Genetic characterization of goutanap virus, a novel virus related to negeviruses, cileviruses and higreviruses

Abstract

Pools of mosquitoes collected in Côte d'Ivoire and Mexico were tested for cytopathic effects on the mosquito cell line C6/36. Seven pools induced strong cytopathic effects after one to five days post infection and were further investigated by deep sequencing. The genomes of six virus isolates from Côte d'Ivoire showed pairwise nucleotide identities of ~99% among each other and of 56%-60% to Dezidougou virus and Wallerfield virus, two insect-specific viruses belonging to the proposed new taxon Negevirus. The novel virus was tentatively named Goutanap virus. The isolate derived from the Mexican mosquitoes showed 95% pairwise identity to Piura virus and was suggested to be a strain of Piura virus, named C6.7-MX-2008. Phylogenetic inferences based on a concatenated alignment of the methyltransferase, helicase, and RNA-dependent RNA polymerase domains showed that the new taxon Negevirus formed two monophyletic clades, named Nelorpivirus and Sandewavirus after the viruses grouping in these clades. Branch lengths separating these clades were equivalent to those of the related genera Cilevirus, Higrevirus and Blunervirus, as well as to those within the family Virgaviridae. Genetic distances and phylogenetic analyses suggest that Nelorpivirus and Sandewavirus might form taxonomic groups on genus level that may define alone or together with Cilevirus, Higrevirus and Blunervirus a viral family.

Figure 1

Phylogenetic relationship of Goutanap virus and Piura virus C6.7-MX-2008. (A) Analysis of the conserved domains of the RNA-dependent RNA polymerase proteins of negeviruses, cileviruses, higreviruses and blunerviruses; (B) Analysis of a gap-free concatenated alignment of fused methyltransferase, helicase and RNA-dependent RNA polymerase domains of members of negeviruses, cileviruses, higreviruses and blunerviruses, as well as representative members of each genus of the Virgaviridae family. ML analyses were based on an 805 amino acid alignment (A) and a 445 amino acid alignment (B) guided by the Blosum62 (A) and Dayhoff (B) substitution matrix using PHYML as implemented in Geneious. Confidence testing was performed with 1000 bootstrap replicates. Virus names and GenBank accession numbers are provided in Table S1.