Molecular detection and epidemiology of astrovirus, bocavirus, and sapovirus in Italian children admitted to hospital with acute gastroenteritis, 2008–2009

Abstract

Although a number of enteric viruses have been identified in children with acute gastroenteritis, the majority of cases of gastroenteritis remain undiagnosed. In order to provide more insights into the epidemiology of enteric viruses that are not included usually in routine diagnostic tests, cases of childhood sporadic gastroenteritis of unknown etiology requiring hospital admission in Parma, Italy, during 2008-2009, were screened for astrovirus (AstV), sapovirus (SaV), and bocavirus (BoV). The stools of 712 children, negative for rotavirus, norovirus, adenovirus, enterovirus, and reovirus, were examined by PCR or RT-PCR for AstV, BoV, and SaV. The prevalence of AstV, BoV, and SaV in the patients examined was 2.1%, 3.2%, 2.4%, respectively, with the viruses being detected mostly in children <3 years of age. AstV strains were characterized by sequencing as types 1, 2, and 4, with a AstV-1 peak occurring in the 2008 fall-winter season. BoV strains were characterized as types 1, 2, and 3, with BoV-3 circulating more frequently in the 2008 autumn and winter season and BoV-2 during March-April 2009. The most common SaVs were GI.2 and GII.1 while GIV and GV SaVs were detected sporadically. Overall, AstV, BoV, and SaV infections accounted for 7.7% of the sporadic cases of acute gastroenteritis with unknown etiology selected for the study. Different virus types and lineages were found to circulate and temporal peaks of virus activity were also demonstrated, suggesting either small clusters of infections or small outbreaks or epidemics in local population.

Lineage diversification and recombination in type-4 human astroviruses

“…Epidemiological investigations for HAstVs worldwide have shown that type-1 HAstV is predominant, while the prevalence of other HAstVs can vary markedly (De Grazia et al, 2011;Medici et al, 2012 Gabbay et al, 2007;Guix et al, 2002;Mustafa et al, 2000;Victoria et al, 2007). Interestingly, type-4 HAstV, along with type-8 HAstV, seems to be associated with infection of older children and with longer duration of diarrhoea (>7 days) (Guix et al, 2002;Silva et al, 2006).…”

“…Surveillance studies for HAstV in Italy identified the circulation of type-4 HAstV strains in 2002 (De Grazia et al, 2011) and again in 2008(De Grazia et al, 2012Medici et al, 2012). Based on a small sequence generated by the diagnostic primers Mon269-Mon270 (Noel et al, 1995) …”

Genetic Heterogeneity and Recombination in Human Type 2 Astroviruses

“…L13745), the 2002 Italian HAstV-2 strains were clearly distinguishable phylogenetically from type 2a and type 2b strains, and they were classified as lineage 2c, along with a number of other strains detected worldwide since the mid-1990s (5). In a similar fashion, in 2009 a novel lineage, 2d, was identified (15). In order to investigate better the extent of the genetic heterogeneity observed in HAstV-2 strains, a 3.2-kb portion at the 3= end of the genome, encompassing an ϳ740-nt-long portion at the 3= end of ORF1b, the full-length ORF2 (2,400 nt), and the 3= untranslated region (3= UTR) (82 nt), was sequenced for two representative strains, ITA/2002/PA65R/ type2c (accession no.…”

“…On the basis of the capsid protein precursor, HAstVs are classified genetically and antigenically into eight types (HAstV-1 to -8) (18). The predominant types appear to vary seasonally and geographically (3,5,10,12,15,23,24), although the relevance of this genetic and antigenic heterogeneity and these temporal and geographical fluctuations is unclear. Epidemiological investigations of HAstVs worldwide have shown that HAstV-1 is predominant, while the prevalence of HAstV-2 can vary markedly (1,5,13,15,21), reaching epidemiological relevance in some geographical settings and seasons (4,9,11,16).…”

“…Discrete sequence variation has been observed within some HAstV types, allowing for distinction of different genetic lineages. Surveillance studies for HAstV in Italy identified the appearance of novel HAstV-2 lineages in 2002 (3,5) and again in 2009 (15). Based on a small sequence generated by the diagnostic primers Mon269 and Mon270 (18) in the 5= region of ORF2 the (D5= region, nt 4571 to 4918 of accession no.…”