Molecular epidemiology of Rotavirus A, causing acute gastroenteritis hospitalizations among children in Nha Trang, Vietnam, 2007-2008: Identification of rare G9P[19] and G10P[14] strains.
Loan Phuong Do1,2
Miho Kaneko1
Toyoko Nakagomi1,3
Punita Gauchan1
Chantal Ama Agbemabiese1
Anh Duc Dang2
Osamu Nakagomi1,3
Affiliations3 institutions
Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
Centre for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
Rotavirus A strain G9P[19] from a child clustered phylogenetically with porcine strains, indicating a likely porcine origin of this genome constellation.
Sequencing of initially untypeable specimens revealed the presence of two unusual strains designated NT0073 and NT0082 possessing G9P[19] and G10P[14], respectively. The genotype constellation of NT0073 (G9‑P[19]‑I5‑R1‑C1‑M1‑A8‑N1‑T7‑E1‑H1) and the phylogenetic trees suggested its origin as a porcine RVA strain causing diarrhea in a 24‑month‑old girl.
Analysis methods
sequencing; phylogenetic analysis
Genomic EvolutionExtraction confidence 0.90
Key finding
Rotavirus A strain G10P[14] from a child showed a genome constellation and phylogenetic placement consistent with artiodactyl (cattle, sheep, or goat) origin.
The genotype constellation of NT0082 (G10‑P[14]‑I2‑R2‑C2‑M2‑A3‑N2‑T6‑E2‑H3) and the phylogenetic trees suggested its origin as an RVA strain of artiodactyl origin (such as cattle, sheep and goats) causing diarrhea in a 13‑month‑old boy.
Analysis methods
sequencing; phylogenetic analysis
Spillover Event2 records
Spillover EventExtraction confidence 0.95
Key finding
A Rotavirus A G9P[19] strain of porcine origin infected a human child, demonstrating animal-to-human spillover in Vietnam.
The genotype constellation of NT0073 (G9-P[19]-I5-R1-C1-M1-A8-N1-T7-E1-H1) and the phylogenetic trees suggested its origin as a porcine RVA strain causing diarrhea in a 24-month-old girl.
Method
sequencing; phylogenetic analysis; genotyping
Study design
cross-sectional study
Transmission direction
animal-to-human
Geographic raw
Nha Trang, Vietnam
Country inferred
Vietnam
Spillover EventExtraction confidence 0.95
Key finding
A Rotavirus A G10P[14] strain of artiodactyl origin infected a human child, representing an animal-to-human spillover event in Vietnam.
The genotype constellation of NT0082 (G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3) and the phylogenetic trees suggested its origin as an RVA strain of artiodactyl origin (such as cattle, sheep and goats) causing diarrhea in a 13-month-old boy.
Method
sequencing; phylogenetic analysis; genotyping
Study design
cross-sectional study
Transmission direction
animal-to-human
Geographic raw
Nha Trang, Vietnam
Country inferred
Vietnam
Cross Species Transmission1 records
Cross Species TransmissionExtraction confidence 0.85
Key finding
Porcine Rotavirus A strain and an artiodactyl Rotavirus A strain were identified, indicating cross-species transmission among non-human animal hosts.
The genotype constellation of NT0073 (G9-P[19]-I5-R1-C1-M1-A8-N1-T7-E1-H1) and the phylogenetic trees suggested its origin as a porcine RVA strain, whereas the genotype constellation of NT0082 (G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3) suggested its origin as an RVA strain of artiodactyl origin (such as cattle, sheep and goats).
