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

Details

• Alternative Title:
  J Clin Virol
• Personal Author:
  Tatusov, Roman L. ; Chhabra, Preeti ; Diez-Valcarce, Marta ; Barclay, Leslie ; Cannon, Jennifer L. ; Vinjé, Jan
• Description:
  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.
  
  
• Subjects:
  Article Caliciviridae Infections Calicivirus Genotype Genotyping Humans Internet K-mer Norovirus Phylogeny Polymerase Sapovirus Typing Tool Web-based

  More +
• Source:
  J Clin Virol. 134:104718
• Pubmed ID:
  33360859
• Pubmed Central ID:
  PMC9029540
• Document Type:
  Journal Article
• Funding:
  CC999999/ImCDC/Intramural CDC HHSUnited States/
• Volume:
  134
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:bf4f2149bb42d82b6662e2350166766763279384351eabfd69c4becdeaacbea4
• Download URL:
  https://stacks.cdc.gov/view/cdc/116653/cdc_116653_DS1.pdf
• File Type:
  [PDF - 170.37 KB ]