Genetic Characterisation of South African and Mozambican Bovine Rotaviruses Reveals a Typical Bovine-like Artiodactyl Constellation Derived through Multiple Reassortment Events

Amy Strydom; Celeste M Donato; Martin M Nyaga; Simone S Boene; Ina Peenze; Milton T Mogotsi; Eva D João; Benilde Munlela; A Christiaan Potgieter; Mapaseka L Seheri; Nilsa de Deus; Hester G O'Neill

doi:10.3390/pathogens10101308

Genetic Characterisation of South African and Mozambican Bovine Rotaviruses Reveals a Typical Bovine-like Artiodactyl Constellation Derived through Multiple Reassortment Events

Pathogens. 2021 Oct 12;10(10):1308. doi: 10.3390/pathogens10101308.

Authors

Amy Strydom¹, Celeste M Donato^{2

3

4}, Martin M Nyaga^{5

6}, Simone S Boene^{7

8}, Ina Peenze⁹, Milton T Mogotsi¹, Eva D João⁷, Benilde Munlela^{7

8}, A Christiaan Potgieter^{10

11}, Mapaseka L Seheri⁹, Nilsa de Deus^{7

12}, Hester G O'Neill¹

Affiliations

¹ Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein 9300, South Africa.
² Enteric Diseases Group, Murdoch Children's Research Institute, Parkville 3010, Australia.
³ Department of Paediatrics, Theniversity of Melbourne, Parkville 3010, Australia.
⁴ Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne 3052, Australia.
⁵ Next Generation Sequencing Unit, University of the Free State, Bloemfontein 9300, South Africa.
⁶ Division of Virology, Faculty of Health Sciences, School of Pathology, University of the Free State, Bloemfontein 9300, South Africa.
⁷ Instituto Nacional de Saúde (INS), Distrito de Marracuene 1120, Mozambique.
⁸ Biotechnology Center, Eduardo Mondlane University, Maputo 1100, Mozambique.
⁹ Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria 0001, South Africa.
¹⁰ Biochemistry, Focus Area Human Metabolomics, North-West University, Potchefstroom 2520, South Africa.
¹¹ Deltamune (Pty) Ltd., Unit 34 Oxford Office Park, 3 Bauhinia Street, Highveld Techno Park, Centurion 0157, South Africa.
¹² Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Maputo 1100, Mozambique.

Abstract

This study presents whole genomes of seven bovine rotavirus strains from South Africa and Mozambique. Double-stranded RNA, extracted from stool samples without prior adaptation to cell culture, was used to synthesise cDNA using a self-annealing anchor primer ligated to dsRNA and random hexamers. The cDNA was subsequently sequenced using an Illumina MiSeq platform without prior genome amplification. All strains exhibited bovine-like artiodactyl genome constellations (G10/G6-P[11]/P[5]-I2-R2-C2-M2-A3/A11/A13-N2-T6-E2-H3). Phylogenetic analysis revealed relatively homogenous strains, which were mostly related to other South African animal strains or to each other. It appears that these study strains represent a specific bovine rotavirus population endemic to Southern Africa that was derived through multiple reassortment events. While one Mozambican strain, MPT307, was similar to the South African strains, the second strain, MPT93, was divergent from the other study strains, exhibiting evidence of interspecies transmission of the VP1 and NSP2 genes. The data presented in this study not only contribute to the knowledge of circulating African bovine rotavirus strains, but also emphasise the need for expanded surveillance of animal rotaviruses in African countries in order to improve our understanding of rotavirus strain diversity.

Keywords: A13 genotype; South Africa and Mozambique; artiodactyl genome constellations; bovine rotavirus; interspecies transmission; transboundary transmission.

Abstract

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