Table 1.
SIVgor-positive gorillas detected in the Campo Ma'an National Park from April 2004 to November 2011
| Individual (CPg ID) | Collection informationa |
Serology result (Inno-Lia HIV-1/2 test)b | SIV-specific PCR resultc |
Genetic profile (consensus multilocus genotype)d |
Sexe | P(ID) HWf | P(ID) Sibf | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Group or cluster | Collection details | Collection date (mo/yr) | Collected sample(s) | Pol | Gp41 | Other | Locus D18S536 | Locus D4S243 | Locus D10S676 | Locus D9S922 | Locus D2S1326 | Locus D2S1333 | Locus D4S1627 | |||||
| ID1 | E | t | 04/04 | CP684, CP685 | + | + | + | FL | 142/146 | 185/193 | 180/192 | 280/280 | 251/263 | 298/318 | 234/274 | F | ** | ** |
| 5n | 12/08 | CP3417 | + | − | − | |||||||||||||
| t | 12/08 | CP3425, CP3426 | + | − | + | env (1,674 bp) | ||||||||||||
| t | 12/08 | CP3428 | + | − | + | |||||||||||||
| ID32 | E | t | 04/04 | CP686 | − | − | − | 146/154 | 193/193 | 180/192 | 280/280 | 251/271 | 298/334 | 234/− | M | * | * | |
| 5n | 12/08 | CP3416 | + | − | + | |||||||||||||
| ID2 | F1 (cf. ID36) | n | 04/06 | CP1434, CP1436 | + | − | + | gp41-nef (1,237 bp) | 146/154 | 173/193 | 196/200 | 276/280 | 255/267 | 298/298 | 234/242 | F | * | * |
| F3 | t | 10/10 | CP6101 | + | − | − | ||||||||||||
| ID70 | F3 | t | 10/10 | CP6097, CP6098, CP6099, CP6100 | + | + | + | 146/146 | 173/189 | 192/196 | 276/280 | 259/271 | 306/314 | 230/238 | M | ** | ** | |
| t | 10/10 | CP6102, CP6103 | + | − | − | |||||||||||||
| ID3 | 02/07 | CP2071 | + | − | − | 146/150 | 181/193 | 196/200 | 268/280 | − | 314/334 | 234/238 | F | |||||
| ID4 | A | n | 02/07 | CP2072, CP2074 | + | + | + | 146/146 | 185/193 | 196/200 | 260/268 | 267/275 | 322/334 | 234/274 | F | * | * | |
| 12n | 02/07 | CP2109, CP2117, CP2118 | + | + | + | |||||||||||||
| 8n | 04/10 | CP5760, CP5761 | + | − | − | |||||||||||||
| t | 04/10 | CP5806 | + | − | − | |||||||||||||
| t | 04/10 | CP5815 | + | − | − | |||||||||||||
| t | 04/10 | CP5851 | + | − | − | |||||||||||||
| 9n | 03/11 | CP6435, CP6437, CP6438 | + | − | − | |||||||||||||
| t | 03/11 | CP6451 | + | − | − | |||||||||||||
| t | 03/11 | CP6473, CP6477 | + | − | − | |||||||||||||
| t | 03/11 | CP6481 | + | − | − | |||||||||||||
| 8n | 03/11 | CP6485, CP6486, CP6495 | + | − | + | |||||||||||||
| 6n | 05/11 | CP6640, CP6641 | + | − | − | |||||||||||||
| t | 05/11 | CP6682 | + | − | + | |||||||||||||
| ID5 | A | 12n | 02/07 | CP2110, CP2111, CP2119, CP2123 | + | − | + | 146/150 | 177/185 | 192/200 | 260/280 | 251/267 | 322/326 | 234/246 | F | ** | ** | |
| 8n | 04/10 | CP5752, CP5803, CP5804, CP5807 | + | − | − | |||||||||||||
| t | 04/10 | CP5849 | + | − | − | |||||||||||||
| 9n | 03/11 | CP6442 | + | − | − | |||||||||||||
| t | 03/11 | CP6453 | + | − | − | |||||||||||||
| t | 03/11 | CP6465, CP6466 | + | − | + | |||||||||||||
| t | 03/11 | CP6476, CP6478 | + | − | − | |||||||||||||
| 8n | 03/11 | CP6488, CP6489 | + | − | − | |||||||||||||
| t | 05/11 | CP6685 | + | − | − | |||||||||||||
| ? | A | t | 05/11 | CP6684 | + | − | − | 146/− | − | − | 268/− | − | 298/− | − | − | |||
| ID65 | A | t | 04/10 | CP5816 | + | − | − | 146/146 | 185/193 | 196/196 | 268/280 | 247/275 | 322/334 | 234/274 | M | ** | ** | |
| t | 04/10 | CP5856, CP5857 | + | − | − | |||||||||||||
| 8n | 03/11 | CP6484 | + | − | − | |||||||||||||
| ID19 | A | 12n | 02/07 | CP2120, CP2121 | − | ND | ND | 146/154 | 181/185 | 192/196 | 264/264 | 255/271 | 318/318 | 242/242 | F | * | * | |
| t | 04/10 | CP5838, CP5839, CP5839bis, CP5848 | +/− | − | − | |||||||||||||
| ? | A | t | 04/10 | CP5802 | + | ND | ND | 146/154 | − | 196/− | 268/− | 251/− | − | − | − | |||
| ID6 | 11 | 12n | 02/07 | CP2094, CP2095 | + | + | − | 146/150 | − | 196/200 | 268/280 | 267/275 | 322/334 | 242/246 | F | * | * | |
| ID7 | 11 | 12n | 02/07 | CP2098 | + | − | − | 146/150 | 185/185 | 196/200 | − | 251/287 | − | 242/242 | F | |||
| ID8 | 11 | 12n | 02/07 | CP2087 | + | − | − | 146/150 | − | 196/200 | − | 267/271 | 354/374 | − | − | |||
| ID9 | C | t | 02/07 | CP2139 | + | + | + | FL | 146/146 | 177/189 | 192/200 | 276/280 | 251/271 | 318/334 | 242/242 | F | ||
| ID10 | C | t | 02/07 | CP2126, CP2132, CP2133, CP2134, CP2135, CP2141 | + | + | + | FL | 146/154 | 173/193 | 180/180 | 276/280 | 255/271 | 298/322 | 230/234 | F | ** | ** |
| 64 (=C?) | 17n | 11/11 | CP6990, CP6991, CP6998 | + | − | − | ||||||||||||
| ID75 | 64 (=C?) | 17n | 11/11 | CP6988 | + | − | − | 146/150 | 173/193 | − | 264/280 | − | 294/322 | 242/242 | F | |||
| ID76 | 64 (=C?) | 17n | 11/11 | CP6989, CP6992 | + | − | + | 146/150 | 193/193 | 196/200 | 280/280 | 267/271 | −/322 | 242/242 | F | |||
| ID77 | 64 (=C?) | 17n | 11/11 | CP7001, CP7002 | + | − | − | 146/158 | 177/181 | 196/200 | 268/272 | 251/271 | 334/334 | 242/274 | F | ** | ** | |
| ID11 | X | t | 11/07 | CP2740, CP2744, CP2746, CP2747, CP2749 | + | − | − | 146/150 | 181/189 | 196/200 | 264/280 | − | 314/318 | 234/234 | M | ** | ** | |
| ID12 | 15 | t | 04/08 | CP2994 | + | − | − | 150/154 | 185/185 | 184/196 | 268/280 | 267/267 | 298/306 | − | F | |||
| ID13 | 16 | 1n | 04/08 | CP3018, CP3019 | + | − | − | 150/154 | 185/185 | 180/180 | 268/280 | − | − | − | M | |||
| ID30 | 20 | 1n | 12/08 | CP3400, CP3401, CP3402, CP3403, CP3404, CP3405, CP3406 | + | + | + | 146/146 | 185/189 | 180/196 | 268/272 | 267/271 | − | 234/242 | M | * | * | |
| 3n | 12/08 | CP3407 | + | − | + | |||||||||||||
| ID31 | 20 | 3n | 12/08 | CP3408, CP3409, CP3410 | + | − | + | 146/146 | 173/189 | 180/196 | 276/280 | 255/267 | 318/322 | 242/274 | M | * | * | |
| t | 12/08 | CP3411 | + | − | + | |||||||||||||
| ID33 | G | t | 12/08 | CP3443 | + | + | + | 142/146 | 169/185 | 180/192 | 276/280 | 251/251 | 298/318 | 230/234 | F | |||
| ID34 | 24 | t | 12/08 | CP3468, CP3469 | + | − | + | gp41-nef (1,207 bp) | 146/150 | 193/193 | 192/200 | 264/276 | 251/255 | 298/334 | 230/242 | M | ** | ** |
| ID35 | F2 | t | 09/09 | CP4758 | + | − | + | 146/146 | 177/189 | 196/200 | 268/280 | 255/271 | 314/334 | 234/274 | M | * | * | |
| 61 (=F2?) | t | 11/11 | CP6970 | + | − | + | ||||||||||||
| ID73 | 61 (=F2?) | t | 11/11 | CP6971 | + | − | + | 146/146 | 177/181 | 196/200 | 264/280 | 267/275 | 322/334 | 242/246 | F | |||
| ID36 | F1 | t | 04/06 | CP1440 | − | − | − | 146/154 | 185/193 | 192/196 | 268/276 | 247/267 | 322/330 | 234/244 | F | ** | ** | |
| F2 | t | 09/09 | CP4759 | + | − | + | ||||||||||||
| ID37 | F2 | t | 09/09 | CP4760 | + | + | + | 146/154 | 177/193 | 192/196 | 264/268 | 251/267 | 334/334 | 234/234 | F | * | * | |
| t | 09/09 | CP4765, CP4766 | + | + | + | |||||||||||||
| 55 (=F2?) | t | 05/11 | CP6631, CP6635 | + | − | − | ||||||||||||
| ID38 | Single | 1n | 09/09 | CP4762, CP4763, CP4764 | + | + | + | 146/150 | 185/193 | 196/200 | 280/284 | 267/275 | 314/322 | 234/242 | M | ** | ** | |
| ? | 31 | 6n | 09/09 | CP4775 | + | − | − | 150/154 | − | − | 268/272 | − | − | 234/246 | M | |||
| ? | 31 | 6n | 09/09 | CP4776 | + | − | − | 142/146 | 189/189 | − | − | − | 298/322 | − | M | |||
| ? | 31 | 6n | 09/09 | CP4779 | + | − | + | 150/150 | − | − | − | − | −/334 | 242/242 | M | |||
| ID66 | 35 | 10n | 04/10 | CP5781 | + | − | + | 150/150 | 185/185 | 200/200 | 264/280 | 247/271 | 334/334 | 238/274 | M | * | * | |
| t | 04/10 | CP5813 | + | ND | ND | |||||||||||||
| t | 03/11 | CP6534 | + | − | + | |||||||||||||
| 11n | 03/11 | CP6555 | + | − | − | |||||||||||||
| ID72 | ? | t | 05/11 | CP6688 | + | − | − | 146/154 | 181/193 | 192/196 | 268/268 | 251/− | 298/298 | 234/274 | F | |||
| ID67 | 35 | t | 04/10 | CP5810 | + | − | − | 150/154 | 181/189 | 180/196 | 260/272 | 267/267 | 322/334 | − | − | |||
| ID60 | 38 | t | 04/10 | CP5827, CP5828, CP5830, CP5831, CP5832, CP5833, CP5834, CP5835, CP5836, CP5837 | + | − | − | 150/150 | 173/185 | 192/196 | 268/276 | 255/275 | 314/− | 242/246 | M | ND | ND | |
| Mixed | 39 | 3n | 10/10 | CP6090, CP6091, CP6092 | + | + | + | F | ||||||||||
| ? | 11/11 | CP6968 | + | ND | + | 146/154 | − | − | −/271 | − | − | M | ||||||
| ID74 | 62 | t | 11/11 | CP6977 | + | − | − | 146/− | 185/193 | 196/200 | 272/272 | −/275 | 322/334 | 234/− | F | |||
| ID78 | 66 | 7n | 11/11 | CP7010 | + | − | − | 146/154 | 181/185 | 188/192 | 268/280 | 271/275 | 306/314 | 242/242 | F | |||
For each gorilla, an ID number was given and the following collection information recorded: collected cluster (01 to 64) or social group (A to H), collection details (t, collected on track; 3n, collected on three nests; n, collected on a nesting site but nests were not counted), collection date, and number of collected samples (multiple samples may have been collected for one individual; SIV sequences are available for samples shown in bold). Eight seropositive samples from the April 2010 field trip that were too degraded to be assigned to an individual are not shown. Samples of poor quality (degraded RNA and/or DNA) are underlined.
+, positive in the Inno-Lia HIV-1/2 serological test; −, negative test result.
Samples confirmed by SIV amplification and sequencing are shown by SIV-specific RT-PCR results (Pol, pol fragment amplification; gp41, env fragment amplification; other, other regions in the genome could be amplified and sequenced; ND, not done; FL, full-length sequence [50]).
The consensus multilocus genotype profile of seven microsatellite loci is given for each gorilla, with two allele sizes per locus. −, repeatedly negative.
F, female; M, male.
The maximum P(ID)HW (**, P < 10−6 ; *, P < 10−3) and P(ID)Sib (**, P < 0.01; *, P < 0.05) values are given for each individual and confirm the matches between samples.