Molecular characterisation of small round structured viruses associated with gastroenteritis in South Africa

Abstract The application of the reverse transcriptase poly‐ merase chain reaction (RT‐PCR) has enabled several morphologically and physically similar small round structured viruses (SRSVs), including the prototype Norwalk virus (NV), to be classified within the Caliciviridae . This technique, using primers directed to the RNA‐dependent RNA polymerase region within the ORF1 of NV, was used to characterise SRSVs associated with epidemic gastroenteritis in adults and sporadic paediatric gastroenteritis in South Africa. Ge‐nomic variation was investigated by sequence analysis of the amplified 209bp cDNA region from six isolates and comparison with other characterised SRSVs including NV. Antigenic variation was investigated by the use of the re‐combinant enzyme immunoassay described recently for the detection of Snow Mountain agent‐like antigen in stool specimens. Two distinct antigenic groups were evident with NV‐like viruses associated with adult gastroenteritis, and Mexico viruslike viruses associated with paediatric gastroenteritis. Viral isolates from two of the outbreaks of adult gastroenteritis showed a high degree of nucleotide sequence identity with NV, i.e., 84% and 98%, respectively, whereas the paediatric isolates showed 92‐95% sequence similarity with the Snow Mountain‐like virus, MxV. These data show concordance between antigenic and genomic analyses. © Wiley‐Liss, Inc.