Figure 1

Screening for lentiviral ERVs. (A) Schematic depiction of the computational screening pipeline. The first step of the best bidirectional hit (BBH) strategy was performed by tblastn search in vertebrate genome database to identify candidate endogenous lentivirus fragments (i). In this step the following Pol amino acid sequences were used as baits: human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), Visna/maedi virus, rabbit endogenous lentivirus type K (RELIK), gray mouse lemur prosimian immunodeficiency virus (pSIVgml), and domestic ferret (Mustela putorius furo) endogenous lentivirus (ELVmpf). The cutoff for the blast search was set at E-value < 10⁻⁵. To filter out non-lentiviral sequences, translated hits were used as a query for backward blastp search against database of retroviral Pol sequences belonging to all retroviral genera (ii). Hits aligned with the best bit score to lentiviral sequences in the backward blast search were further analyzed. (B). Graph shows bit scores of all lentiviral candidate hits ordered by species in which they were found. Each species is represented by different color. Newly discovered lentiviral sequence in colugo (ELVgv) as well endogenous lentiviruses in rabbit [3], domestic ferret [6], and gray mouse lemur [4],[5] are indicated. Previously published endogenous lentivirus sequences were excluded as baits for their corresponding host species (e.g. RELIK against the rabbit genome) to avoid identical matching of the hits.