PMC

The amino acid identities are shown for the four LSV proteins (RdRp, G, N, and NSs). A sliding window of 50 bp was used. GenBank accession numbers are reported in the text.

CPE is shown at 24, 48, 72, 96, and 120 hours post-inoculation (hpi). Uninfected controls at 120 hpi are also shown.

For the RdRp, glycoprotein, and N protein, Gouleako virus is included as an outgroup to the phleboviruses (tan). Gouleako virus, the closest known bunyavirus relative to phleboviruses, is a member of a proposed new genus in the family Bunyaviridae . Also shown color-coded are the Uukuniemi (blue), Bhanja (red), and SFTS (green) clades of known tick-borne phleboviruses. GenBank accession numbers are reported in the text.

(A) Using a rapid computational pipeline, reads identified as bunyaviruses by SNAP nucleotide alignment (orange) or RAPSearch amino acid alignment (dark red) were mapped to the assembled LSV genome. The coverage (y-axis) achieved at each position along the genome (x-axis) is plotted on a logarithmic scale. (B) De novo assembly of the LSV genome using the PRICE assembler (3 rounds of 15 cycles each) and LSV seed sequences (“S”) identified from (A). (C) The genome structure of LSV. Boxes represent open reading frames (ORFs) corresponding to the RdRp, G, N, and NSs proteins, flanked by noncoding regions, which are indicated by lines. Coding directions are indicated by arrows. (D) Mapping of the actual deep sequencing reads derived from LSV to the final assembled genome. The coverage (y-axis) achieved at each position along the genome (x-axis) is plotted on a logarithmic scale. GenBank accession numbers are reported in the text. Abbreviations: kb, kilobases; bp, base pairs.