Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences.
J Clin Virol
; 134: 104718, 2021 01.
Article
em En
| MEDLINE
| ID: mdl-33360859
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.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Infecções por Caliciviridae
/
Norovirus
/
Sapovirus
Limite:
Humans
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article