Study Design and Setting; We conducted a cross-sectional study among women in the fishing communities of Kigungu and Kasenyi fish landing sites along the shores of Lake Victoria, Entebbe peninsula. Sample collection procedures were performed by a trained nurse at the Post Abortive Care Unit of Entebbe General Hospital. Samples were in under 3 hours, transported to and analysed at the UVRI-IAVI HIV Vaccine Program Laboratory located within the Uganda Virus Research Institute (UVRI), Entebbe.
Study Population and Sampling; Participants were females aged 18 to 49 years, HIV seronegative, not pregnant and must have been residents of the study area for at least 3 months prior to enrolling into the study. All participants gave a written informed consent before enrolment into the study. Eligible participants who were experiencing menstrual bleeding at their clinic visit were rescheduled approximately 7 days from the last day of menstrual bleeding. Female participants with an Intra-Uterine Device (IUD) were excluded due to a risk of the IUD dislodgement during the cytobrush sample collection procedure. Cytobrush samples with visible blood stains were excluded to avoid PBMC contamination of CMCs.
Alcohol Use Disorder Identification Test (AUDIT) questionnaire administration and categorization of participants; The standard WHO-AUDIT questionnaire was administered to all participants. Total AUDIT scores were calculated and participants were assigned as Alcohol Consumers (27 participants) or alcohol non-consumers (26 participants) based on WHO’s cut-off score of > = 8/40 and < 8/40 and respectively prior to sample collection.
HIV Screening and Pregnancy testing; HIV was tested using the Uganda Ministry of Health’s Rapid Diagnostic Test (RDT) algorithm. Briefly, samples were first tested on the Determine HIV-1/2 Ag/Ab Combo-Antibody test [6], non-reactive results were immediately reported [33]. Samples reactive on the Determine HIV-1/2 Ag/Ab Combo-Antibody RDT were tested on the HIV1/2 STAT-PAK RDT [7] and if reactive, results were reported as such. Samples with discordant results between Determine and STAT-PAK methods were tested on the SD Bioline HIV-1/2 Antibody test [1], the results of which were reported as final. Testing for pregnancy was done using the QuickVue One Step HCG Combo test (Quidel, CA) on the urine samples.
Cervical Mononuclear Cells (CMCs) and Blood sample collection; CMCs were collected using the Cytobrush (Fisher Scientific, USA). Two cervical Cytobrush samples (one for the phenotyping assay and another for the HIV-1 pseudo-virus infectivity assay) were collected from each consenting participant by a trained Nurse using a sterile Cytobrush under speculum examination. A Cytobrush was gently inserted into the cervical os and rotated at 360 degrees. The cytobrush was then immediately retracted and placed into 50ml of RPMI-1640 supplemented with 1%Penicillin/Streptomycin/Amphotericin B and 2% Fetal Bovine Serum (FBS) and placed on ice. Samples were transported to the laboratory on ice for processing within 3 hours of collection. Additionally, 10mls of heparinized venous blood sample was collected from each participant to serve as a comparator for CMCs.
CMC processing; CMC isolation was performed as described elsewhere [34]. In brief cytobrush samples were vortexed for 2 minutes. The cytobrush was then squeezed between the thumb and index finger, and subjected to several rotating motions while the tip was still in the media. The procedure was repeated in R10 media (RPMI 1640 supplemented with 10% FBS) for all the CMCs to be released into suspension. The CMCs in suspension were filtered through a 100µm nylon cell strainer (Fisher Scientific, USA) into a newly labelled 50 ml conical tube (BD, USA). This CMC suspension was centrifuged for 10 minutes at 500g without brakes. The supernant was gently disposed of and the CMC pellet resuspended by gentle agitation in PBS supplemented with 2%FBS. The Cytobrush sample of one participant (from the alcohol consumer group) was excluded from laboratory analysis due to visible blood contamination of the cytobrush sample.
Peripheral Blood Mononuclear Cells (PBMC) separation; PBMCs were isolated from heparinized blood using the Ficoll-Histopaque density gradient centrifugation method [35]. Briefly, 10mls of anti-coagulated blood was gently layered over 10mls of Ficoll-Histopaque solution in a 50ml conical tube (BD, USA) and centrifuged at 400xg, 220C for 40 minutes. The mononuclear cell layer that is between the plasma layer and Ficoll-Histopaque layer was carefully pipetted into another 50ml conical tube (BD, USA) and washed twice with 10ml PBS at 400xg, 220C for 10 minutes followed by cell counting.
CD4 + T cell phenotyping; Surface staining was performed as follows: 800,000 cells of isolated CMC and PBMC were incubated at 40C for 30 minutes with antibodies (with conjugated fluorochromes) targeting CD4-BV650, CD3-AF700, CCR4-PECy7, CXCR3-BV510, CCR5-PECY759, Beta7-PerCP/Cy5.5, Beta1-APC, Alpha 4-PE-Green and LIVE/DEAD-NIR-APC-Cy7 CD4. Cells were then washed in 2 ml of PBS (with 2% FBS) at 640g for 4 minutes at room temperature. Cells were fixed by adding 200µl of 1X CellFIX solution (BD, USA) and incubated for 15 minutes at 4 0C wrapped in aluminum foil and washed as before. The stained fixed cell pellet was re-suspended in 200µl of PBS (with 2%FBS) and kept in the fridge (40C) wrapped and acquired on an LSR II Flow Cytometer. CD3 + CD4 + T cell phenotype was identified from the isolated CMCs and PBMCs based on their size and granularity using a FSC/SSC plot (Supplementary Fig. 1A (i)) and B (i)), doublets by a FSC-A/FSC-H plot (Supplementary Fig. 1A(ii) and B (ii)), live and dead cell were separated using a Live-Dead NIR/SSCA plot (Supplementary Fig. 1A (iii) and B (iii)), and CD3:CD4 double positives identified by a CD4/CD3 plot (Supplementary Fig. 1A (iv) and B (iv)). Integrin receptor expressing CD4 + T cells were identified by gating for α4+, β1+ and β7 + from the CD3 + CD4 + gate using a α4+, β1 + or β7+ /CD4 + plot (Supplementary Fig. 3).
Green Fluorescent Protein (GFP)-tagged pseudo-virus production; GFP-tagged pseudo-virus was obtained from the “Elite study” where production was performed using, with adaptation, a method described by Nasri et al, 2014. In summary, the single cycle GFP-tagged pseudo-virus were produced by transfection of 100mg of each plasmid (envelope and backbone + transfer vector and packaging vector) as follows; CIY + VSVG (Pan tropic); CIY + ADA (R5 tropic HIV) and CIY + YU-2(R5 tropic HIV) in cultures of 100,000 cell lines per well followed by incubation for 3 days. Pseudo-virus in the cell culture supernatants were harvested and titrated by transduction of HEK 293T cells. The cells were then transduced by serial dilution of vector and the GFP expressing cells were analyzed using flow cytometry. Titrated pseudo-viruses were aliquoted in 1.0mLs and frozen until used in the infectivity assays.
HIV-1 entry assay; To measure susceptibility to HIV entry, 100ul of CMCs and PBMCs were spinoculated (1700xg, 2hrs, 17°C, with brakes) and cultured with either 0.5 MOIs of GFP-tagged HIV-1 pseudo-virus particles (infection well) or RPMI (mock well) in 48 flat bottomed well plates (Fisher Scientific, USA) at 37oC and 0.5% CO2 for 36 hours to allow viral entry to occur. Contents of each culture well were transferred into a labelled FACS tube (BD Bioscience, UK) and washed in 2mls of PBS with 2% FBS (640xg for 4 min). Cells were then surface stained with CD4-BV650, CD3-AF700, CCR5-PE-CF594, Alpha4-PE-green, Beta7-PerCP-Cy5.5, Beta 1 (CD49d)-647-APC and LD-NIR-APC-Cy7 surface marker antibodies as described above. Both Immunophenotyping and HIV entry were then measured by acquiring cells on an LSR II flow cytometer (BD Biosciences, UK). HIV viral entry was measured by the frequency of CD3 + CD4 + T cell expressing GFP. The GFP + CD3 + CD4 + T cells were gated for using a GFP+/CD4 + plot from the CD3 + CD4 + gate (Supplementary Fig. 2).
Data analysis; Flow cytometry data was acquired on the LSRII Flow cytometer. Data from FACSDIVA was analyzed using FlowJo software v10.11 and exported to Microsoft Excel. Statistical analysis was performed using GraphPad Prism V6 software. Comparison of CD4 + T cell phenotype frequencies and Viral entry of CD4 + T cells between the alcohol consumers and non-consumer control group was assessed using non-parametric Mann- Whitney U-test and a P value of less than 0.05 was considered significant at a confidence interval of 95%.