in the end of 2005 to the middle of 2006 with 0% (0/16)and 23.5% (8/34) of positive specimen, respectively. There were more A/H1N1 isolates in 2005 - 2006 with 21.4% (12/56), 43.8% (7/16) and 76.5% (26/34) of positive specimen, respectively, but declined obviously in 2007 - 2008 accounting for only 0% (0/44) and 5.0% (7/139). Influenza B virus was more popular in 2004 to 2005 with 42.9% (24/56) and 56.2% (9/16), respectively, and not isolated from 2006 to 2007, then increased in 2008 accounting for 34.5% (48/139). Phylogenetic tree of HA showed that A/H1N1 isolates in the same year clustered from 2005 to 2008, and most A/H3N2 isolated were homologous in the same year during 2004 - 2008 while some were inserted to the clusters of near years and more distinguished sequences appeared. A/H1N1 and A/H3N2 isolates were all similar to the vaccine strains recommended by WHO. The distribution of influenza type and subtype kept on changing each year, but A/H3N2 dominated in most years. A/H1N1 and A/H3N2 in the same year clustered, but some A/H3N2 of near years were and evolved faster with more distinguished strains appeared in same interval. Generally, HA of influenza A isolates in Shanghai during 2004 to 2008 were similar to the WHO reference strains.