Molecular characterization of highly pathogenic avian influenza clade 2.3.4.4b H5N8 viruses in terns and other coastal birds in South Africa in 2018

Abstract

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 significance to the clusters was found. Multiple sequence alignments were investigated to identify genetic markers. No strong adaptive host pressures were evident. Results indicated that there may have been a single introduction of the virus into the coastal bird population, possibly from the terrestrial wild bird population. The terrestrial strains were basal to the coastal bird strains, but still not closely related. The coastal bird viruses have a common ancestor with the Namibian outbreaks that occurred at the beginning of 2019 and they may have been the source of the Namibian outbreaks. Alternatively, an introduction of the virus into the Namibian birds could have been independent of the South African incursions.