The PTAP sequence duplication in HIV-1 subtype C Gag p6 in drug-naive subjects of India and South Africa

Sharma, Shilpee; Aralaguppe, Shambhu G.; Abrahams, Melissa-Rose; Williamson, Carolyn; Gray, Clive; Balakrishnan, Pachamuthu; Saravanan, Shanmugam; Murugavel, Kailapuri G.; Solomon, Suniti; Ranga, Udaykumar

doi:10.1186/s12879-017-2184-4

BMC Infectious Diseases

Table 1 The clinical profile of the study subjects belonging to two different clinical cohorts of India

From: The PTAP sequence duplication in HIV-1 subtype C Gag p6 in drug-naive subjects of India and South Africa

(A) The YRG CARE cohort, n = 30
Subject ID	Year of Diagnosis	Enrolment date	Age/ Gender	Time (months from the date of enrolment)												GenBank Accn. No.
				PVL			CD4						CD8
				M0	M12	M24	M0	M6	M12	M18	M24	M30	M0	M12	M24	gag
T-001	22–05–2002	26–11–2010	28/F	12074	29617	60953	560	569	525	530	645	355	1633	1804	1273	KT152633
T-002	22–01–2002	06–12–2010	34/F	15354	16293	6852	517	855	740	879	565	584	610	762	734	KP890700–11
T-004	15–03–2004	16–12–2010	29/F	33784	36627	112577	553	442	508	359	321	296	>2000	>2000	1910	KT152674–686
T-005	13–12–2003	20–12–2010	26/F	912	x	x	770	x	x	x	x	x	>2000	x	x	KT152634
T-006	25–08–2008	29–12–2010	28/F	1638	24773	x	527	480	409	547	x	x	1513	1199	x	KP890712–21
T-007	27–10–2007	30–12–2010	26/F	<150	263	722	958	799	1016	886	1311	x	859	992	1380
T-008	17–10–2008	20–01–2011	30/F	34640	172183	x	468	480	484	432	476	415	1158	1083	901	KP890722-38
T-009	24–08–2006	24–01–2011	27/F	14672	76956	24797	695	x	603	x	330	x	1927	1930	928	KP890739-45
T-010	22–02–1996	29–01–2011	39/F	<150	<150	<150	641	785	813	NA	525	x	880	1105	679
T-011	14–10–2004	29–01–2011	42/F	45583	7780	107965	823	559	489	533	575	x	1071	1191	1043	KP890746–61
T-012	20–09–2008	03–02–2011	30/F	<150	<150	x	1380	NA	1549	1964	x	x	1142	1071	x
T-013	20–04–2005	02–12–2011	25/F	438	3877	4528	856	580	816	718	502	724	1214	1424	1164	KT152635–37
T-014	28–10–2002	16–02–2011	35/F	2888	4578	x	553	484	376	436	425	x	1000	743	973	KT152638–42
T-015	11–05–2002	25–02–2011	36/F	542	3120	x	920	1000	820	880	830	x	1237	1097	1321	KT152643–47
T-016	22–10–2007	09–08–2011	38/F	1664	1401	x	730	x	653	x	x	x	1535	1366	x	KT152648–49
T-017	20–12–2006	27–09–2011	36/F	5598	x	x	504	332	325	x	x	x	2000	>2000	x	KT152650–52
T-018	16–03–2007	29–08–2011	34/M	6645	x	150244	519	563	483	452	446	x	1751	1732	1283	KT152653–56
T-019	31–05–2007	19–09–2011	39/M	63722	x	x	238	x	x	x	x	x	1379	x	x	KT152658
T-020	03–12–2008	11–12–2011	35/M	<150	489	x	459	x	x	x	x	x	>2000	x	x	KT152659
T-021	14–06–2008	14–10–2011	52/M	31410	x	x	676	651	641	x	x	x	884	861	x
T-022	20–07–2007	19–12–2011	38/M	6625	46553	x	624	522	558	488	x	x	>2000	>2000	x	KT152660–63
T-023	12–08–2004	23–02–2012	39/F	<150	x	x	987	x	x	x	x	x	1195	x	x
T-024	19–02–2007	28–02–2012	50/F	541	x	x	914	1179	1570	1574	x	x	1174	>2000	x	KT152664
T-025	11–06–2007	07–03–2012	38/F	1294	4369	x	789	950	693	x	x	x	1724	1968	x	KT152665
T-026	11–07–2007	15–03–2012	54/F	197	<150	974	907	x	1215	x	922	x	1345	1517	1748
T-027	29–04–2005	26–03–2012	36/F	<150	x	x	1195	630	x	x	x	x	767	x	x
T-028	25–05–2007	19–04–2012	28/F	162112	x	x	398	318	x	x	x	x	885	x	x	KT152666-68
T-029	31–12–2007	28–04–2012	30/F	1659	1504	x	618	694	599	545	x	x	1362	x	x	KT152669-70
T-030	22–12–2005	03–05–2012	42/F	284879	1E + 06	x	545	410	368	x	x	x	1352	x	x	KT152672-73
T-031	28–06–1999	09–06–2012	24/F	753	x	x	819	x	x	x	x	x	1091	x	x
(B) The Nellore cohort, n = 35
Subject-ID	Enrolment date	Age/ Gender	Cell count		PVL											GenBank Accession No.
Subject-ID	Enrolment date	Age/ Gender	CD4	CD8	PVL											Gag
INDO-SA-NLR2001	26–09–2011	23/F	608	1035	25149
INDO-SA-NLR2002	26–09–2011	32/F	589	927	26186											KT124420–21
INDO-SA-NLR2003	26–09–2011	69/M	1140	1192	548											KT124422
INDO-SA-NLR2004	26–09–2011	43/F	1012	1240	6070											KT124423–24
INDO-SA-NLR2005	26–09–2011	35/F	599	773	5713											KT124425–27
INDO-SA-NLR2006	26–09–2011	46/F	659	1185	662											KT124428
INDO-SA-NLR2007	26–09–2011	40/M	546	912	11986											KT124429–31
INDO-SA-NLR2008	26–09–2011	46/M	1289	1175	3687											KT124432–33
INDO-SA-NLR2010	26–09–2011	32/F	989	1497	251											KT124434–36
INDO-SA-NLR2011	26–09–2011	28/F	582	642	2704											KT124437
INDO-SA-NLR2012	28–09–2011	28/F	1087	1420	6070											KT124438–39
INDO-SA-NLR2014	28–09–2011	55/M	766	>2000	88645											KT124440–41
INDO-SA-NLR2015	28–09–2011	34/F	1019	>2000	21108											KT124442–43
INDO-SA-NLR2016	28–09–2011	29/F	631	1465	26363											KT124444–46
INDO-SA-NLR2017	28–09–2011	39/M	581	1050	8972											KT124447–49
INDO-SA-NLR2018	28–09–2011	35/F	825	1637	6493											KT124450–52
INDO-SA-NLR2019	28–09–2011	35/F	1085	1078	185											KT124453
INDO-SA-NLR2020	28–09–2011	38/M	570	1268	70025											KT124454–56
INDO-SA-NLR2022	28–09–2011	38/M	1489	1470	<150											KT124457
INDO-SA-NLR2023	28–09–2011	28/M	8.2	>2000	<150
INDO-SA-NLR2024	14–10–2011	30/F	984	1279	340
INDO-SA-NLR2025	14–10–2011	30/M	500	825	3423											KT124458–60
INDO-SA-NLR2026	14–10–2011	18/M	1015	1546	8733											KT124461–63
INDO-SA-NLR2028	14–10–2011	34/F	711	1409	24480											KT124464–65
INDO-SA-NLR2029	14–10–2011	35/F	1148	1290	<150
INDO-SA-NLR2030	14–10–2011	39/F	1185	1041	<150
INDO-SA-NLR2031	14–10–2011	50/F	1007	498	<150
INDO-SA-NLR2032	14–10–2011	45/M	671	821	9468											KT124466–68
INDO-SA-NLR2036	14–10–2011	27/M	860	1715	3332											KT124469–70
INDO-SA-NLR2037	14–10–2011	29/M	732	>2000	1505											KT124471–72
INDO-SA-NLR2038	31–10–2011	33/M	669	777	26542											KT124473
INDO-SA-NLR2039	31–10–2011	47/M	925	1111	4563295											KT124474–75
INDO-SA-NLR2040	31–10–2011	29/M	1181	978	<150
INDO-SA-NLR2041	31–10–2011	45/M	888	1237	56445											KT124476–77
INDO-SA-NLR2042	02–12–2011	26/F	1280	>2000	4797											KT124478

Note: Accession Numbers. KP890700-KP890762 and KT152677-686: Full-length gag sequences of six subjects (T002, T004, T006, T008, T009 and T011) at M0 time-point as determined using the plasmid clone sequencing strategy. The rest of the sequences were determined by direct sequencing of the PCR amplicons of the same subjects at the follow-up time-points
M: The month of sample collection at 6 month interval from baseline M0
X: Information not available
−: Failed PCR amplification
PVL: Plasma viral load (number of RNA copies/ml)
CD4 and CD8: cell count (cells/μl)

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ISSN: 1471-2334

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