Enterovirus Genotyping Tool Methods

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

1. The initial step performs an 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 asgenus enterovirus, species enterovirus A, B, C or D in step 1. Sequences of each enterovirus species are analysed sperately using a different reference set. For each submitted sequence that overlaps sufficiently (at least 100nt) with VP1, an alignment is performed using ClustalW and a phylogenetic tree (NJ) is constructed with the HKY851 method using PAUP*2 software. HKY85 is a likelyhood method with 100 bootstrap replicates. The alignment contains the sequence together with the pre-aligned reference sequences for each (sero)type. In the PAUP* log file also the bootstrap tree is presented. 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

Regions supported by the tool

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Flowchart of the genotyping process