Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region

Abstract

Astroviruses are single-stranded, positive-sense RNA viruses that are associated with gastroenteritis in humans and animals. We describe a reverse transcription-polymerase chain reaction (RT-PCR) assay using primers targeted to a nonstructural protein coding region that allowed sensitive detection and genetic typing of representative strains of seven astrovirus serotypes. Phylogenetic analysis of the nucleotide sequences of PCR products from the reference strains and several wild isolates indicated two distinct genogroups of sequences in open reading frame 1a (ORF 1a). These genogroups correlated with serotype: genogroup A included strains of types 1 to 5, while genogroup B included strains of types 6 and 7. This phylogenetic arrangement differs from the nearly equidistant clustering of serotypes seen when comparing nucleotide sequences from either ORF 1b or ORF 2. It is possible that recombination was responsible for the observed difference in genetic relationships.

Lineage diversification and recombination in type-4 human astroviruses

“…Although other diagnostic primers are available in the ORF1a, ORF1b, ORF2 and 3 0 UTR (Belliot et al, 1997;Guix et al, 2005;Jakab et al, 2004;Noel et al, 1995) the Mon260-Mon270 primer pair has been adopted and used in several epidemiological studies worldwide as it is able to amplify all HAstV types and the sequence information of the amplified region is suitable to predict serotype specificity. Taking advantage of the high conservation in the 3 0 end of ORF2 and in the 3 0 UTR, other consensus primers (prBEG/JWT4-Mon2) (Jakab et al, 2004) have been designed at the 3 0 end of ORF2 (D3 0 region).…”

Detection of Enteric Viruses in Fecal Specimens from Nonbacterial Foodborne Gastroenteritis Outbreaks in Tokyo, Japan between 1966 and 1983

“…For samples that were also positive for other viruses by real-time PCR, conventional PCR was performed to identify the virus. The primer sets F22 and R2, Beg9 and End9, Beg and End, Mon244 and Mon245, and hex1885 and hex1913 were used to amplify the partial SaV capsid, RVA VP7, RVC VP7, AstV capsid, and AdV hexon genes, respectively, as previously described (23)(24)(25)(26)(27).…”

“…PCR products from other enteric viruses were directly sequenced using the method described above and were classified as previously reported (24,26,27,33,34). In addition, the Basic Local Alignment Search Tool (BLAST; http://blast.ncbi.nlm.nih.gov) was used to identify homologous genes (35).…”

An epidemiological study of enteric viruses in sewage with molecular characterization by RT-PCR and sequence analysis

“…Published sets of oligonucleotide primers were used for rotaviruses (Gouvea et al 1990), human astroviruses (Belliot et al 1997), enteroviruses (Zoll et al 1992) and HAV (Cromeans et al 1987). For human noroviruses, three set of primers located in the conserved RNA polymerase region were used: the primers designed by Ando et al (1995) yield a 123 bp product, those designed by Green et al (1995) yield a 113 bp product, and those designed by Jiang et al…”