Mendes, AdrianoLentsoane, OliviaAllam, MushalKhumalo, Zamantungwa Thobeka HappinessIsmail, ArshadCoetzer, Jacobus A.W.Venter, Marietjie2023-03-222023-03-222022-07-05Mendes, A.; Lentsoane, O.; Allam, M.; Khumalo, Z.; Ismail, A.; Coetzer, J.A.W.; Venter, M. Phylogenetic Characterisation of the Full Genome of a Bagaza Virus Isolate from Bird Fatalities in South Africa. Viruses 2022, 14, 1476. https://DOI.org/10.3390/v14071476.1999-4915 (online)10.3390/v14071476http://hdl.handle.net/2263/90168DATA AVAILABLITY STATEMENT : The full genome sequence reported in this study can be found on Genbank under the accession ID MW463911.SUPPLEMENTARY MATERIAL : TABLE S1 and TABLE S2.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.en© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.FlavivirusFull genome sequenceIsrael turkey meningoencephalomyelitis virusPhylogeneticsBagaza virus (BAGV)Article