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 1310 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 s) than BLAST (150 s) or phylogenetic analyses approaches.
Conclusions: The web-based HuCaT tool supports rapid and accurate genotyping of human noroviruses and sapoviruses.
Keywords: Calicivirus; Genotyping; Norovirus; Polymerase; Sapovirus; Typing tool; Web-based; k-mer.
Published by Elsevier B.V.