Genetic diversity of species A rotaviruses detected in clinical and environmental samples, including porcine-like rotaviruses from hospitalized children in the Philippines.
Animals
Child, Hospitalized
Child, Preschool
Feces
/ virology
Genetic Variation
Genome, Viral
Genotype
Humans
Infant
Infant, Newborn
Molecular Typing
Philippines
/ epidemiology
Phylogeny
Retroviridae Proteins
/ genetics
Rivers
/ virology
Rotavirus
/ classification
Rotavirus Infections
/ epidemiology
Rotavirus Vaccines
Sequence Analysis, DNA
Swine
/ virology
Environmental water
Philippines
Rotavirus
Viral evolution
Viral gastroenteritis
Journal
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
ISSN: 1567-7257
Titre abrégé: Infect Genet Evol
Pays: Netherlands
ID NLM: 101084138
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
14
02
2020
revised:
09
07
2020
accepted:
13
07
2020
pubmed:
21
7
2020
medline:
26
10
2021
entrez:
21
7
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32687980
pii: S1567-1348(20)30296-3
doi: 10.1016/j.meegid.2020.104465
pii:
doi:
Substances chimiques
Retroviridae Proteins
0
Rotavirus Vaccines
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
104465Informations de copyright
Copyright © 2020. Published by Elsevier B.V.