A Review of Flaviviruses that Have No Known Arthropod Vector

Abstract

Most viruses in the genus Flavivirus are horizontally transmitted between hematophagous arthropods and vertebrate hosts, but some are maintained in arthropod- or vertebrate-restricted transmission cycles. Flaviviruses maintained by vertebrate-only transmission are commonly referred to as no known vector (NKV) flaviviruses. Fourteen species and two subtypes of NKV flaviviruses are recognized by the International Committee on Taxonomy of Viruses (ICTV), and Tamana bat virus potentially belongs to this group. NKV flaviviruses have been isolated in nature almost exclusively from bats and rodents; exceptions are the two isolates of Dakar bat virus recovered from febrile humans and the recent isolations of Sokoluk virus from field-collected ticks, which raises questions as to whether it should remain classified as an NKV flavivirus. There is evidence to suggest that two other NKV flaviviruses, Entebbe bat virus and Yokose virus, may also infect arthropods in nature. The best characterized bat- and rodent-associated NKV flaviviruses are Rio Bravo and Modoc viruses, respectively, but both have received limited research attention compared to many of their arthropod-infecting counterparts. Herein, we provide a comprehensive review of NKV flaviviruses, placing a particular emphasis on their classification, host range, geographic distribution, replication kinetics, pathogenesis, transmissibility and molecular biology.

Keywords: bat; flavivirus; genomic organization; host range; no known vector; rodent; transmission; vertebrate-specific.

Figure 1

Phylogenetic tree for genus Flavivirus. Complete polyprotein amino acid sequences were aligned using MUSCLE [46]. A maximum likelihood phylogenetic tree was estimated using the Bayesian Markov chain Monte Carlo method implemented in MrBayes Version 3.2.3 [45] sampling across the default set of fixed amino acid rate matrices, with ten million generations, discarding the first 25% as burn-in. The figure was produced using FigTree v1.4.2. (http://tree.bio.ed.ac.uk/software/figtree/). The tree is midpoint-rooted; nodes are labelled with posterior probability values if different from 1.00, and poorly-supported branches are also colored differently. Species names are color-coded as follows: classical insect-specific flaviviruses, blue; dual-host affiliated insect-specific flaviviruses, green; NKV flaviviruses, red; mosquito/vertebrate flaviviruses, purple; tick/vertebrate flaviviruses, black. dISFs: dual-host affiliated insect-specific flaviviruses.

Figure 2

Phylogenetic tree for Rio Bravo virus (RBV)-group partial NS5 sequences. A 1011-nucleotide (nt) region of NS5 corresponding to nt 8952–9962 of JQ582840 (RBV) was used in order to include several additional NKV flaviviruses, for which only partial NS5 sequences are available. The sequences form a gapless nucleotide sequence alignment. A maximum likelihood phylogenetic tree was estimated using the Bayesian Markov chain Monte Carlo method implemented in MrBayes Version 3.2.3 [45] using the general time reversible (GTR) substitution model with the gamma-distributed rate variation across sites and a proportion of invariable sites. Chains were run for one million generations, with the first 25% discarded as burn-in. The figure was produced using FigTree v1.4.2. (http://tree.bio.ed.ac.uk/software/figtree/). Based on the full-genus tree (Figure 1), Apoi virus (APOIV) was selected as an outgroup to root the tree. Nodes are labelled with posterior probability values if different from 1.00, and poorly-supported branches are also colored differently.

Figure 3

Relative UpA and CpG frequencies in different flavivirus species. UpA and CpG frequencies were calculated in two different ways. (A) In each sequence, the numbers of UpA and CpG dinucleotides and A, C, G and U mononucleotides were counted. Dinucleotide frequencies, f_XpY, were expressed relative to their expected frequencies, f_X × f_Y, in the absence of selection. (B) Since codon usage reflects dinucleotide bias, but can also be subject to other selective pressures (e.g., for translational speed or accuracy) that, due to co-evolution of dinucleotide and codon preferences in the host, may lead to the same dinucleotide biases, we also calculated dinucleotide biases independent of codon (and amino acid) usage. To factor out codon and amino acid usage, 1000 shuffled ORF sequences were generated for each virus sequence. In each shuffled sequence, the original amino acid sequence and the original total numbers of each of the 61 codons were maintained, but synonymous codons were randomly shuffled between the different sites where the corresponding amino acid is used in the original sequence. Then, the UpA and CpG frequencies in the original sequence were expressed relative to their mean frequencies in the codon-shuffled sequences. Because codon usage is factored out, the UpA and CpG relative frequencies tend to be less extreme in (B) compared to (A). Since many sequences lack complete UTRs, for consistency, both analyses of all species were restricted to the polyprotein ORF. Each point represents a single flavivirus sequence. Points and selected species names are color-coded as follows: Classical insect-specific flaviviruses, blue; Dual-host affiliated insect-specific flaviviruses, green; NKV flaviviruses, red; Mosquito/vertebrate flaviviruses, purple; Tick/vertebrate flaviviruses, black. Virus names refer to NKV flaviviruses (red points). GenBank accession numbers are the same as those used in Figure 1.