Genotyping and clinical factors in pediatric diarrhea caused by rotaviruses: one-year surveillance in Surabaya, Indonesia

Abstract

Background: Rotavirus infections are a major cause of diarrhea in children in both developed and developing countries. Rotavirus genetics, patient immunity, and environmental factors are thought to be related to the severity of acute diarrhea due to rotavirus in infants and young children. The objective of this study was to provide a correlation between rotavirus genotypes, clinical factors and degree of severity of acute diarrhea in children under 5 years old in Surabaya, Indonesia.

Methods: A cross-sectional study was conducted in children aged 1-60 months with acute diarrhea hospitalized in Soetomo Hospital, Surabaya, Indonesia from April to December 2013. Rotavirus in stool specimens was identified by ELISA and genotyping (G-type and P-type) using multiplex reverse transcription PCR. Severity was measured using the Ruuska and Vesikari scoring system. The clinical factors were investigated included patient's age (months), hydration, antibiotic administration, nutritional state, co-bacterial infection and co-viral infection.

Results: A total of 88 children met the criteria; 80.7% were aged 6-24 months, watery diarrhea was the most common type (77.3%) and 73.6% of the subjects were co-infected with bacteria, of which pathogenic Escherichia coli was the most common (42.5%). The predominant VP7 genotyping (G-type) was G2 (31.8%) and that of VP4 genotyping (P-type) was P[4] (31.8%). The predominant rotavirus genotype was G2P[4] (19.3%); G1P[4] and G9P[4] were uncommon with a prevalence of 4.5%. There were significant differences between the common genotype and uncommon genotype with respect to the total severity score of diarrhea (p <0.05). G3, G4 and G9 were significantly correlated with severe diarrhea (p = 0.009) in multivariate analyses and with frequency of diarrhea (>10 times a day) (p = 0.045) in univariate analyses, but there was no significant correlation between P typing and severity of diarrhea. For combination genotyping of G and P, G2P[4] was significantly correlated with severe diarrhea in multivariate analyses (p = 0.029).

Conclusions: There is a correlation between rotavirus genotype and severity of acute diarrhea in children. Genotype G2P[4] has the highest prevalence. G3, G4, G9 and G2P[4] combination genotype were found to be associated with severe diarrhea.

Keywords: Clinical factors; Genotyping; Pediatrics; Rotavirus diarrhea.

Figure 1

Gel electrophoreses from stool samples. PCR amplification result for G-type. Lane M: DNA Step Ladder marker, lane 1 (881 bp, full length VP7 RT-PCR product: positive control), lane 2 (G1, 618 bp), lane 4 (G4, 452 bp), lane 5 (G2, 521 bp), lane 6 (G3, 682 bp), lanes 7 and 8 (G9, 179 bp). (−): negative control.

Figure 2

Gel electrophoreses from stool samples. PCR amplification result for P-type. Lane M (DNA Step Ladder), lane (+): positive control (663 bp, full length VP4 gene), lanes 1 (P[4], 362 bp), lanes 2 and 4 (P[8], 224 bp), lane 3 (P[10], 462 bp), lane 5 (P[9], 270 bp) and lane 6 (P[6]P[8], 146 bp and 224 bp). Lane (−): negative control.

Figure 3

Gel electrophoreses from stool samples. PCR amplification result for P-type. Lane M (DNA Step Ladder), lane (+): positive control (663 bp, full length VP4 gene), lane 7 (P[6]P[8], 146 bp and 224 bp), lane 8 (P[6], 146 bp) , lane 9 and 10 (P[9], 270 bp), and lane 11 (P[4]P[9], 362 bp and 270 bp). Lanes (−): negative control.