Prevalence and genomic characterization of rotavirus group A genotypes in piglets from southern highlands and eastern Tanzania

Joseph J Malakalinga; Gerald Misinzo; George M Msalya; Mariana J Shayo; Rudovick R Kazwala

doi:10.1016/j.heliyon.2022.e11750

Prevalence and genomic characterization of rotavirus group A genotypes in piglets from southern highlands and eastern Tanzania

Heliyon. 2022 Nov 23;8(11):e11750. doi: 10.1016/j.heliyon.2022.e11750. eCollection 2022 Nov.

Authors

Joseph J Malakalinga^{1

2

3}, Gerald Misinzo^{2

4}, George M Msalya⁵, Mariana J Shayo⁶, Rudovick R Kazwala¹

Affiliations

¹ Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, PO Box 3021, Morogoro, Tanzania.
² SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania.
³ Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, PO Box 9524, Dar es Salaam, Tanzania.
⁴ Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, PO Box 3019, Morogoro, Tanzania.
⁵ Department of Animal, Aquaculture, and Range Sciences, College of Agriculture, Sokoine University of Agriculture, PO Box 3004, Morogoro, Tanzania.
⁶ Muhimbili University of Health and Allied Sciences, Department of Biological and Pre-clinical Studies, PO Box 65001, Dar es Salaam, Tanzania.

Abstract

Animals have been identified as the potential reservoirs of rotavirus group A (RVA) for human infection. However, very little is known regarding the genotype and genomic profiles of circulating RVA in Tanzanian piglets. The rotavirus genetic diversity and genome analysis was assessed among piglets from Southern highlands and Eastern Tanzania. A total of 241 faecal samples were collected from piglets in the regions of Mbeya, Iringa, and Morogoro. RVA was detected and genotyped using reverse transcription polymerase chain reaction (RT-PCR). Sanger dideoxynucleotide cycle sequencing of the viral protein (VP) 4 and VP7 genes was afterwards performed to confirm the RT-PCR results. Selected genotypes were subjected to whole genome sequencing. The overall prevalence of RVA was 35.26% (85/241) in piglets (30.58% in Mbeya, 43.75% in Iringa and 31.16% in Morogoro). Upon genotyping, the G genotypes were G4 (26), G9 (10), G3 (6), G5 (3) and the remaining 40 were untypeable, while the P genotype, were P[6] (35), P[13] (3) and the remaining 47 were untypeable. The G4P[6] were the predominant genotype followed by G3P[6], G3P[13], G4P[13] and G5P[13] were most common genotypes combinations. On phylogenetic analysis, G4 was grouped to lineage V, sublineages VIIa and VIIc, G9 to lineage I, G5 to lineage II, G3 to lineage IV, P[6] to lineage V and sublineage Ic and the P[13] to lineage IV. We revealed amino acid differences between the circulating G4 and the G4 in the ProSystems RCE vaccine used in pigs. The whole genome reveals genomic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1, G5-P[x]-I5-R1-C1-M1-A8-N1-Tx-E1-H1, G3/G4-P[13]/P[6]-Ix-R1-C1-M1-A8-N1-T1-E1-H1, G3-P[6]-Ix-R1-C1-M1-A8-N1-Tx-E1-H1 and G9-P[x]-Ix-R1-C1-M1-Ax-N1-Tx-E1-H1. The VP7 gene of G9, the VP4 gene of P[6] and NSP4 (E1) gene of some genotypes clustered together and closely related to humans origin or porcine-human reassortant strains with nucleotide similarities ranging from 97.90% to 99.74% from neighboring countries, implying possibility intragenogroup reassortment and interspecies transmission. The higher strain diversity observed within the gene segments highlight the importance of genomic analysis and continuous monitoring of RVA genotypes. Further research is needed to determine the risk factors associated with RVA infection in Tanzanian pigs in order to properly design a control program.

Keywords: Genetic diversity; Piglets; Rotavirus group A; Sequencing; Tanzania; VP4 gene; VP7 gene.