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Table 2 Microorganisms amplified in this study

From: Old zoonotic agents and novel variants of tick-borne microorganisms from Benguela (Angola), July 2017

Microorganisms Target gene Amblyomma variegatum
(2: 5N, 1M)a 		Hyalomma truncatum
(3: 1M, 5F)a 		Rhipicephalus decoloratus
(16: 24M, 83F)a 		Rhipicephalus duttoni
(2: 1M, 2F)a 		Rhipicephalus evertsi mimeticus
(1: 1F)a 		Rhipicephalus sp.
(1: 1 M)a
Rickettsia spp. ompA R. africae
(100;CP001612)
2 (5N, 1M) 		R. aeschlimannii (100;HQ335157)
3 (1M, 5F) 		R. africae
(100; CP001612)
1 (9M) 		– – –
Anaplasma/Neoehrlichia/Ehrlichia spp. groESL – – Ehrlichia spp.
(100; MW054557)
6 (44F) 		– – –
Ehrlichia spp. gltA NP NP Ehrlichia spp.
(96.9–97.0; KX987353)b
6(44F) 		NP NP NP
16S rRNAc NP NP Ehrlichia sp.
(99.9; AF497581)
1 (9F)d 		NP NP NP
Borrelia spp. flaB – – – – – –
glpQ – – – – – –
Coxiella burnetii IS1111 – – – – – –
Coxiella/Francisella spp. rpoB Coxiella spp.
(98.9–99.2; KP985305)
2 (5N, 1M) 		SNC Coxiella spp.
(100; KP985329)
16 (24M,38F) 		Coxiella sp.
(95.9; KP985337)
2 (1M, 2F) 		Coxiella sp.
(99.1; KP985331)
1 (1F) 		Coxiella sp.
(97.8;KP985337)
1 (1M)
groEL Coxiella spp.
(99.5; KP985486)
2 (5N, 1M) 		Francisella sp.
(96.8;CP013022, CP012505)e
1 (4F) 		Coxiella spp.
(100; KP985510)
16 (24M, 38H) 		Coxiella sp.
(97.3; KY678195)
2 (1M, 2F) 		Coxiella sp.
(98.2; KY678195)
1 (1F) 		Coxiella sp.
(98.3;CP011126)
1 (1M)
  16S rRNAc NP Francisella sp.
(99.6; AB001522)
1 (4F)f 		Coxiella sp.
(99.4; JQ480818)
1 (5H)d 		NP NP NP
Spiroplasma spp. rpoB – – Spiroplasma spp.
(99.4; KP967687)g
3 (24M) 		– – –
16S rRNA NP NP Spiroplasma spp.
(98.7–100; KP967685)h
3 (24M) 		NP NP NP
Theileria spp./Babesia spp. 18S rRNA Babesia spp.
(91.4; AB734390)
2 (5N, 1M) 		– B. bigemina
(100; KF606863)
2 (10F) 		– – –
Babesia spp. ITS 1 Babesia spp.
(70.9; LK391709)
2 (5N, 1M) 		NP B. bigemina
(98.8–100; EF458251)h
2 (10H) 		NP NP NP
ITS 2 Babesia spp.
(74.7; EF186914)
2 (5N, 1M) 		NP B. bigemina
(99.5; EF458266)
2 (10F) 		NP NP NP
  1. Data show the species names and the highest identity with public sequences (%; GenBank accession number) followed by the number of pools in which the microorganisms have been detected and, in brackets, the number of ticks from each pool
  2. N: nymphs; M: males; F: females; SNC: sequences not conclusive; NP: not performed
  3. aNumbers in brackets indicate (number of pools: number of ticks and developmental stage); btwo genetic variants were identified; cpan-bacterial PCR assay; dPCR assay performed to four samples, but because this is a pan-bacterial PCR assay (Additional file 1:Table S1), the bacterium was only amplified from one sample; ewith 87.6% and 65% query cover, this genotype reached 98.2% and 98.7% identity with Francisella sp. detected in soft and hard ticks, respectively (MW287617 and KY678032); fwith 92% query cover, this genotype reached 99.8% identity with Francisella sp. amplified from Hyalomma truncatum (JF290387); gwith 42% query cover, the sequences are identical to available Spiroplasma sequences from Rhipicephalus decoloratus (MK267083-4), but also to those detected in other Rhipicephalus and Ixodes species (MK267073-7, MK267082, MK267085); hNucleotide sequences show several ambiguous bases
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