Genomic characterization of human astrovirus type 6 Katano virus and the establishment of a rapid and effective reverse transcription-polymerase chain reaction to detect all serotypes of human astrovirus

Abstract

We previously reported that human astrovirus type 6 (HAstV T6) was the etiologic agent of a large-scale outbreak of acute gastroenteritis that occurred in 1991 in Katano City, Osaka, Japan [Oishi et al., 1994]. The two representative strains, Katano virus K23 and K24, have been analyzed by sequencing the open reading frame 2 (ORF2) region after amplification by reverse transcription-polymerase chain reaction (RT-PCR). The ORF2 region of HAstV T6 strains, including K23, was found to be about 20 bp smaller than those of other types. There was 94% nucleotide sequence identity and 95% amino acid sequence identity between K23 and K24, with the Oxford strains belonging to HAstV T6. The high homology of the ORF2 region between the Katano and Oxford strains shows intratype genomic stability, irrespective of time and place of virus isolation. Comparing sequences of ORF2 of different HAstV serotypes, we established a rapid and highly sensitive detection system for HAstV types using RT-PCR with the AC230/AC1' primer set designed from the 5'-terminal end region of ORF2. This RT-PCR system seems very useful in detecting at least two different viruses in a single PCR test tube using AC230/AC1' in addition to the NV81/82, SM82 primer sets. Thus, our rapid and effective detection system may contribute to the epidemiologic characterization of astrovirus infections as well as Norwalk-like viruses.