Ecology and molecular epidemiology of H9N2 avian influenza viruses isolated in Israel during 2000-2004 epizootic.

The first two isolates of H9N2 influenza virus were picked up from turkey and chicken hosts in May 2000, but the actual epizootic of the low pathogenicity avian influenza (LPAI) H9N2 virus started in December 2001, following a 1.5-year period of silence, during which the H10N7 and H6N3 influenza viruses were isolated sporadically. The outbreak of the H9N2 influenza began in northern Israel, from where the epizootic spread all over the country. Damage was relatively limited because of the widespread use of an inactivated vaccine. Single isolates were recorded in commercial ostrich and goose flocks, and in a wild pigeon. Apart from the routine serological tests, the diagnostics used the RT-PCR (reverse transcription polymerase chain reaction) test with type-specific primers related to the M and nucleoprotein (NP) genes, and a set of subtype-specific primers related to all the haemagglutinin (HA) and neuraminidase (NA) subtypes. All the primers were specially constructed. The part coding for N-terminus of the H chain of the HA gene of 61 out of 400 isolates was sequenced. The isolates showed a high rate of mutability, and differed distinctly from the H9 prototype strain; they belong to the same phylogenetic lineage divided into three sublineages, one of which exhibited a unique cleavage-site motif RSKR. The result indicates that two parallel evolutionary trends originated from the same local "prototype" isolate.