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Article

Phylogenetic Characterisation of the Full Genome of a Bagaza Virus Isolate from Bird Fatalities in South Africa

1
Zoonotic Arbo- and Respiratory Virus Research Program, Centre for Viral Zoonoses, University of Pretoria, Pretoria 0007, South Africa
2
Sequencing Core Facility, National Institute of Communicable Disease, Johannesburg 2192, South Africa
3
Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria 0001, South Africa
*
Author to whom correspondence should be addressed.
Viruses 2022, 14(7), 1476; https://doi.org/10.3390/v14071476
Submission received: 22 April 2022 / Revised: 26 June 2022 / Accepted: 28 June 2022 / Published: 5 July 2022
(This article belongs to the Special Issue Flaviviruses and Flavivirus Vaccines)

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 3′UTR 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 3′UTR 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.
Keywords: flavivirus; Bagaza virus; full genome sequence; Israel turkey meningoencephalomyelitis virus; phylogenetics flavivirus; Bagaza virus; full genome sequence; Israel turkey meningoencephalomyelitis virus; phylogenetics

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MDPI and ACS Style

Mendes, 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

AMA Style

Mendes A, Lentsoane O, Allam M, Khumalo Z, Ismail A, Coetzer JAW, Venter M. Phylogenetic Characterisation of the Full Genome of a Bagaza Virus Isolate from Bird Fatalities in South Africa. Viruses. 2022; 14(7):1476. https://doi.org/10.3390/v14071476

Chicago/Turabian Style

Mendes, Adriano, Olivia Lentsoane, Mushal Allam, Zamantungwaka Khumalo, Arshad Ismail, Jacobus A. W. Coetzer, and Marietjie Venter. 2022. "Phylogenetic Characterisation of the Full Genome of a Bagaza Virus Isolate from Bird Fatalities in South Africa" Viruses 14, no. 7: 1476. https://doi.org/10.3390/v14071476

APA Style

Mendes, A., Lentsoane, O., Allam, M., Khumalo, Z., Ismail, A., Coetzer, J. A. W., & Venter, M. (2022). Phylogenetic Characterisation of the Full Genome of a Bagaza Virus Isolate from Bird Fatalities in South Africa. Viruses, 14(7), 1476. https://doi.org/10.3390/v14071476

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