relationship of reference database with ICTV

[Former user]

I wonder whether the classification of viruses in reference database follows Refseq or ICTV .

[Ben Bolduc]

Depending on the database selected, vConTACT2 will use either an ICTV-only taxonomy, or NCBI’s taxonomy reinforced with ICTV. The challenge with using ICTV only, is that its taxonomy covers such a small percentage of viral sequences available in NCBI that classification becomes more challenging.

vContact2 has taken a somewhat perilous position by using NCBI taxonomy, then updating any genomes with ICTV taxonomy with that taxonomy. This can cause some issues for some viral groups, especially if one subset of a viral group has been updated with ICTV whereas an adjacent subset hasn’t been covered by ICTV. Then you get a weird group where half the genomes are using ICTV and the other half are still NCBI. That said, the effect is negligible, with less than 1% change in the network classification.

[Ben Bolduc]

Clarification.