Abstract
BackgroundEnteritis is caused by a spectrum of viruses that is most likely not fully characterised. When testing stool samples by cell culture, virus isolates are sometimes obtained which cannot be typed by current methods. In this study we used VIDISCA, a virus identification method which has not yet been widely applied, on such an untyped virus isolate.ResultsWe found a human parechovirus (HPeV) type 1 (strain designation: BNI-788st). Because genomes of contemporary HPeV1 were not available, we determined its complete genome sequence. We found that the novel strain was likely the result of recombination between structural protein genes of an ancestor of contemporary HPeV1 strains and nonstructural protein genes from an unknown ancestor, most closely related to HPeV3. In contrast to the non-structural protein genes of other HPeV prototype strains, the non-structural protein genes of BNI-788st and HPeV3 prototype strains did not co-segregate in bootscan analysis with that of other prototype strains.ConclusionHPeV3 nonstructural protein genes may form a distinct element in a pool of circulating HPeV non-structural protein genes. More research into the complex HPeV evolution is required to connect virus ecology with disease patterns in humans.
Highlights
Enteritis is caused by a spectrum of viruses that is most likely not fully characterised
A simpler method, termed Virus Discovery cDNA AFLP (VIDISCA), uses cell culture supernatants treated by DNase digestion in a modified cDNA Amplified Fragment Length Polymorphism (AFLP) analysis
The virus isolate could be passaged to uninfected cells but showed no detectable neutralisation if subcultured with several different pools of polyclonal anti-enterovirus sera
Summary
Enteritis is caused by a spectrum of viruses that is most likely not fully characterised. The Picornaviridae are a highly diversified family of nonenvevloped plus-strand RNA viruses, many of which are pathogenic for humans Their full genetic and phenotypic spectrum is unknown and novel picornavirus strains keep being discovered [1,2]. Large work has been invested in recent years in the development of methods for discovering new and unknown viruses Sophisticated approaches, such as highly redundant cDNA arrays, high-throughput cDNA library analysis, and ultradeep sequencing have been successfully used [3,4,5,6,7]. These methods are expensive and require expert knowledge, prohibiting their use in general diagnostic laboratories.
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