Enterovirus Genotyping Tool

Software version 2.23.0

Tool version 2.17

The (sero)typing process consists of up to two steps:

1. The initial step performs a nucleotide blast scan, using Blastn. The submitted sequence is blasted against a set of whole genome sequences for determination of the genus within the Picornaviridae family and the species for enterovirus (enterovirus A, B, C, and D and rhinovirus A, B and C). The start and end positions of the fragment are determined. A genus/species is only assigned if the relative blastscore >1.5. The relative blastscore is the highest blastscore divided by the next highest blastscore of the submitted sequence with the whole genome sequence of another genus/species. Besides this relative score an absolute cutoff is used: the E value < 1E-5, as a measure for statistic significance.
2. This second step is performed for sequences which were identified as genus enterovirus, species enterovirus A, B, C or D in step 1. Sequences of each enterovirus species are analysed separately using a different reference set. For each submitted sequence that overlaps sufficiently (≤ 100nt) with VP1, an alignment is performed using Blast/Aga and a phylogenetic tree (NJ) is constructed. For each (sero)type two, in some cases more, reference sequences have been selected, representing the level of variance within the cluster. The reference strains in this tool have been selected based on the picornavirus home page