Abstract:
Bagaza virus (BAGV), a member of the Ntaya serogroup in the Flavivirus genus of the
Flaviviridae, was isolated from the brain tissue of a Himalayan monal pheasant that died following
neurological signs in Pretoria, South Africa in 2016. Next-generation sequencing was carried out
on this isolate resulting in a genome sequence of 10980nt. The full genome sequence of this isolate,
designated ZRU96-16, shared 98% nucleotide identity with a BAGV isolate found in Culex univitattus
mosquitoes from Namibia and 97% nucleotide identity with a Spanish BAGV sequence isolated from
an infected partridge. In total, seven amino acid variations were unique to ZRU96-16 after alignment
with other BAGV and Israel turkey meningoencephalomyelitis (ITV) genomes. The 30UTR sequence
of ZRU96-16 was resolved with sufficient detail to be able to annotate the variable and conserved
sequence elements within this region. Multiple sequence alignment of the 30UTR suggested that it
could be useful in lineage designation as more similar viruses carried similar mutations across this
region, while also retaining certain unique sites. Maximum likelihood phylogenetic analysis revealed
two clusters containing both BAGV and ITVs from Europe, the Middle East and Africa. Broadly,
temporal clustering separated isolates into two groups, with one cluster representing viruses from
the 1960–2000’s and the other from 2010 onwards. This suggests that there is consistent exchange of
BAGV and ITV between Europe and Africa. This investigation provides more information on the
phylogenetics of an under-represented member of the Flaviviridae and provides an avenue for more
extensive research on its pathogenesis and geographic expansion.
