| Summary: | Dissertation (MSc (Veterinary Research))--University of Pretoria, 2020. The Gs/GD (goose/Guangdong) highly pathogenic (HP) H5 influenza virus detected in China in 1996 has since evolved into genetically distinct clades and subclades. In June 2017, clade 2.3.4.4b H5N8 highly pathogenic avian influenza (HPAI) caused the first notifiable avian influenza outbreaks in gallinaceous poultry in South Africa. It spread rapidly and caused outbreaks in all provinces of the country. Farmed ostriches, commercial and backyard poultry, zoological collections and wild birds were infected. The first coastal birds that became infected were reported in December 2017, when major die-offs of terns and other coastal bird species started to occur in the southern regions of the Western and Eastern Cape provinces. Outbreaks in the area continued until June 2018. This was the first report of major mortalities from HPAI in coastal birds in South Africa since an outbreak of HPAI H5N3 was reported in common terns (Sterna hirundo) in 1961 (Rowan, 1962). The study objective was to isolate H5N8 HPAI viruses from coastal birds and to carry out molecular characterization by full genome sequencing. Viruses isolated from terns, cormorants, penguins, gulls and an oystercatcher from December 2017 to May 2018, were sequenced using Ion Torrent sequencing. Phylogenetic analysis of the eight gene segments of each isolate was used to compare them with H5N8 viruses responsible for outbreaks in terrestrial avian species in South Africa in 2017, and with selected viruses that circulated in 2017 in other parts of Africa. Radial trees of the gene segments of the coastal bird isolates were also prepared for better visualization of clustering of the viruses to assess reassortment. Two clusters within each of segments 4, 5, 7 and 8 could be distinguished. Three clusters were evident in segment 6. There was relatively greater variation in the polymerase gene segments (Segments 1, 2 and 3) but no distinct clusters within any of them were apparent. No biological ...
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