Phylogenetic studies of South African influenza A viruses: 1997–1999

Background: The National Institute for Virology (NIV) in Johannesburg has an active surveillance programme to monitor influenza activity and to obtain viral isolates for characterisation at both the antigenic and the molecular level. These data also provide a clearer understanding of the genetic relationships of the South African viruses with those circulating in other countries. Methods: Influenza A H3N2 and H1N1 viruses isolated from 1997 to 1999 were analysed by sequence analysis of the viral haemagglutinin gene, and phylogenetic relationships were determined. Results: Most influenza activity was due H3N2 viruses, while H1N1 activity was generally low. The H3N2 viruses responsible for the major epidemic in 1998 were found to be due to the introduction of the antigenically distinct A/Sydney/5/97-like strains into the country in April. The 1999 H3N2 isolates exhibited drift from the A/Sydney/5/97 virus at the genetic level and shared a close homology with some recent Australian and New Zealand virus isolates. Phylogenetic analysis revealed that several 1997 H1N1 isolates were similar to the A/Wuhan/371/95-like variants. These were the first H1N1 viruses of this lineage to be isolated in the Southern Hemisphere. The 1998 and 1999 H1N1 isolates were genetically more related to the previous A/Jhb/82/96 vaccine strain than to the 1999 A/Beijing/262/95 vaccine strain. Conclusions: These studies have shown that the viruses present in South Africa during a specific year are not always closely related to those in other Southern Hemisphere countries and thus provide a valuable contribution to the Southern Hemisphere vaccine formulation decision.