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Open AccessArticle

Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

1
Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
2
Virology Laboratory, Department of Pathology & Microbiology, University Teaching Hospital, Adult and Emergency Hospital, Lusaka 10101, Zambia
3
Department of Paediatrics & Child Health, School of Medicine, University of Zambia, Ridgeway, Lusaka RW50000, Zambia
4
World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo
5
Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa
6
South African Medical Research Council, 1 Soutpansberg Road, Pretoria 0001, South Africa
*
Author to whom correspondence should be addressed.
Pathogens 2020, 9(8), 663; https://doi.org/10.3390/pathogens9080663
Received: 24 July 2020 / Revised: 14 August 2020 / Accepted: 14 August 2020 / Published: 17 August 2020
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans. View Full-Text
Keywords: whole-genome; genotype constellation; interspecies transmission; reassortment; porcine; porcine-like human whole-genome; genotype constellation; interspecies transmission; reassortment; porcine; porcine-like human
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Maringa, W.M.; Mwangi, P.N.; Simwaka, J.; Mpabalwani, E.M.; Mwenda, J.M.; Peenze, I.; Esona, M.D.; Mphahlele, M.J.; Seheri, M.L.; Nyaga, M.M. Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia. Pathogens 2020, 9, 663.

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