VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A Schäffer; Eneida Hatcher; Linda Yankie; Lara Shonkwiler; J Rodney Brister; Ilene Karsch-Mizrachi; Eric P Nawrocki

In the DP dataset, for which only VADR was tested, 37 sequences failed. Twenty-eight failed because no similarity to any RefSeq in the reference library was detected (noannotn alert). Twenty of these are likely not dengue virus sequences but rather from Aedes aergypti or Aedes albopictus, the mosquito vectors of Dengue virus as they contain one of those species names in the sequence description. Three of the other nine sequences that failed did so because they are reverse complemented (revcompl alert). Three others fail because the blastx alignments do not extend far enough relative to the nucleotide-based CDS endpoints (indf5pst or indf3pst alerts). One failed because it had an internal stop in the polyprotein CDS (cdsstopp alert). One failed because its stem loop feature that is supposed to be found upstream of the CDS lacked similarity to the RefSeq in the first 30 nucleotides (lowsim5f alert). The final sequence failed because it was classified as coming from a different species in family Flaviviridae, namely West Nile virus (incgroup alert).