Phylogenetic studies of influenza B viruses isolated in southern Africa: 1998–2001

Influenza B viruses isolated in southern Africa during the period from 1998 to 2001 were analysed by sequence analysis of the viral haemagglutinin HA1 subunit and the phylogenetic relationships were determined. Influenza B activity varied considerably in South Africa during the 4-year study period with no activity detected in 2000. Phylogenetic analysis revealed that viruses isolated in 1998 from a localised outbreak in Durban belonged to two distinct sub-lineages. Some of the influenza B viruses isolated throughout South Africa in 1999 as well as several viruses obtained from Mozambique in the same year were closely related to the B/Yamanashi/166/98-like viruses. In contrast, the majority of the 1999 isolates, represented by B/Johannesburg/5/99, exhibited considerable drift from the B/Yamanashi/166/98 stain. The viruses isolated during the 2001 season fell into two sub-lineages, one of which had evolved from the B/Johannesburg/5/99-like viruses and the other which had evolved from the group of viruses that included one of the 1998 Durban isolates. These molecular epidemiological studies reveal a diverse and complex pattern of influenza B virus strains circulating in southern Africa.