title: An automated genotyping tool for enteroviruses and noroviruses.
abstract: BACKGROUND
  Molecular techniques are established as routine in virological laboratories and virus typing through (partial) sequence analysis is increasingly common. Quality assurance for the use of typing data requires harmonization of genotype nomenclature, and agreement on target genes, depending on the level of resolution required, and robustness of methods.
  
  
  OBJECTIVE
  To develop and validate web-based open-access typing-tools for enteroviruses and noroviruses.
  
  
  METHODS
  An automated web-based typing algorithm was developed, starting with BLAST analysis of the query sequence against a reference set of sequences from viruses in the family Picornaviridae or Caliciviridae. The second step is phylogenetic analysis of the query sequence and a sub-set of the reference sequences, to assign the enterovirus type or norovirus genotype and/or variant, with profile alignment, construction of phylogenetic trees and bootstrap validation. Typing is performed on VP1 sequences of Human enterovirus A to D, and ORF1 and ORF2 sequences of genogroup I and II noroviruses. For validation, we used the tools to automatically type sequences in the RIVM and CDC enterovirus databases and the FBVE norovirus database.
  
  
  RESULTS
  Using the typing-tools, 785(99%) of 795 Enterovirus VP1 sequences, and 8154(98.5%) of 8342 norovirus sequences were typed in accordance with previously used methods. Subtyping into variants was achieved for 4439(78.4%) of 5838 NoV GII.4 sequences.
  
  
  CONCLUSIONS
  The online typing-tools reliably assign genotypes for enteroviruses and noroviruses. The use of phylogenetic methods makes these tools robust to ongoing evolution. This should facilitate standardized genotyping and nomenclature in clinical and public health laboratories, thus supporting inter-laboratory comparisons.
authors.affiliation: Laboratory of infectious diseases, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3720BA Bilthoven, The Netherlands. annelies.kroneman@rivm.nl
authors.forename: A
authors.initials: A
authors.lastname: Kroneman
authors.forename: H
authors.initials: H
authors.lastname: Vennema
authors.forename: K
authors.initials: K
authors.lastname: Deforche
authors.forename: H
authors.initials: H
authors.lastname: v d  Avoort
authors.forename: S
authors.initials: S
authors.lastname: Peñaranda
authors.forename: M S
authors.initials: MS
authors.lastname: Oberste
authors.forename: J
authors.initials: J
authors.lastname: Vinjé
authors.forename: M
authors.initials: M
authors.lastname: Koopmans
mesh_terms: D001331:Automation / Q000379:methods*; D004770:Enterovirus / Q000145:classification* / Q000235:genetics*; D005838:Genotype; D006801:Humans; D020407:Internet; D058889:Molecular Typing / Q000379:methods*; D029322:Norovirus / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D014764:Viral Proteins / Q000235:genetics; D014773:Virology / Q000379:methods*
chemical_list: D014764:Viral Proteins