Table 1.
Characteristics of included studies.
| Author (publication year) | Subjects & Sample sizes | Study site | Age, median [IQR] | Gender | Race | ART initiation and ART duration | CD4+ T-cell counts (cells/μL) | HIV RNA (copies/ml) | Sample type | Platforms | Methods of sequencing | RF |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Kazer (2020) | From FRESH cohort; 4 patients |
NA | 22.5 (21, 24) | NA | NA | Only number 3 patient-initiated ART 2.3 years after baseline | Pre-infection: 884 (676.75, 916); baseline: 238 (212, 335.25); Week 1: 157 (140.5, 214.5); Week 2: 347 (244.5, 389.5); Week 3: 190.5 (74.5, 373.5); Week 4: 501 (322.5, 585); Month 4: 196 (140.75, 353.5); Year 1: 659 (510.5, 823.5). | NA | PBMC | BD SORP FACSAria II | Integrated single-cell analysis | 22 |
| Wang (2020) | 6 HIV-infected individuals, 4 healthy individuals | U.S.A. | 46 (30.5, 58.25); two without specific age | 1 female, 9 male | NA | Yes (except 1 HIV controller) | 451 (227, 629.25); HIV controller: unknown. |
3 donors with a high viral load and 3 with a low viral load (>100,000 and < 20) | PBMC | 10x Genomics | scRNA-seq | 23 |
| Liu (2020) | 25 HIV patients (virologically suppressed) | NA | 57 (51, 62) | Male: 17; Female: 8 | African American (17), White/Caucasian (6),Hispanic (1), Asian (1) | 181 (105, 246) months | NA | Virologically suppressed | PBMC and leukapheresis sample | NA | Sort-Seq | 24 |
| de Armas (2019) | 6 HIV patients, 6 non-HIV patients | NA | HIV: 64 (62, 66.75); non-HIV: 64 (61.25, 66). | HIV group: 5 male, 1 female; non-HIV group: 3 male, 3 female | NA | Yes | NA | Virologically suppressed on ART | PBMC | Illumina MiSeq (BD) |
Single cell gene expression analysis | 25 |
| Farhadian (2018) | Virologically suppressed HIV (3 patients) versus. healthy control (2 participants, none had active neurological disease or other infection) | U.S.A. | HIV participants: 47(40, 49); uninfected participants: 54(51.5, 56.5) | All male | NA | Yes | Nadir CD4+ T-cells [infected participants]: 237.5(157.75, 317.25); current CD4+ T-cells [infected participants]: 391(424, 967). nadir CD4+ T-cells [uninfected participants]: NA; current CD4+ T-cells [uninfected participants]:848.5(811.75, 885.25). | Infected participants: plasma HIV RNA levels <20 for more than 1 year; CSF HIV RNA: 68.5 (53.25,83.75) |
CSF and blood | NA | scRNA-seq | 26 |
| Josefsson (2013) | Chronically infected with HIV-1 (Fiebig stage VI); 5 patients |
U.S.A. | 29.9 (29.7, 33.2) | 5 male | White/Latino: 2; Black: 3 | Untreateda | 484 (220, 758); 2 patients (3, 4) had CD4+ percent <14 %. Palpable lymph nodes were identified in the axilla or inguinal regions and entire lymph nodes were excised. | 9991 (6195,35576) | Lymph node tissue; PBMC | NA | Single-cell sequencing | 27 |
| Holla (2021) | HIV:HCs = 3:3 (sc-RNA seq) | U.S.A. | NA |
HIV: 1 female, 2 male; Healthy donors: 3 female |
HIV: African (Zimbabwe),Multirace/Hispanic, African American; Healthy donor: African American |
NA | HIV1: 1366; HIV2: 458; HIV3: 677 |
HIV1: <40, HIV2: 185, HIV3: 1353 |
PBMC | Illumina HiSeq 3000 platform | Pipeliner RNA-seq | 57 |
| Angin (2019) | Non-ART and virologically suppressed HICs (n = 5) and cART individuals (n = 5). Longitudinal follow-up (4,6,8,10,12,14 days after diagnosis/infection) |
HIV controllers: ANRS CO21 Codex cohort; cART: ANRS PRIMO cohort or CHU Kremlin-Bicêtre and CHU Georges Pompidou in Paris. |
NA | NA | NA | ART group has initiated ART for at least 2 years | NA |
HIV controllers whose last five consecutive plasma HIV RNA were <400; ART group: virologically suppressed |
PBMC | Fluidigm | Single-cell gene expression | 28 |
| Nguyen (2019) | 12 HIV controllers, 14 ART, 18 CP, 7 Acute | San Francisco (USA),Mexico, Philadelphia | 52 (47–59), 40 (32–58), 31 (24–37) and 23 (20–27) | 10 male: 1 female (male transform to female); 8 male, 1 female, 5 unknown; 10 male, 1 female, 7 unknown; 7 male | NA | NA |
HIV controller group: 881 (660–1172); ART group: 544 (359–601); Chronic progressor group: 348 (175–521); Acute group: 306 (238–370) |
HIV controller group: <40; ART group: <40; Chronic progressor group: 51396 (12845–213173); Acute group: 1996027 (1297461–4421034) |
PBMC; lymph node tissue | HiSeq 4000 (Illumina) | Integrated single-cell approach (Illumina Nextera) | 29 |
| Varadarajan (2011) | HIV controllers (2 patients) versus. untreated viremic progressors (2 patients) | U.S.A. | NA | NA | NA | No | NA | HIV controllers (<50); untreated viremic progressors (>2000, median, 3692, range 189–34172) | PBMCs | SMART-RACE RT-PCR kit (BD). | TCR α and β chain sequencing | 30 |
| Saluzzo (2021) | Cohort 1 (HIV ‘late ART’, 3 patients and 3 healthy donors); cohort 2 (HIV ‘early ART’, 6 patients, 11 controls), cohort 3 (HIVSeq 5 controls) and cohort 4 (HIV HPV: HIV-infected patients [n = 11] and HIV- patients [n = 10]). | Vienna | NA | NA | NA | Yes; Cohort 1: after diagnosis (average 50 months) and was on therapy for more than 5 years at time of tissue sampling; Cohort 2: immediately after diagnosis (average 13 ± 12 days). |
Cohort 1: nadir at diagnosis (<350, average 209 ± 130). Cohort 2: average 507 ± 154. |
Cohort 1: <1000 | Skin, Blood (PBMC) | 10x Genomics, the Illumina NovaSeq platform |
scRNA-seq and scTCRαβ-seq | 34 |
| Rato (2017) | HIV: non-infected CD4+ T-cells from high (∼40 % GFP+) and low (∼10 % GFP+) permissive individuals. 1 high and 1 low permissive donor; 2 uninfected CD4+ T-cell donors (3 for validation) |
NA | NA | NA | NA | NA | NA | NA | PBMC (followed by CD4+ T-cell isolation using negative selection and magnetic separation) | Fluidigm C1 platform | scRNA-seq and Bulk RNA-seq | 33 |
| Wanjalla (2021) | HIV-positive non-diabetes (Group 1, 5 patients) versus. HIV-positive diabetes (Group 2, 6 patients) versus. HIV-negative diabetes (Group 3, 5 patients) | U.S.A. | Group 1 (41 [31,32]) versus. Group 2 (53[43, 55.5]) versus. Group 3 (49 [33,34]) | Group 1 (4M, 1F) versus. Group 2 (4M, 2F) versus. Group 3 (3M, 2F) | Group 1 (2 African American, 2 Caucasian, 1 other) versus. Group 2 (4 African American, 2 Caucasian) versus. Group 3 (5 Caucasian) | Yes, on long-term ART (1.5–20.35 years) |
Group 1: CD4+ T-cells at start: 655 [500, 661]; current CD4+ T-cells:1133 [781, 1256]; Group 2: CD4+ T-cells at start: 513.5 [304.25, 683.75]; current CD4+ T-cells: 823.5 [554.75, 950.5] |
HIV-1 RNA<50 for the 12 months prior to adipose biopsy | Adipose tissue, blood [PBMC] | Illumina MiSeq (for sc-TCR sequencing); Illumina NextSeq (for 3′ and 5′ RNaseq) | SMART seq2 and MARS-seq approach | 35 |
| Murray (2020) | 6 HIV patients | U.S.A. | 46 (31.25, 51.75) | Male: Female = 5:1 | NA | 3 start ART [6 (4, 9.5) years]; 3 ART-naïve | Normal levels of CD4+ T-cells in the blood, i.e.,∼500–1500 CD4+ T-cells |
ART-treated individuals: 2 with HIV RNA<50; 1 with HIV RNA<400; ART-naïve individuals: 5970; 304,742; 19,998 |
mDCs | Illumina | ScRNA-seq | 31 |
NA: not applicable.
a
1 patient had received transient ART but had not undergone any consistent therapy for over 2 years prior to biopsy.