Rotavirus genotypes in sewage treatment plants and in children hospitalized with acute diarrhea in Italy in 2010 and 2011

Abstract

Although the molecular surveillance network RotaNet-Italy provides useful nationwide data on rotaviruses causing severe acute gastroenteritis in children in Italy, scarce information is available on rotavirus circulation in the general Italian population, including adults with mild or asymptomatic infection. We investigated the genotypes of rotaviruses present in urban wastewaters and compared them with those of viral strains from clinical pediatric cases. During 2010 and 2011, 285 sewage samples from 4 Italian cities were tested by reverse transcription-PCRs (RT-PCRs) specific for rotavirus VP7 and VP4 genes. Rotavirus was detected in 172 (60.4%) samples, 26 of which contained multiple rotavirus G (VP7 gene) genotypes, for a total of 198 G types. Thirty-two samples also contained multiple P (VP4 gene) genotypes, yielding 204 P types in 172 samples. Genotype G1 accounted for 65.6% of rotaviruses typed, followed by genotypes G2 (20.2%), G9 (7.6%), G4 (4.6%), G6 (1.0%), G3 (0.5%), and G26 (0.5%). VP4 genotype P[8] accounted for 75.0% of strains, genotype P[4] accounted for 23.0% of strains, and the uncommon genotypes P[6], P[9], P[14], and P[19] accounted for 2.0% of strains altogether. These rotavirus genotypes were also found in pediatric patients hospitalized in the same areas and years but in different proportions. Specifically, genotypes G2, G9, and P[4] were more prevalent in sewage samples than among samples from patients, which suggests either a larger circulation of the latter strains through the general population not requiring medical care or their greater survival in wastewaters. A high level of nucleotide identity in the G1, G2, and G6 VP7 sequences was observed between strains from the environment and those from patients.

FIG 1

Distribution of RVA-positive sewage samples (2011) and samples from pediatric AGE cases (2010 to 2012) in Naples, Bari, Palermo, and Sassari, by month.

FIG 2

Phylogenetic dendrograms based on partial VP7 sequences of genotypes G1 (a), G2 (b), G3 and G9 (c), and G6 (d) and on partial VP4 nucleotide sequences of genotypes P[8], P[4], P[14], P[19], P[6], and P[9] (e). RVA strains from Italy were detected in sewage and clinical samples. All sequences obtained from GenBank are named as described previously by Matthijnssens et al. (7), and G and P genotypes are indicated on the right. Environmental samples are marked with filled circles; AGE samples are marked with filled triangles. The scale bar at the bottom of the tree indicates the number nucleotide substitutions/site. Bootstrap values (2,000 replicates) are shown at the branch nodes; values of <70 are not shown.

FIG 2

Phylogenetic dendrograms based on partial VP7 sequences of genotypes G1 (a), G2 (b), G3 and G9 (c), and G6 (d) and on partial VP4 nucleotide sequences of genotypes P[8], P[4], P[14], P[19], P[6], and P[9] (e). RVA strains from Italy were detected in sewage and clinical samples. All sequences obtained from GenBank are named as described previously by Matthijnssens et al. (7), and G and P genotypes are indicated on the right. Environmental samples are marked with filled circles; AGE samples are marked with filled triangles. The scale bar at the bottom of the tree indicates the number nucleotide substitutions/site. Bootstrap values (2,000 replicates) are shown at the branch nodes; values of <70 are not shown.