Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences

Abstract Background The family Caliciviridae consists of a genetically diverse group of RNA viruses that infect a wide range of host species including noroviruses and sapoviruses which cause acute gastroenteritis in humans. Typing of these viruses relies on sequence-based approaches, and therefore there is a need for rapid and accurate web-based typing tools. Objective To develop and evaluate a web-based tool for rapid and accurate genotyping of noroviruses and sapoviruses. Methods The Human Calicivirus Typing (HuCaT) tool uses a set of curated reference sequences that are compared to query sequences using a k-mer (DNA substring) based algorithm. Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. Results The HuCaT tool was validated with a set of 1,310 norovirus and 239 sapovirus sequences covering all known human norovirus and sapovirus genotypes. HuCaT tool assigned genotypes to all queries with 100% accuracy and was much faster (17 seconds) than BLAST (150 seconds) or phylogenetic analyses approaches. Conclusions The web-based HuCaT tool supports rapid and accurate genotyping of human noroviruses and sapoviruses.