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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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