TY - JOUR
T1 - Genetic diversity of species A rotaviruses detected in clinical and environmental samples, including porcine-like rotaviruses from hospitalized children in the Philippines
AU - Imagawa, Toshifumi
AU - Saito, Mayuko
AU - Yamamoto, Dai
AU - Saito-Obata, Mariko
AU - Masago, Yoshifumi
AU - Ablola, Adrianne C.
AU - Tandoc, Amado O.
AU - Segubre-Mercado, Edelwisa
AU - Lupisan, Socorro P.
AU - Oshitani, Hitoshi
N1 - Funding Information:
We thank the staff of Molecular Biology Laboratory at RITM for supporting laboratory analyses, the staff of EVRMC and Asian Foundation for Tropical Medicine for collection of clinical samples, and Dapat C, Gaylon R, Angulo R, Hijada JR for the technical support. This study was funded by Japan Initiative for Global Research Network on Infectious Diseases (J-GRID), Japan Agency for Medical Research and Development (AMED) and Grants-in-Aid for Research Activity Start-up, JSPS KAKENHI Grant Number 23890016.
Funding Information:
We thank the staff of Molecular Biology Laboratory at RITM for supporting laboratory analyses, the staff of EVRMC and Asian Foundation for Tropical Medicine for collection of clinical samples, and Dapat C, Gaylon R, Angulo R, Hijada JR for the technical support. This study was funded by Japan Initiative for Global Research Network on Infectious Diseases (J-GRID), Japan Agency for Medical Research and Development (AMED) and Grants-in-Aid for Research Activity Start-up, JSPS KAKENHI Grant Number 23890016 .
Publisher Copyright:
© 2020
PY - 2020/11
Y1 - 2020/11
N2 - Rotaviruses are the major cause of severe acute diarrhea in infants and young children. Rotaviruses exhibit zoonosis and thereby infect both humans and animals. Viruses detected in urban rivers possibly reflect the presence of circulating viruses in the catchment. The present study investigates the genetic diversity of species A rotaviruses detected from river water and stool of hospitalized children with acute diarrhea in Tacloban City, the Philippines. Species A rotaviruses were detected by real-time RT-PCR and their genotypes were identified by multiplex PCR and sequencing of partial regions of VP7 and VP4. Rotaviruses were detected in 85.7% (30/35) of the river water samples and 62.7% (151/241) of the clinical samples. Genotypes of VP7 in the river water samples were G1, G2, G3, G4, G5, and G9, and those of VP4 were P[3], P[4], P[6], P[8], and P[13]. Genotypes of viruses from the clinical samples were G2P[4], G1P[8], G3P[8], G4P[6], G5P[6], and G9P[8]. Among those, G2P[4] in clinical samples (77.9%, 81/104) and P[4] of VP4 in river water samples (67.5%, 56/83)) were the most frequently detected rotavirus genotypes. However, G5 was the more frequently detected than G2 in the river water samples (42% vs. 13%) which may be originated from porcine rotavirus. Sequence analyses of eleven gene segments revealed one G5P[6] and two G4P[6] rotaviruses in the clinical samples, wherein, several gene segments were closely related to porcine rotaviruses. The constellation of these rotavirus genes suggests the emergence of reassortment between human and porcine rotavirus due to interspecies transmission. Although two commercial rotavirus vaccines are available now, these vaccines are designed to confer immunity against the major human rotaviruses. Constant monitoring of viral variety in populated areas where humans and domestic animals live in close proximity provides vital information related to the diversity of rotaviruses in a human population.
AB - Rotaviruses are the major cause of severe acute diarrhea in infants and young children. Rotaviruses exhibit zoonosis and thereby infect both humans and animals. Viruses detected in urban rivers possibly reflect the presence of circulating viruses in the catchment. The present study investigates the genetic diversity of species A rotaviruses detected from river water and stool of hospitalized children with acute diarrhea in Tacloban City, the Philippines. Species A rotaviruses were detected by real-time RT-PCR and their genotypes were identified by multiplex PCR and sequencing of partial regions of VP7 and VP4. Rotaviruses were detected in 85.7% (30/35) of the river water samples and 62.7% (151/241) of the clinical samples. Genotypes of VP7 in the river water samples were G1, G2, G3, G4, G5, and G9, and those of VP4 were P[3], P[4], P[6], P[8], and P[13]. Genotypes of viruses from the clinical samples were G2P[4], G1P[8], G3P[8], G4P[6], G5P[6], and G9P[8]. Among those, G2P[4] in clinical samples (77.9%, 81/104) and P[4] of VP4 in river water samples (67.5%, 56/83)) were the most frequently detected rotavirus genotypes. However, G5 was the more frequently detected than G2 in the river water samples (42% vs. 13%) which may be originated from porcine rotavirus. Sequence analyses of eleven gene segments revealed one G5P[6] and two G4P[6] rotaviruses in the clinical samples, wherein, several gene segments were closely related to porcine rotaviruses. The constellation of these rotavirus genes suggests the emergence of reassortment between human and porcine rotavirus due to interspecies transmission. Although two commercial rotavirus vaccines are available now, these vaccines are designed to confer immunity against the major human rotaviruses. Constant monitoring of viral variety in populated areas where humans and domestic animals live in close proximity provides vital information related to the diversity of rotaviruses in a human population.
KW - Environmental water
KW - Philippines
KW - Rotavirus
KW - Viral evolution
KW - Viral gastroenteritis
UR - http://www.scopus.com/inward/record.url?scp=85088375098&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85088375098&partnerID=8YFLogxK
U2 - 10.1016/j.meegid.2020.104465
DO - 10.1016/j.meegid.2020.104465
M3 - Article
C2 - 32687980
AN - SCOPUS:85088375098
VL - 85
JO - Infection, Genetics and Evolution
JF - Infection, Genetics and Evolution
SN - 1567-1348
M1 - 104465
ER -
