Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children

Abstract

We report a naturally occurring human astrovirus (HAstV) strain detected in two different geographic locations. We identified two isolates of this strain in a diarrhea outbreak at a child care center in Houston, Texas; and two isolates in diarrhea stool samples from two children in Mexico City. All four isolates were detected in stool samples by enzyme immunoassay (EIA). One of the Mexican isolates was typed by EIA and all four isolates were HAstV-5 by typing RT-PCR. The four isolates were >97% nucleotide-identical in two different genomic regions: ORF1a (246 nt), and the 3' end of the genome (471 nt). One isolate from each geographic location was further sequenced in the transition region from ORF1b to ORF2 (1255 nt) and this region of the two isolates showed > or = 99% nt identity. Phylogenetic analyses of sequences of eight HAstV antigenic types and the novel strain in the transition region demonstrated the new strain being closely related to HAstV-3 in ORF1b, but closest to HAstV-5 in ORF2. These results and high sequence identity among all HAstV antigenic types in the transition region and RNA structural predictions supported a potential recombination site at the ORF1b/ORF2 junction. This is the first evidence that recombination occurs among human astroviruses.

Lineage diversification and recombination in type-4 human astroviruses

“…There was a 8-nt overlap between the 3 0 end of ORF1b and the start of ORF2. The highly conserved nt stretch 5 0 -ATT-TGGAGNGGNGGACCNAAN 5-8 ATGNC-39, believed to be part of a promoter region for synthesis of subgenomic RNA, was retained upstream the ORF2 start codon (Walter et al, 2001). …”

“…The deduced amino acid (aa) sequence of the capsid precursor was determined and an alignment generated to assess the rate of aa variation across the various ORF2 regions (Walter et al, 2001). The aa variation within type-4 HAstVs reached 6.8% in the N-terminal domain (aa 1-424), 8.1% in the HVR hypervariable region (aa 425-688) and 23.7% in the highly acidic C-terminal domain.…”

“…By Simplot analysis (Fig. 2B) the crossover site was mapped to the ORF1b/ORF2 region, upstream the highly conserved promoter region for synthesis of subgenomic RNA (Walter et al, 2001). …”

Novel human astroviruses: challenges for developing countries

“…The upstream conserved RNA sequence from the ORF2 initiation codon might play a key role in the regulation of the capsid gene expression. This region was identified as a hotspot for RNA recombination [41].…”

“…The infection rate ranged from 2 to 6 % for hospitalized children with acute diarrhoea and 5-17 % for acute diarrhoea cases from the community [3]. In both developed and developing countries, HAstV infection was associated with diarrhoea episodes and ranged from 3 to 12 and 2 to 26 % respectively [18,23,29,34,40,41].…”