Epidemiology, molecular genetic, and evolutionary analysis of humanrotavirus a infection in Thailand

Abstract

Rotavirus A (RVA) infection remains one of the major causes of viral diarrhea in young children worldwide. Despite the success of RVA vaccines including RotaTeq in significantly reducing morbidity and disease severity associated with hospitalization, national immunization against RVA have only just begun in Thailand in 2020. Consequently, possible RV vaccine shedding among pediatric vaccine recipients has not been rigorously documented here.The first part of my study was summarize the virology, disease burden, prevalence, distribution of genotypes and seasonality of RVs, and the current status of RV vaccination in Southeast Asia (Cambodia, Indonesia, Lao People’s Democratic Republic, Malaysia, Myanmar, Philippines, Singapore, Thailand, and Vietnam) from 2008 to 2018. According to the RV surveillance data for Southeast Asia, 40.78% of all diarrheal disease in children were caused by RV infection. Mortality was inversely related to socioeconomic status. The most predominant genotype distribution of RV changed from G1P[8] and G2P[4] into the rare and unusual genotypes G3P[8], G8P[8], and G9P[8]. Although the predominat strain has changed, but the seasonality of RV infection remains unchanged. Rotavirus vaccine is highly cost effective in Southeast Asia countries because the ratio between cost per disability-adjusted life years (DALY) averted and gross domestic product (GDP) per capita is less than one.

For the second part of my project done during the coronavirus pandemic of 2020 and 2021, I received 257 diarrhea samples from four sentinel hospitals in Thailand. Only 25 samples (9.7%) tested positive for RVA and G3P[8] was the predominant genotype. Eight samples contained multiple RVA strains based on detailed sequence analysis of the VP7 and VP4 genes, of which two samples possessed RVA with genetic similarity to the vaccine strains in RotaTeq. Genome constellation of one sample (B8019) was consistent with G1P[8] vaccine strain reassortant. Another sample (B7711) contained G1, G2, G3, G4, P[5], and P[8] vaccine strains, as well as equine-G3P[4] wildtype RVA. Neither report of diarrhea from RVA infection after RotaTeq vaccination nor simultaneous shedding of vaccine-derived and wildtype RV infection has previously been described in Thailand. These results suggest the need for increased awareness of RVA-associated diarrhea following routine vaccination and demonstrate evidence of possible co-infection with wild-type RVA shortly after vaccination.

Although rotavirus vaccines are available in many parts of the world and are effective in reducing the overall incidence of rotavirus infection, it remains a major cause of diarrhea in less-developed countries including Thailand. Among various RVA strains, the increasingly common genotype G3 (defined by the VP7 gene) has been identified in both humans and animals. Our previous epidemiological surveillance in Bangkok found several unusual non-vaccine-like G3 strains in patients with diarrhea. For the third part of my study, I sequenced and characterized the genomes of seven of these G3 strains, which formed combinations with genotypes P[4], P[6], P[9], and P[10] (defined by the VP4 gene). Interestingly, I identified a bat-like RVA strain with the genome constellation G3-P[10]-I3-R3-C3-M3-A9-N3-T3-E3-H6, which has not been previously reported in the literature. The amino acid residues deduced from the nucleotide sequences of our G3 strains differed at the antigenic epitopes to those of the VP7 capsid protein of the G3 strain in RotaTeq vaccine. Although it is not unusual for the segmented genomes of RVA to reassort and give rise to emerging novel strains, the atypical G3 strains I identified suggest possible animal-to-human RVA zoonotic spillover even in Bangkok.

The fourth part of my project examined viral zoonosis because rotavirus infection can cause diarrhea in many animal species. A 2 year-old indoor female Siamese cat was ill with a mucus-bloody diarrhea and tested positive for rotavirus by real-time reverse-transcription polymerase chain reaction (RT-PCR). Subsequent conventional RT-PCR and nucleotide sequence analysis revealed a rotavirus G3P[9] genotype with the genome constellation G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3. From phylogenetic analysis, the VP4, VP7, NSP1, NSP3, NSP4, and NSP5 genes were closely related to human/feline-like rotavirus, while VP1, VP2, VP3, VP6, and NSP2 genes were genetically closest to human bovine-like rotavirus. Although this G3P[9] strain was previously reported in Korea, which infected a 9 year-old girl (strain CAU-12-2-51) a decade ago, it has never been documented in Thailand and its emergence is enigmatic.

In summary, my thesis research projects collectively advances our knowledge of an important vaccine-preventable virus with a major impact in improving the understanding of disease biology in Thailand and elsewhere around the world.