Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil

Abstract

Ticks are ectoparasites spread worldwide and are well known as vectors of many viruses of great importance to human and animal health. However, the viral diversity in ticks is still poorly understood, particularly in South America. Here we characterized the viral diversity present in Rhipicephalus microplus parasitizing cattle in the southern region of Brazil using metagenomics. Our study revealed the presence of viruses that had not been previously described in the region, including lihan tick virus (Phenuiviridae family) and wuhan tick virus 2 (Chuviridae family), as well as expands the biogeography of jingmen tick virus (Flaviviridae family) in Brazil. Also, we described three novel tymoviruses (Tymovirales order), named guarapuava tymovirus-like 1 to 3. We described the genomic and phylogenetic characterization of these viruses. Our study sheds light on the viral diversity of Rhipicephalus microplus in South America, and also expands the biogeography of tick viruses that were previously described only in Asia.

Figure 1

Maximum likelihood phylogenies of new strains of Jingmen tick virus. Phylogenies were constructed on nucleotides alignments, (a) segment 1 (NS5-like) based on TN + F + I nucleotides substitution model, (b) segment 3 (NS3-like) based on TIM3 + F + I nucleotides substitution model, (c) segment 2 (Glycoprotein) based on TIM3 + F + G4 nucleotides substitution model and (d) segment 4 (VP2-VP3) based on TNe + I nucleotides substitution model. Phylogenies are midpoint rooted for clarity of presentation. The scale bar indicates evolutionary distance in numbers of substitutions per nucleotides sites. Taxons are colored according to geographical location, and the hosts were denoted with a silhouette. The legends for the colors are shown on the left. The black circles indicate the main nodes with maximum likelihood bootstrap support levels above 75% bootstrap replicates.

Figure 2

Maximum likelihood phylogenies of new strains of Lihan tick virus into Phenuiviridae family. Phylogenies were constructed on amino acids alignments sequences of nucleoprotein (a) and RNA-dependent RNA polymerase (b) based on LG + I + G4 amino acids substitution model. Phylogenies are midpoint rooted for clarity of presentation. The scale bar indicates evolutionary distance in numbers of substitutions per amino acids sites. Taxons are colored according to geographical location, and the host was denoted with a silhouette. The legends for the colors are shown on the left. The black circles indicate the main nodes with maximum likelihood bootstrap support levels above 75% bootstrap replicates.

Figure 3

Maximum likelihood phylogeny of new strains of Wuhan tick virus 2 into Chuviridae family. Phylogeny was constructed on amino acids alignments sequences with RNA-dependent RNA polymerase based on LG + I + G4 amino acids substitution model. Phylogeny was midpoint rooted for clarity of presentation. The scale bar indicates evolutionary distance in numbers of substitutions per amino acids sites. Taxons are colored according to geographical location, and the host was denoted with a silhouette. The legends for the colors are shown on the left. The black circles indicate the main nodes with maximum likelihood bootstrap support levels above 75% bootstrap replicates.

Figure 4

Genome organization of novel tymoviruses (a). The ORF1 polyprotein and coat gene are shown in blue and pink, respectively. The respective nucleotides positions of elements in genome are shown at the bottom of figures. Dashed-lines indicate the incomplete gene. (b) Maximum likelihood phylogeny of novel tymoviruses into Tymovirales order. Phylogeny was constructed on amino acids alignments sequences with ORF1 polyprotein based on LG + I + G4 amino acids substitution model. Phylogeny was midpoint rooted for clarity of presentation. The scale bar indicates evolutionary distance in numbers of substitutions per amino acids sites. Taxons are colored according to geographical location, and the host was denoted with a silhouette. The legends for the colors are shown on the left. The black circles indicate the main nodes with maximum likelihood bootstrap support levels above 75% bootstrap replicates.

Figure 5

Map of sample collection sites in the southern region of Brazil. Black dots represent the name of the collection sites in each state.