Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus

Abstract

Tamana bat virus (TABV, isolated from the bat Pteronotus parnellii) is currently classified as a tentative species in the genus Flavivirus. We report here the determination and analysis of its complete coding sequence. Low but significant similarity scores between TABV and memberviruses of the genus Flavivirus were identified in the amino acid sequences of the structural, NS3 and NS5 genes. A series of cysteines located in the envelope protein and the most important enzymatic domains of the virus helicase/NTPase, methyltransferase and RNA-dependent RNA polymerase were found to be highly conserved. In the serine-protease domain, the catalytic sites were conserved, but variations in sequence were found in the putative substrate-binding sites, implying possible differences in the protease specificity. In accordance with this finding, the putative cleavage sites of the TABV polyprotein by the virus protease are substantially different from those of flaviviruses. The phylogenetic position of TABV could not be determined precisely, probably due to the extremely significant genetic divergence from other member-viruses of the family Flaviviridae. However, analysis based on both genetic distances and maximum-likelihood confirmed that TABV is more closely related to the flaviviruses than to the other genera. These findings have implications for the evolutionary history and taxonomic classification of the family as a whole : (i) the possibility that flaviviruses were derived from viruses infecting mammals rather than from mosquito viruses cannot be excluded ; (ii) using the current criteria for the definition of genera in the family Flaviviridae, TABV should be assigned to a new genus.

Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes

“…Thirdly, the polymerases of numerous viruses that specifically infect mammalian cells (pestiviruses, hepaciviruses and Tamana bat virus) are phylogenetically related to those of flaviviruses (de Lamballerie et al, 2002) and there is little chance that these viruses originated from the genome of mosquitoes in recent times; for example, it has been suggested that the common ancestor of hepaciviruses GB virus A and C existed 35 mya in primates (Charrel et al, 1999).…”

“…2). The region of the flavivirus polyprotein homologous to the CSA ORF includes several cleavage sites for the viral serine proteinase, a series of cysteine residues (in the NS1 gene) and enzymic motifs (in the NS3 gene) responsible for serine protease and helicase/NTPase activities, which are widely conserved among flaviviruses (de Lamballerie et al, 2002). These sites and motifs are present and conserved in the CSA sequence, and the hydropathy profile of the protein deduced by conceptual translation of the ORF sequence is remarkably similar to that of the homologous region of KRV polyprotein (Fig.…”

Ngoye virus: a novel evolutionary lineage within the genus Flavivirus

“…This virus was isolated in 1973 from an insectivorous bat in Trinidad (Price, 1978) and for 25 years it remained a taxonomic enigma. It was shown recently to constitute a highly divergent evolutionary lineage within the flaviviruses, constituting a sister group to all other known taxa (de Lamballerie et al, 2002). In contrast to CFAV and KRV, TABV infects only vertebrates and does not replicate in arthropod cells.…”

“…The corresponding amino acid sequence was then aligned with those of other flaviviruses by using the MUSCLE algorithm (Edgar, 2004). The highly divergent TABV was excluded from this analysis, as a previous study failed to identify its precise phylogenetic position (de Lamballerie et al, 2002). Phylogenetic trees were estimated by using the maximum-likelihood (ML) method available in TREE-PUZZLE (Strimmer & von Haesler, 1996), with 10 000 puzzling steps.…”

Characterization of a Novel Flavivirus from Mosquitoes in Northern Europe That Is Related to Mosquito-Borne Flaviviruses of the Tropics

“…Phylogenetically, the insect viruses form a divergent outgroup that may represent a primordial flavivirus lineage. Apart from the insect flaviviruses, the other recently discovered novel flaviviruses represent highly divergent lineages, such as Tamana bat virus (13), and Ngoye virus (20). Recently, a novel flavivirus, Nounané virus (NOUV) was isolated from a novel mosquito vector species, Uranotaenia mashonaensis in Côte d'Ivoire (23), and was shown to be phylogenetically related to the human pathogenic mosquito-borne flaviviruses.…”