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

• Authors: Roman L Tatusov, Cherokee Nation Assurance, Arlington; Preeti Chhabra, National Center for Immunization and Respiratory Diseases; Marta Diez-Valcarce, Emory University; Leslie Barclay, National Center for Immunization and Respiratory Diseases; Jennifer L Cannon, National Foundation for the Centers for Disease Control and Prevention Inc., Atlanta; J Vinjé, National Center for Immunization and Respiratory Diseases
• Journal Title: JOURNAL OF CLINICAL VIROLOGY
• Volume: Volume 134
• Publisher: Elsevier | 2021-01-01
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1016/j.jcv.2020.104718
• Subjects: Health Sciences, Public Health
• Keywords: Norovirus; Sapovirus; Calicivirus; Typing tool; Genotyping; Polymerase; k-mer; Web-based

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 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.