Typing tool

Norovirus and Sapovirus

The family Caliciviridae consist of 11 genera [1] of which viruses belonging to the Norovirus and Sapovirus genera cause epidemic and endemic acute gastroenteritis (vomiting and diarrhea) in people of all ages. The clinical symptoms of norovirus and sapovirus gastroenteritis are indistinguishable.

Both noroviruses and sapoviruses are genetically and antigenically highly diverse. The non-enveloped virus particles are 27-40 nm in diameter and have a single-stranded positive-sense RNA genome of 7.1-7.7 kb in length. In human noroviruses, this genome is divided into three open reading frames (ORF1-3) whereas sapoviruses consist of 2 ORFs (see Figure).

Based on phylogenetic clustering of complete VP1 amino acid sequences, noroviruses can be classified into 10 established (GI - GX) and 2 tentative genogroups, of which viruses from GI, GII, GIV, GVIII and GIX (formerly GII.15) infect humans [2]. Each genogroup can be further divided into genotypes (9 GI, 26 GII, 2 GIV, 1 GVIII, and 1 GIX). In addition, based on clustering of nucleotide sequences of the polymerase region at least 14 GI polymerase (GI.P) types and 37 GII.P types have been described [2]. Among sapoviruses, viruses belonging to GI, GII, GIV and GV indect humans.

To genotype GI and GII noroviruses, most laboratories amplify relative short sequences spanning the 3’-end of ORF1 (polymerase region) and 5’-end of ORF2 (major capsid protein gene). These sequences can be generated in separate RT-PCR reactions or in a single, genogroup-specific, RT-PCR assay [3].

This human calicivirus typing tool uses a BLAST-like algorithm to type both the polymerase region (P-type) and the capsid (genotype) of GI, GII, GIV, GVIII, and GIX (formerly GII.15) noroviruses as well as capsid genotyping of GI, GII, GIV and GV sapoviruses [4] against a database of norovirus and sapovirus reference sequences. Genotypes are assigned following classification criteria agreed upon by the Norovirus Classification Working Group [2, 5].

Reference sequences

The reference sequences used in this typing tool are updated on a regular basis. They are listed under Reference sequences tab and are all available in GenBank.

Citations:

pdf 1. Vinjé J, Estes MK, Esteves P, Green KY, Katayama K, Knowles NJ, L'Homme Y, Martella V, Vennema H, White PA, ICTV Report Consortium.
ICTV Virus Taxonomy Profile: Caliciviridae.
J Gen Virol. 2019 Oct 1. doi: 10.1099/jgv.0.001332. (2019).
pdf 2. Chhabra P, de Graaf M, Parra G, Chan MC-W, Green KY, Martella V, Wang Q, White PA, Katayama K, Vennema H, Koopmans MPG, Vinjé J.
Updated classification of norovirus genogroups and genotypes.
J Gen. Virol. 100 (10):1393-1406 (2019).
pdf 3. Cannon JL, Barclay L, Collins NR, Wikswo ME, Castro CJ, Magaña LC, Gregoricus N, Marine RL, Chhabra P, Vinjé J.
Genetic and epidemiologic trends of norovirus outbreaks in the United States from 2013 to 2016 demonstrated emergence of novel GII.4 recombinant viruses.
J. Clin. Microbiol. 55 2208–2221 (2017).
pdf 4. Oka T, Wang Q, Katayama K, Saif LJ,
Comprehensive review of human sapoviruses.
Clin Microbiol Rev. 28 32-53 (2015).
pdf 5. Kroneman A, Vega E, Vennema H, Vinjé J, White PA, Hansman G, Green K, Martella V, Katayama K, Koopmans M,
Proposal for a unified norovirus nomenclature and genotyping.
Arch Virol. 158 2059-2068 (2013).