Figure legends
Figure 1. Map of the three neighbouring counties of Busia, Bungoma, and Kakamega showing the livestock markets and slaughterhouses from which arthropod samples were collected .
Figure 2. Melt rate profiles. (A) CCHF virus RdRp amplicons, (B) Theileria/Babesia 18S rRNA amplicons, (C) Anaplasma16SrRNA amplicons, and (D) Rickettsia/Coxiella 16S rRNA amplicons. PC: positive control. Ra: Rh. appendiculatus . Rd:Rh. decoloratus .
Figure 3. Maximum likelihood phylogeny of Crimean-Congo haemorrhagic fever virus strains inferred from 34 aligned 434-nt segments of the L-segment (RdRp gene). GenBank accession numbers and country of origin are indicated for each sequence. Accession numbers for sequences from this from this study are in bold. Isolation sources in applicable sequences are also highlighted. Bootstrap values at the major nodes are of percentage agreement among 1,000 replicates. The branch length scale represents substitutions per site. The gaps indicated in the branches to the Nairobi sheep disease outgroup represent 0.8 substitutions per site. The sequences from this study fall into African genotype II as indicated by the vertical bars.
Figure 4. Maximum likelihood phylogeny of apicomplexan protozoa inferred from 32 aligned 502-nt segments of the 18S rRNA gene. GenBank accession numbers and isolation sources are indicated for each sequence. Accession numbers for sequences from this study are in bold. Bootstrap values at the major nodes are of percentage agreement among 1,000 replicates. The branch length scale represents substitutions per site.
Figure 5. Maximum likelihood phylogeny of tick-associatedCoxiella endosymbionts inferred from 33 aligned 279-nt segments of the 16S rRNA gene. GenBank accession numbers and tick species of origin are indicated for each sequence. Accession numbers for sequences from this study are in bold Bootstrap values at the major nodes are of percentage agreement among 1,000 replicates. The branch length scale represents substitutions per site. The gaps indicated in the branches to the L. pneumophila outgroup represent 0.12 substitutions per site. Sequences from this study and those from GenBank fall into three genotypes: A = Coxiella burnetii; BCoxiella endosymbionts of Amblyomma spp. ticks; C= Coxiella endosymbionts of Rhipicephalus spp. ticks; D = Coxiella endosymbionts of Dermacentor andAmblyomma spp. ticks.