Outbreak of diarrhoea in piglets caused by novel rotavirus genotype G4P[49] in north-western district of Bangladesh, February 2014

Isolation, characterization and whole-genome analysis of G9 group a rotaviruses in China: Evidence for possible Porcine-Human interspecies transmission

Group A rotaviruses (RVAs) are major causes of severe gastroenteritis in infants and young animals. To enhance our understanding of the relationship between human and animals RVAs, complete genome data are necessary. We screened 92 intestinal and stool samples from diarrheic piglets by RT‒PCR targeting the VP6 gene, revealing a prevalence of 10.9%. RVA was confirmed in two out of 5 calf samples. We successfully isolated two porcine samples using MA104 cell line. The full-length genetic constellation of the two isolates were determined to be G9-P[23]-I5-R1-C1-M1-A8-N1-T7-E1-H1, with close similarity to human Wa-like and porcine strains. Sequence analysis revealed the majority of genes were closely related to porcine and human RVAs. Phylogenetic analysis revealed that these isolates might have their ancestral origin from pigs, although some of their gene segments were related to human strains. This study reveals evidence of reassortment and possible interspecies transmission between pigs and humans in China.

Prevalence and genetic diversity of rotavirus in Bangladesh during pre-vaccination period, 1973-2023: a meta-analysis

Introduction

Rotavirus infection is a major cause of mortality among children under 5 years in Bangladesh. There is lack of integrated studies on rotavirus prevalence and genetic diversity during 1973 to 2023 in Bangladesh.

Methods

This meta-analysis was conducted to determine the prevalence, genotypic diversity and seasonal distribution of rotavirus during pre-vaccination period in Bangladesh. This study included published articles on rotavirus A, rotavirus B and rotavirus C. We used Medline, Scopus and Google Scholar for published articles. Selected literatures were published between 1973 to 2023.

Results

This study detected 12431 research articles published on rotavirus. Based on the inclusion criteria, 29 of 75 (30.2%) studies were selected. Molecular epidemiological data was taken from 29 articles, prevalence data from 29 articles, and clinical symptoms from 19 articles. The pooled prevalence of rotavirus was 30.1% (95% CI: 22%-45%, p = 0.005). Rotavirus G1 (27.1%, 2228 of 8219) was the most prevalent followed by G2 (21.09%, 1733 of 8219), G4 (11.58%, 952 of 8219), G9 (9.37%, 770 of 8219), G12 (8.48%, 697 of 8219), and G3 (2.79%, 229 of 8219), respectively. Genotype P[8] (40.6%, 2548 of 6274) was the most prevalent followed by P[4] (12.4%, 777 of 6274) and P[6] (6.4%, 400 of 6274), respectively. Rotavirus G1P[8] (19%) was the most frequent followed by G2P [4] (9.4%), G12P[8] (7.2%), and G9P[8], respectively. Rotavirus infection had higher odds of occurrence during December and February (aOR: 2.86, 95% CI: 2.43-3.6, p = 0.001).

Discussion

This is the first meta-analysis including all the studies on prevalence, molecular epidemiology, and genetic diversity of rotavirus from 1973 to 2023, pre-vaccination period in Bangladesh. This study will provide overall scenario of rotavirus genetic diversity and seasonality during pre-vaccination period and aids in policy making for rotavirus vaccination program in Bangladesh. This work will add valuable knowledge for vaccination against rotavirus and compare the data after starting vaccination in Bangladesh.

Molecular epidemiological investigation of group A porcine rotavirus in East China

Group A porcine rotavirus (RVA) is a serious threat to the breeding industry worldwide, which was associated with severe diarrhea in piglets. However, the prevalence and molecular characterizations of RVA circulating in farms of East China remains largely unknown. Five hundred and ninety-four samples were collected from 35 farms in East China from September 2017 to December 2019. The results showed that 16.8% was positive for RVA of all samples. Among different types of samples, the highest positive rate of RVA was intestinal samples (19.5%), and among pigs at different growth stages, the highest detection rate of RVA in piglets was 18.5%. Furthermore, the VP7 and VP4 genes of nine positive samples were sequenced for alignment and phylogenetic analysis. Phylogenetic analysis revealed that the nine isolates belong to four kinds of genotype combinations correspondingly: G9P[7](5/9), G5P[13](2/9), G9P[13](1/9), and G5P[7](1/9).The data suggested that multiple genotypes combinations of RVA were circulating in pigs in East China. Thus, it's necessary to continuously survey the prevalence of RVA in pigs, aiding the rational application of vaccines or other measures for the prevention and control of RVA spread.

New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method

Nanopore sequencing of virus genomes represented by segmented RNA (e.g. rotaviruses) requires the development of specific approaches. Due to the massive use of rotavirus vaccines, the relevance of monitoring the genetic diversity of circulating strains of group A rotaviruses (RVA) increased. The WHO recommended method of multiplex type-specific PCR does not allow genotyping of all clinically significant strains of RVA and identifying inter-strain differences within the genotype. We have described a new principle of amplification of RVA gene segments using six primers for reverse transcription and one universal primer for PCR for nanopore sequencing. The amplification of RVA genome was tested on clinical samples and three phylogenetically distant laboratory RVA strains, Wa (G1P[8]), DS-1 (G2P[4]) and 568 (G3P[3]). The developed protocol of sample preparation and nanopore sequencing allowed obtaining full-length sequences for gene segments of RVA, including the diagnostically significant segments 9 (VP7), 4 (VP4) and 6 (VP6) with high accuracy and coverage. The accuracy of sequencing of the rotavirus genome exceeded 99.5 %, and the genome coverage varied for different strains from 59.0 to 99.6 % (on average 86 %). The developed approach of nanopore sequencing of RVA genome could be a prospective tool for epidemiological studies and surveillance of rotavirus infection.