High prevalence of circulating DS-1-like human rotavirus A and genotype diversity in children with acute gastroenteritis in Thailand from 2016 to 2019

Abstract

Background: Human rotavirus A (RVA) infection is the primary cause of acute gastroenteritis (AGE) in infants and young children worldwide, especially in children under 5 years of age and is a major public health problem causing severe diarrhea in children in Thailand. This study aimed to investigate the prevalence, genotype diversity, and molecular characterization of rotavirus infection circulating in children under 15 years of age diagnosed with AGE in Thailand from January 2016 to December 2019.

Methods: A total of 2,001 stool samples were collected from children with gastroenteritis (neonates to children <15 years of age) and tested for RVA by real-time polymerase chain reaction (RT-PCR). Amplified products were sequenced and submitted to an online genotyping tool for analysis.

Results: Overall, 301 (15.0%) stool samples were positive for RVA. RVA occurred most frequently among children aged 0-24 months. The seasonal incidence of rotavirus infection occurred typically in Thailand during the winter months (December-March). The G3P[8] genotype was identified as the most prevalent genotype (33.2%, 100/301), followed by G8P[8] (10.6%, 32/301), G9P[8] (6.3%, 19/301), G2P[4] (6.0%, 18/301), and G1P[6] (5.3%, 16/301). Uncommon G and P combinations such as G9P[4], G2P[8], G3P[4] and G3P[9] were also detected at low frequencies. In terms of genetic backbone, the unusual DS-1-like G3P[8] was the most frequently detected (28.2%, 85/301), and the phylogenetic analysis demonstrated high nucleotide identity with unusual DS-1-like G3P[8] detected in Thailand and several countries.

Conclusions: A genetic association between RVA isolates from Thailand and other countries ought to be investigated given the local and global dissemination of rotavirus as it is crucial for controlling viral gastroenteritis, and implications for the national vaccination programs.

Keywords: Acute gastroenteritis; DS-1-like; Rotavirus A.

Figure 1. Age distribution of RVA infection among children in Thailand from January 2016 to December 2019. Bar graphs denote the total number of RV-positive samples.

Figure 2. Distribution of RVA genotypes between January 2016 and December 2019. The monthly number of samples from children diagnosed with AGE is shown in grey. Bar graphs show the number of RV-positive cases.

Figure 3. Phylogenetic tree of the VP6, VP7 and VP4 genes. The tree was constructed using the Tamura 3-parameter model, and the maximum likelihood method with 1,000 replicates bootstrapping and bootstrap values >70% considered significant.

(A) Partial VP6 gene analyzed in this tree contained 361 nucleotides, (B) partial VP7 gene analyzed in this tree contained 561 nucleotides and (C) partial VP four gene analyzed in this tree contained 438 nucleotides.