The Incursion and Spread of Highly Pathogenic Avian Influenza H5N8 Clade 2.3.4.4 Within South Africa

The report of a mass die-off of white-winged terns (Chlidonias leucopterus) along the shores of Lake Victoria in Uganda in January 2017 was a warning that highly pathogenic avian influenza (HPAI) H5N8 clade 2.3.4.4 had entered the avian populations of the African Rift Valley. In early June 2017, Zimbabwe reported an outbreak of the virus in commercial breeder chickens near Harare, and on June 19, 2017, the first case of HPAI H5N8 was confirmed in a broiler breeder operation near Villiers, Mpumalanga Province, South Africa, representing the first ever notifiable influenza in gallinaceous poultry in South Africa. Forty viruses were isolated from wild birds, backyard hobby fowl, zoo collections, commercial chickens, and commercial ostriches over the course of the outbreak and full genomes were sequenced and compared to determine the epidemiologic events in the introduction and spread of clade 2.3.4.4 H5N8 across the country. We found that multiple virus variants were involved in the primary outbreaks in the north-central regions of South Africa, but that a single variant affected the southernmost regions of the continent. By November 2017 only two of the nine provinces in South Africa remained unaffected, and the layer chicken industry in Western Cape Province was all but decimated. Two distinct variants, suggesting independent introductions, were responsible for the first two index cases and were not directly related to the virus involved in the Zimbabwe outbreak. The role of wild birds in the incursion and spread was demonstrated by shared recent common ancestors with H5N8 viruses from West Africa and earlier South African aquatic bird low pathogenicity avian influenza viruses. Improved wild bird surveillance will play a more critical role in the future as an early warning system.