Malakalinga Joseph J, Misinzo Gerald, Msalya George M, Shayo Mariana J, Kazwala Rudovick R
Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania; SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro, Tanzania; Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, P.O. Box 9524, Dar es Salaam, Tanzania.
SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro, Tanzania; Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro, Tanzania.
Acta Trop. 2023 Jun;242:106902. doi: 10.1016/j.actatropica.2023.106902. Epub 2023 Mar 21.
Rotavirus group A genomic characterization is critical for understanding the mechanisms of rotavirus diversity, such as reassortment events and possible interspecies transmission. However, little is known about the genetic diversity and genomic relationship of the rotavirus group A strains circulating in Tanzania. The genetic and genomic relationship of RVA genotypes was investigated in children under the age of five. A total of 169 Fecal samples were collected from under-five with diarrhea in Mbeya, Iringa and Morogoro regions of Tanzania. The RVA were screened in children under five with diarrhea using reverse transcription PCR for VP7 and VP4, and the G and P genotypes were determined using Sanger dideoxynucleotide cycle sequencing. Whole-genome sequencing was performed on selected genotypes. The overall RVA rate was 4.7% (8/169). The G genotypes were G3 (7/8) and G6 (1/8) among the 8 RVA positives, while the P genotypes were P[6] (4/8) and P[8] (2), and the other two were untypeable. G3P[6] and G3P[8] were the identified genotype combinations. The genomic analysis reveals that the circulating G3P[8] and G3P[6] isolates from children under the age of five with diarrhea had a DS-1-like genome configuration (I2-R2-C2-M2-axe-N2-T2-E2-H2). The phylogenic analysis revealed that all 11 segments of G3P[6] were closely related to human G3P[6] identified in neighboring countries such as Uganda, Kenya, and other African countries, implying that G3P[6] strains descended from a common ancestor. Whereas, G3P[8] were closely related to previously identified equine-like G3P[P8] from Kenya, Japan, Thailand, Brazil, and Taiwan, implying that this strain was introduced rather than reassortment events. We discovered amino acid differences at antigenic epitopes and N-linked glycosylation sites between the wild type G3 and P[8] compared to vaccine strains, implying that further research into the impact of these differences on vaccine effectiveness is warranted. The phylogenic analysis of VP7 also identified a bovine-like G6. For the first time in Tanzania, we report the emergence of novel equine-like G3 and bovine-like G6 RVA strains, highlighting the importance of rotavirus genotype monitoring and genomic analysis of representative genotypes.
A组轮状病毒的基因组特征对于理解轮状病毒多样性机制至关重要，例如重配事件和可能的种间传播。然而，对于坦桑尼亚流行的A组轮状病毒株的遗传多样性和基因组关系知之甚少。本研究调查了五岁以下儿童中A组轮状病毒（RVA）基因型的遗传和基因组关系。从坦桑尼亚姆贝亚、伊林加和莫罗戈罗地区五岁以下腹泻儿童中总共收集了169份粪便样本。使用针对VP7和VP4的逆转录PCR对五岁以下腹泻儿童进行RVA筛查，并使用桑格双脱氧核苷酸循环测序法确定G和P基因型。对选定的基因型进行全基因组测序。总的RVA检出率为4.7%（8/169）。在8例RVA阳性样本中，G基因型为G3（7/8）和G6（1/8），而P基因型为P[6]（4/8）和P[8]（2/8），另外两例无法分型。G3P[6]和G3P[8]是鉴定出的基因型组合。基因组分析显示，来自五岁以下腹泻儿童的流行G3P[8]和G3P[6]分离株具有DS-1样基因组构型（I2-R2-C2-M2-axe-N2-T2-E2-H2）。系统发育分析表明，G3P[6]的所有11个基因片段与在乌干达、肯尼亚等邻国以及其他非洲国家鉴定出的人G3P[6]密切相关，这意味着G3P[6]毒株源自一个共同祖先。而G3P[8]与先前在肯尼亚、日本、泰国、巴西和台湾鉴定出的马样G3P[P8]密切相关，这意味着该毒株是引入的而非重配事件。我们发现野生型G3和P[8]与疫苗株相比，在抗原表位和N-连接糖基化位点存在氨基酸差异，这意味着有必要进一步研究这些差异对疫苗效力的影响。VP7的系统发育分析还鉴定出一种牛样G6。我们首次在坦桑尼亚报告了新型马样G3和牛样G6 RVA毒株的出现，突出了轮状病毒基因型监测和代表性基因型基因组分析的重要性。
