Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Phylogenetic Characterisation of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir

Version 1 : Received: 27 January 2021 / Approved: 2 February 2021 / Online: 2 February 2021 (13:32:42 CET)

A peer-reviewed article of this Preprint also exists.

Wampande, E.M.; Waiswa, P.; Allen, D.J.; Hewson, R.; Frost, S.D.; Stubbs, S.C. Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir. Microorganisms 2021, 9, 438. Wampande, E.M.; Waiswa, P.; Allen, D.J.; Hewson, R.; Frost, S.D.; Stubbs, S.C. Phylogenetic Characterization of Crimean-Congo Hemorrhagic Fever Virus Detected in African Blue Ticks Feeding on Cattle in a Ugandan Abattoir. Microorganisms 2021, 9, 438.

Journal reference: Microorganisms 2021, 9, 438
DOI: 10.3390/microorganisms9020438

Abstract

Crimean-Congo haemorrhagic fever virus (CCHFV) is the most geographically widespread tick-borne virus. However, African strains are poorly represented in sequence databases. In addition, almost all sequence data have been obtained from cases of human disease, while information regarding circulation of the virus in tick and animal reservoirs is severely lacking. Here, we characterise the complete coding region of a novel CCHFV strain, detected in African blue ticks (Rhipicephalus (Boophilus) decoloratus) feeding on cattle in an abattoir in Kampala, Uganda. These cattle originated from a farm in Mbarara, a major cattle-trading hub for much of Uganda. Phylogenetic analysis indicates that the newly sequenced strain belongs to the African genotype II clade, which predominantly contains the sequences of strains isolated from West Africa in the 1950’s and South Africa in the 1980’s. Whilst, the viral S (nucleoprotein) and L (RNA polymerase) genome segments shared >90% nucleotide similarity with previously reported genotype II strains, the glycoprotein-coding M segment shared only 80% nucleotide similarity with the next most closely related strains, which were from India and China. This segment also displayed a large number of non-synonymous mutations previously unreported in genotype II strains. Characterisation of this novel strain adds to our limited understanding of the natural diversity of CCHFV circulating in both ticks and in Africa. Such data can be used to inform the design of vaccines and diagnostics, as well as studies exploring the epidemiology and evolution of the virus for the establishment of future CCHFV control strategies.

Supplementary and Associated Material

https://zenodo.org/record/4282999#.YBkrdpP7TaY: Supplemetary sequence alignments and phylogenetic treefiles

Subject Areas

Crimean-Congo hemorrhagic fever virus; hemorrhagic fever; viral genomics; Rhipicephalus (Boophilus) decoloratus; Rhipicephalus; ticks

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