South African HIV-1 subtype C transmitted variants with a specific V2 motif show higher dependence on α4β7 for replication.

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Figure 5

Viruses with P/SDI/V motifs are associated with BV and are more frequent among South Africa subtype C viruses. a P/SDI/V α4β7 binding motifs were significantly associated with concurrent BV infection as compared to those with LDI/L motifs (17/18 P/SDI/V motifs vs. 7/12 LDI/L motifs; *p = 0.026, Fisher exact test). b Fold differences of mean cytokine levels in CVL and plasma among 25 and 28 individuals respectively in the CAPRISA 002 cohort separated based on those that have P/SDI/V motifs (green, n = 15 and n = 17) and those that have LDI/L motifs (blue, n = 10 and n = 11). The intensity of the respective colours is indicative of the fold differences between the two groups (green = greater fold difference in P/SDI/V group; blue = greater fold difference in LDI/L group) which is ranked based on the CVL profile. c Global frequency of the P/SDI/V motif (green), LDI/V/L motif (blue) and other motifs (grey) among sequences from subtypes A, B, C and D from the Los Alamos database. Further breakdown of subtype C sequences according to the country of origin is shown in the box. Viruses from South Africa showed the highest frequency of P/SDI/V motifs (35%) with those from the CAPRISA 002 cohort exceeding this (48%; n = 20). d A maximum likelihood tree inferred using Fasttree of all subtype C gp160 sequences from the LANL database (n = 776) rooted on the 1959 Zaire sequence with HXB2 as an outgroup. Nodes are coloured according to the α4β7 binding motif (positions 179–181), South African sequences indicated by dotted lines and CAPRISA sequences indicated by red lines.

South African HIV-1 subtype C viruses show a higher frequency of P/SDI/V motifs

Among the 42 women where viral sequence data was available, 20 (48%) were infected with viruses that contained P/SDI/V motifs, exceeding those with LDI/V/L motifs (n = 14; 33%) (Figure 5c). To explore whether this was typical of global viruses, we analysed ~4,700 unique V1/V2 sequences from the Los Alamos National Laboratory (LANL) HIV database with information on genetic subtype, route of transmission, sex of individual and region. HIV-1 subtype C showed the highest prevalence of viruses with P/SDI/V motifs (18%), in contrast to subtypes A, B and D (2, 3 and 8% P/SDI/V motifs respectively). When subtype C sequences were broken down by region, however, the increased frequency of the P/SDI/V motif was almost completely accounted for by South African viruses. Of 781 sequences from South Africa, excluding sequences from the CAPRISA 002 cohort, 273 (35%) had the P/SDI/V motif. This is in contrast to other regions where subtype C circulates, including Tanzania, Malawi, Botswana and Zambia where the frequency of the P/SDI/V motif was less than 8%. Since many South African sequences were from women and the route of transmission is predominantly heterosexual, we compared gender and transmission route across all sequences in the database. However, no significant differences were noted between the groups (not shown).

When the phylogeny of full-length subtype C gp160 sequences (n = 776) was examined the enrichment of non-LDI/L motifs in South African sequences (indicated by the dotted lines) was found to be due to founder effects (Figure 5d). Two distinct South African lineages with founders that had PDI motifs with branch support of 0.955 and 0.999 were identified. These data suggest that the high frequency of P/SDI/V motifs is not typical of subtype C viruses in general, but rather represents a signature of South African subtype C viruses.

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Discussion

While it is generally accepted that gp120 binds α4β7 via a tri-peptide motif in V2, its role in HIV infection is controversial [19–21, 27, 29]. Using viruses from the well-characterized CAPRISA acute infection cohort, we were able to show that interaction with α4β7 was common but highly variable between isolates from different individuals as well as within an individual over time. Furthermore, T/F viruses with a P/SDI/V tri-peptide motif bound α4β7 more efficiently and had higher dependence on α4β7 for replication compared to those with an LDI/V motif. Notably, the P/SDI/V genotype was more common among South African subtype C viruses. The disproportionate distribution of P/SDI/V genotypes in the South African-based CAPRISA cohort may in part explain why this study has enabled us to more clearly define a role for α4β7 in HIV infection.

Our study used infectious viruses from the same individuals over multiple time points, and to our knowledge, includes the largest collection of T/F viruses investigated for α4β7 dependence linked to extensive clinical and laboratory data. For those individuals where we had complete longitudinal datasets (CAP88, CAP200 and CAP206), we found α4β7 dependence was high for the T/F viruses but decreased during acute infection. However, high dependence on α4β7 was not a feature common to all T/F viruses and is therefore unlikely to be a transmission signature. The loss of high reactivity also coincides with migration to the target tissue after which α4β7 would no longer provide any selective advantage [32]. Many of the chronic viruses tested also had high α4β7 dependence but its role at this stage of infection is less clear. Comparison of the longitudinal sequences from these 3 participants revealed no changes in the α4β7 binding motif except for CAP200, who was dually-infected. However, we noted changes in other regions such as V5 and gp41. Glycan changes in V5, that forms part of the conformational epitope for CD4 binding mAbs such as VRC01 [33] may affect α4β7 reactivity as the integrin is in close proximity to CD4 on the cell surface [9, 34]. Similarly, changes in gp41 may impact on membrane fusion and viral incorporation, with one of the changes, L568R, associated with a reduction in the ability of HIV-1 envelope protein expressing cells to fuse with target cells [34]. Regardless, the absence of common changes between the T/F and acute/early viruses in V1/V2 suggests that regions outside this domain influence α4β7 reactivity. We did find that α4β7 dependence was weakly associated with higher glycan density and longer V1/V2 loops. This is at odds with Nawaz et al. [27], although both studies found that shorter C3/V4 domain lengths was associated with increased α4β7 binding affinity. In addition to this, we found the presence or absence of specific glycans correlated with α4β7 reactivity. The under-representation of PNG332 in viruses with high α4β7 dependence and the reciprocal overrepresentation of PNG334 is intriguing as the 332 glycan has been found to occur less frequently in T/F viruses [35]. These findings suggest that while differences in predicted glycan occupancy alone cannot explain α4β7 reactivity, their position may impact the ability of the tri-peptide motif to access α4β7 on the cell surface. Recent data suggests that the tri-peptide motif is occluded in the pre-fusion trimer structure [36], however this crystalline structure does not account for the significant flexibility and entropy associated with the variable domains of gp120 in which transient exposure of the α4β7 binding site is plausible. Non-functional trimers on the surface of HIV could also provide additional opportunities for viral particles to bind α4β7 [37].

STIs have been identified as a major cause of inflammatory cytokine upregulation and immune cell recruitment to the genital mucosa [38] increasing HIV risk [39–41]. Both HSV-2 and Chlamydia trachomatis infection increase the number of α4β7+ CD4+ T cells in the genital tissue [7, 30, 42]. Bacterial vaginosis, a common syndrome characterised by a shift in vaginal flora composition [43], has been identified as a specific risk factor for HIV acquisition, also influencing genital tract cytokine concentrations [40, 44, 45]. In this study, we found that BV diagnosis at the time of HIV infection was associated with T/F viruses that had high α4β7 dependence for replication, but found no such associations with STI’s. In a recent study by Masson et al., BV in the CAPRISA cohort upregulated inflammatory cytokines while downregulating chemokines in the CVL, in contrast to chlamydia and HSV-2 [46]. Chemokines are essential for the chemotaxis of effector cells, suggesting that BV may be associated with a reduction in target cells in the genital mucosa, favouring viruses with enhanced α4β7 reactivity. However, since the data presented here does not prove causality, it is possible that the increased α4β7 dependence is merely a feature of viruses transmitted in these conditions. This is corroborated by our observation that individuals infected with viruses with P/SDI/V motifs were more likely to have BV at the time of infection. Overall, BV-associated changes in the genital cytokine milieu may modulate the mucosal barrier favouring the transmission of viruses with P/SDI/V α4β7 binding motifs that have a high dependence on the integrin.

We also found that IL-7 levels in genital secretions at transmission were associated with α4β7 dependence of T/F viruses. Recently, Cimbro et al. demonstrated that IL-7 induces expression and functional activation of α4β7 in vitro and in vivo [47]. The levels of IL-7 required to upregulate the integrin, however, are associated with lymphopenia; an immunological state only generated late in HIV infection. It is therefore unlikely that the levels induced in the CVL at the time of infection would be sufficient to influence α4β7 expression. Interestingly, other cytokines upregulated by BV, such as IL-8 and IL-1α [48–51] were also associated with α4β7 dependence in CVL, but not in plasma, suggesting that that the most relevant impact of the cytokines on α4β7 is at the site of transmission. Furthermore, all 3 cytokines were associated with the P/SDI/V α4β7 binding motif, further suggesting that BV may play a significant role in determining the level of α4β7 interaction at transmission.

This study is the first to fully explore the effect of different α4β7 sequence binding motifs on α4β7 reactivity. Transmitted viruses with P/SDI/V motifs, present in only 8% of global viruses, were associated with a higher dependence on α4β7 for replication and bound better to the integrin. LDI/L/V motifs which most closely resemble those of the natural ligand MAdCAM-1 (LDT) and fibronectin (LDV) are more common in global sequences accounting for 78% of all circulating variants. In addition to the LDT motif, the integrin-binding loop of MAdCAM-1 contains a downstream SDT motif that is responsible for stabilisation of the interaction [52]. Interestingly, an α4β7 antagonist containing the SDV/T motif was more potent than one containing an LDT motif [53]. This suggests that different motifs display different affinities for the ligand, similar to the observation in this study that viruses with P/SDI/V motifs have a higher reactivity with α4β7 as compared to LDI/V motifs.

Unexpectedly, we found that 48% of women in the CAPRISA 002 cohort and 35% of all South African sequences had P/SDI/V motifs, significantly higher than what is seen in other countries where HIV-1 subtype C circulates. This is due in part to founder effects, with two South African lineages having founder viruses with a PDI motif. The introduction and maintenance of this motif in South African viruses may be as a result of an immunological feature of people in this region. α4β7 expression is known to be regulated by ATRA, a metabolite of vitamin A [54]. Vitamin A deficiency is common in the South African population as compared to other sub-Saharan African countries; with 19% of pregnant women having serum retinol <0.70 µmol/l, higher than Botswana, Malawi or Tanzania [55]. It is therefore possible that vitamin A deficiency may result in decreased expression of α4β7, leading to the selection of viruses with a α4β7 binding motifs that have a greater affinity for the integrin in this population. In addition, the exact composition of the microbiota in BV has not been fully elucidated, and it is possible that this may differ from region to region; possibly creating a unique environment in the South African population. This data highlights the importance of fully characterising individual epidemics, even those caused by the same subtype.

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Conclusions

Collectively, these data suggest a role for α4β7 in HIV infection that changes over time and that is impacted during transmission by a number of factors including the sequence of the α4β7 binding motif, cytokine milieu and BV in the genital tract. This may have particular relevance for South Africa where a higher frequency of α4β7-dependent V2 motifs were present among HIV-1 subtype C transmitted/founder viruses. Further understanding of the interaction between the virus and the integrin might provide additional opportunities for devising vaccine and therapeutic strategies.

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Methods

Ethics statement

Ethical approval was received for the CAPRISA 002 Acute Infection Study from the University of KwaZulu-Natal, University of Cape Town and University of Witwatersrand. All participants provided written informed consent for the CAPRISA 002 study with tacit agreement to adhere to regular clinic visits and blood draws. Approval for this particular study was granted by the University of the Witwatersrand.

Study participants

Participants in the CAPRISA 002 Acute Infection cohort, established in 2004 [26] were derived from prospective cohorts of high-risk HIV negative South African women [46]. Clinical and laboratory monitoring including CD4 count, viral load and testing for STIs and BV were performed routinely [26, 40] on all participants at enrolment and regularly thereafter. Eleven participants, where cloned longitudinal envelopes from the transmitted/founder and/or acute infections were available, were selected for the α4β7 binding and replication studies. Participants in the parent CAPRISA 002 cohort with sequence (n = 42), laboratory-diagnosed STIs or BV (n = 28) and cytokine (n = 25) data were available for a larger correlates study.

Testing for STIs and BV

A gynaecological examination was performed and two vulvovaginal swabs were collected [40]. Swabs were screened for C. trachomatis, N. gonorrhoeae, M. genitalium, HSV and T. vaginalis by PCR. BV was diagnosed by Gram staining using Nugent’s criteria (a score ≥7 indicates BV).

Cell lines

The TZM-bl cell line engineered from CXCR4-positive HeLa cells to express CD4, CCR5, and a firefly luciferase reporter gene (under control of the HIV-1 LTR) was obtained from the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH (developed by Dr. John C. Kappes, and Dr. Xiaoyun Wu [56, 57]). The 293T cell line was obtained from Dr George Shaw (University of Alabama, Birmingham, AL, USA). Cell lines were cultured at 37°C, 5% CO₂ in DMEM containing 10% heat-inactivated fetal bovine serum (Gibco BRL Life Technologies) with 50 ug/ml gentamicin (Sigma) and disrupted at confluency by treatment with 0.25% trypsin in 1 mM EDTA (Sigma).

Isolation and stimulation of CD4+ T lymphocytes from whole blood

CD4+ T cells were isolated to a purity of 99% from healthy blood donors using RosetteSep Human CD4+ T cell Enrichment Cocktail (Stem Cell Technologies, Canada) as per the manufacturer’s protocol. Isolated cells were cultured with 10 µM all-trans retinoic acid (ATRA) (Sigma-Aldrich, MO, USA), 50 ng/ml OKT3 (anti-CD3 antibody) (eBioscience, CA, USA) and 20 U/ml IL-2 (Roche Applied Sciences, Germany) in RPMI media supplemented with 20% heat inactivated fetal bovine serum for 6 days at 37°C, 5% CO₂ [3]. The purity of the CD4+ T cell population as well as the upregulation of α4β7 by ATRA was confirmed routinely by flow cytometry. Donors were designated as responders or non-responders based on whether ATRA treatment upregulated the α4β7+ population of lymphocytes as shown in Additional file 3. Only 25% of donors responded to ATRA treatment similar to what was shown in a study by Arthos et al. [3] and only these donors were used in further experiments.

Flow cytometry surface staining

Isolated CD4+ T cells from ATRA-treated responders were stained with optimally titrated fluorescently labelled antibodies: CD3 energy coupled dye (ECD Beckham Coulter, France), CD4-Quantum dot 605 (Invitrogen, Carlsbad, CA, USA), anti-human CD49d (Integrin alpha 4) R-Phycoerythrin (PE) (eBioscience, CA, USA), anti-human/mouse integrin β7 fluorescein isothiocyanate (FITC) (eBioscience, CA, USA) and Aqua Fluorescent Reactive Dye (Invitrogen, Molecular Probes, Carlsbad) in 1% BSA/PBS staining buffer in the dark for 30 min at 4°C and fixed in 0.1% paraformaldehyde/PBS. Fluorescence minus one controls were used to define the gating strategy and compensation was done using anti-mouse Igκ BD CompBeads. Acquisition of all samples was performed on a FACSAria (BD Biosciences) and analysis done on FlowJo X software (TreeStar Ashland, OR, USA).

Production of infectious viruses and pseudoviruses

Cloned HIV-1 gp160 envelope genes derived by single genome amplification as previously described [58] from selected CAPRISA participants were used to produce infectious virions. Mutant envelopes were generated as detailed in Table 1 with QuikChange Lightning Kit (Stratagene) and confirmed by DNA sequencing. Infectious envelope clones (IECs), were generated by re-amplifying the gp160 env gene from the envelope plasmids and co-transfecting the PCR product with the pHIVΔenvBstEllnef-hisD backbone (a gift from Dr Daniel Kuritzkes) which were constructed as described elsewhere [59]. Two infectious molecular clones (IMCs) which contain full proviral genomes derived from participants CAP210 and CAP239 and representative of the T/F viruses were also used. The SF162 IMC was from David Montefiori at Duke University, NC. The IMC plasmids were transfected in 293T cells and both IECs and IMCs were incubated at 37°C, 5% CO₂ for 72 h following which the media was changed to fresh DMEM with 10% FBS. After a week of incubation in 293T cells, 1 ml of the viral supernatant was spinoculated for 60 min at 1,200 g, 30°C with activated CD8+ depleted PBMCs at 5 × 10⁶ cells/ml and the spinoculation was repeated the next day. Viral growth was monitored by an in-house p24 antigen ELISA as described previously [60]. p24 positive cultures were expanded into T25 flasks with fresh CD8 depleted PBMCs and following a week of incubation, the viral supernatant was removed, filtered with a 0.2 nm micropore filter and aliquoted for freezing at −70°C. All viruses inputs were titrated to a TCID₅₀/ml of 25 as described elsewhere [56, 57].

Table 1

Mutations introduced into the α4β7 binding motif of T/F viruses

Individual	Type	α4β7 binding motifa	IEC
CAP225 T/F	Wild type	SDI	✓
	Mutant	LDI	Did not grow
CAP88 T/F	Wild type	PDI	✓
	Mutant	LDI	Did not grow
CAP200 T/F	Wild type	SDV	✓
	Mutant	LDI	Did not grow
CAP8 T/F	Wild type	LDI	✓
	Mutant	PDI	✓
CAP256 T/F	Wild type	LDL	✓
	Mutant	SDI	✓

^aIntroduced mutations are in italics.

Sequence analysis

Full length env sequences from the CAPRISA 002 cohort were assembled and edited using Sequencher v.4.5 and Bioedit v.7.0.5.3. Number and positions of predicted N-linked glycans were estimated using the N-GlycoSite tool [61]. Variable domain lengths and relative positions of predicted glycans were determined with reference to HXB2 numbering. For relative frequency of predicted glycan sites, envelopes that showed α4β7 reactivity above the mean were defined as having high α4β7 dependence (n = 33) and those with values below the mean were considered to have low α4β7 dependence (n = 27). The frequency of predicted glycans (excluding those in the variable regions that are difficult to align accurately) were expressed as a proportion of either high or low α4β7 dependent sequences. V1/V2 sequences downloaded from Los Alamos National Laboratory HIV database were selected as single unique sequences per individual. These sequences were further stratified by country of sampling, genetic subtype, mode of transmission and gender of infected individual. Phylogeny of gp160 of subtype C viruses (n = 776) was assessed using the Shimodaira–Hasegawa test and Fasttree to determine a maximum-likelihood tree and branch support.

Flow cytometry based α4β7-virus binding assays

α4 and β7 encoding plasmids synthesised by Origene (Rockville, MD, USA) were co-transfected using 4 µg of each plasmid into 293T cells with X-tremeGENE Transfection Reagent (Roche) or Polyethyleimine Max (Polysciences, Inc., Warrington, PA, USA) and incubated at 37°C, 5% CO₂ for 2 days. The transfected cells were removed gently with 1 mM EDTA/PBS, following which the co-expression of α4β7 was determined by flow cytometric staining using CD49d (integrin α4)-PE (eBioscience, CA, USA) and anti-human/mouse integrin β7 FITC as described above. The gating strategy was single (FSC-H/FSC-A), live (FSC/Aqua vital negative) and α4β7⁺ (α4-PE/β7-FITC) 293T cells. Two types of binding assays were done; namely a competition binding assay and a direct binding assay. In the first, α4β7 transfected 293T cells (1 × 10⁵ cells/ml) were incubated in the presence or absence of the Act-1 mAb (targets the α4β7 dimer) obtained from the NIH AIDS Research and Reference Reagent Program or the HP2/1 mAb (Beckman Coulter, France) which targets the α4 subunit only, for 15 min followed by the addition of the either IECs or IMCs for 25 min. Cells were stained as above. Binding to α4β7 was defined as the percentage difference between the median fluorescence intensity (MFI) of α4-PE and β7-FITC of α4β7-transfected cells without an inhibitory mAb or virus and the MFI α4β7-transfected cells with an inhibitory mAb or virus. The direct binding assay was carried out in a similar way except that the cell-virus complexes were stained for p24-FITC (KC57, Beckman Coulter) and the percentage p24 positive cells gated on single live 293T cells were compared between 293T untransfected (background) and α4β7 transfected 293T cells as a representation of bound virus.

α4β7 mediated virus replication inhibition assay

ATRA-treated CD4+ T lymphocytes (25 μl of 4 × 10⁶ cells/ml) from a responder individual were either incubated with 25 μl of media (virus control), 10 μg/ml anti-CD4 monoclonal antibody (positive control), 275 pM inhibiting monoclonal antibody HP2/1 (targeting α4 subunit) or 2.2 pM Act-1 (targets α4β7) for an hour at 37°C at 5% CO2. Both HP2/1 and Act-1 mAb concentrations were optimised by titration in the α4β7-mediated virus capture inhibition assay, noting the concentration at which effectiveness of blocking viral replication was highest. 100 μl containing 25 TCID₅₀ of IECs and IMCs were incubated for 2 h in triplicate with the cells in a 96-well plate, followed by two washes with fresh IL-2 media (5% IL-2 at 200 U/ml, 20% FBS and RPMI media) at 1,200 g for 5 min at 25°C. 100 µl of culture supernatant was harvested every 2 days without disturbing the cells for a period of 10 days with removed volume replaced with fresh IL-2 media. Collected supernatants were lysed using 1.25% Empigen/TBS solution and stored at 4°C before assessing p24 levels by ELISA. Percentage dependency on α4β7 was calculated as the percentage of difference in p24 between untreated samples (virus control) and p24 on samples treated with HP2/1 or Act-1 relative to untreated controls at the exponential growth phase of the latter. These single points were unique for each virus based on steepness of the gradient of the kinetic growth curve.

Cytokine measurements in CVLs and plasma

CVLs (10 ml sterile saline) for cytokine measurements were collected, centrifuged and supernatants stored at −80°C. CVLs were not collected from menstruating participants. Blood was collected by venepuncture into acetate citrate dextran vacutainer tubes, plasma isolated and stored at −80°C. CVLs were pre-filtered by centrifugation using 0.2 μm cellulose acetate filters (Sigma, USA). The concentrations of 32 cytokines were measured using LINCOplex Human Cytokine and High Sensitivity Human Cytokine kits (LINCO Research, USA). Human Cytokine LINCOplex kits included Epidermal growth factor (EGF), eotaxin/CCL11, fractalkine/CX₃CL1, G-CSF, IFN-α, IL-1α, IL-1Ra, IL-12p40, IL-15, IL-17, IFN-γ-induced protein (IP)-10/CXCL10, MCP-1/CCL2, MIP-1α/CCL3, MIP-1β/CCL4, RANTES/CCL5, sCD40L, soluble IL-2 receptor α (sIL-2Rα), transforming growth factor (TGF)-α and vascular endothelial growth factor (VEGF). Thirteen cytokines were measured in CVL and plasma using High Sensitivity LINCOplex kits: IL-1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8/CXCL8, IL-10, IL-12p70, IL-13, GM-CSF, IFN-γ and TNF-α. The lower limit of detection of these kits ranged between 0.01 and 27.65 pg/ml for each of the cytokines. Data was collected using a Bio-Plex™ Suspension Array Reader (Bio-Rad Laboratories Inc^®) and a 5 PL regression formula was used to calculate cytokine concentrations from the standard curves (BIO-Plex™ manager software version 4). IFN-α and MIP-3α were measured in CVLs using ELISA (R&D Systems). Cytokine concentrations below the assay lower limit of detection were reported as the mid-point between the lowest concentrations measured for each cytokine and zero.

Statistical analysis

Paired data with only two groups were assessed by paired t test or Wilcoxon matched pairs signed rank test, and in groups with three or more sets by the repeated measures one way ANOVA with pairwise comparisons adjusted for multiple comparisons using Tukey’s method. Unpaired data were assessed for significance by the Mann–Whitney test, or the one way ANOVA and the Fisher exact test was used to determine the significance of categorical groupings. While Spearman’s correlation was used to assess linear correlations, correlations were adjusted for multiple comparisons using a false discovery rate (FDR) step down procedure (STATA version 12, StataCorp, College Station, TX, USA). A mixed linear model was fitted to assess significance in cases where there were multiple comparisons with repeated measures and were corrected for duration of infection. Observations of p < 0.05 were defined as significant. Statistics and graphs were done with GraphPad Prism 5 and STATA 12.

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Authors’ contributions

SIR performed, designed and analysed experiments and wrote the manuscript. ESG designed experiments and NNM assisted with flow cytometry analysis. DJS, CW and LW provided statistical and evolutionary analysis of binding motifs. BEL produced all α4β7 binding site mutants and CKW advised and produced structure visualisations. LM (Lindi Masson) and JSP provided cytokine data and NG provided clinical data on the CAPRISA cohort. QAK and SSAK are responsible for the conceptualisation of the CAPRISA cohorts. PLM and LM (Lynn Morris) analysed, advised and wrote the manuscript. All authors read and approved the final manuscript.

Acknowledgements

We are grateful to participants of the CAPRISA Acute Infection cohort for providing samples, and to the clinical/laboratory staff at CAPRISA for their commitment to the study. We also thank Mary Phoswa for assistance in the production of the viruses and isolation of PBMCs and Dr Lyle McKinnon for constructive advice on the manuscript. We are grateful to Florette Treurnicht (UCT) and Haitao Ding (University of Alabama at Birmingham) for the generation of the CAP210 and CAP239 IMCs.

This project was funded by a research Grant from K-RITH to ESG and bursaries from PRF and NRF to SIR. We also thank CHAVI-ID and CAPRISA. CAPRISA is funded by the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes for Health (NIH), and U.S. Department of Health and Human Services (Grant: AI51794). PLM is a Wellcome Trust Intermediate Fellow in Public Health and Tropical Medicine (Grant 089933/Z/09/Z).

Compliance with ethical guidelines

Competing interests The authors declare that they have no competing interests.

Additional files

Additional file 1:^{(588K, pdf)}

α4β7-virus binding assays. (A) α4β7 expressed on transfected 293T cells (red) and not on the surface of untransfected 293T cells (black) confirmed by flow cytometry were used for direct binding and competition assays. (B) Infectious viruses represented by p24-FITC MFI bound to α4β7 transfected 293T cells shown in red but not to untransfected 293 cells shown in black, representative of 4 independent experiments. (C) Viral attachment of CAP88 T/F in the presence of HP2/1 and Act-1 was inhibited in the p24 direct binding assay (red and blue respectively), representative of 5 independent experiments.

Additional file 2:^{(361K, pdf)}

IECs and IMCs show similar binding to and dependence on α4β7 for replication. IECs and IMCs of CAP210 T/F and CAP239 T/F bound to α4β7 at similar levels as defined by (A) p24 binding assay where the dashed line represents IMC binding and the solid line represents IEC binding and (B) the competition assay. SF162 IEC and IMC also bound similarly see Figure 1A. (C) All three viruses showed no differences between their IECs and respective IMCs in dependence on α4β7 for replication. All results are representative of three experiments with error bars representing SEM. No differences were significant by the paired t test.

Additional file 3:^{(1.4M, pdf)}

Characterisation of a responder and non-responder to ATRA treatment. CD4 cells were treated with ATRA for 6 days and stained for α4 and β7. An example of a non-responder is shown in A and a responder in B with an increase in the percentage of cells with α4 and β7 co-expression.

Additional file 4:^{(803K, pdf)}

Titration of α4β7 inhibitors for maximal inhibition of viral replication. (A) A decreasing shift in PE florescence relative to the experimental control (ATRA treated CD4 + T cells alone shown in black); is indicated in a dose-dependent manner between 0.0022-30 nM (i) HP2/1 and (ii) Act-1 concentrations (red and blue graduations respectively). All samples were gated on single live CD4 + T lymphocytes. (B) Change in median fluorescent intensity (MFI) with the 30 nM being the most saturating concentration for blocking of the integrin by both mAbs. Both A and B are representative of four repeated experiments, with the bars showing the mean and error bars, the SEM. (C) The same ATRA activated responders were infected with a T/F virus CAP88.2.00.17-5A and incubated with (i) HP2/1 and (ii) Act-1 between 0.0022-30 nM (red and blue graduations respectively) and monitored over 10 days by p24-ELISA. The virus control (no inhibitory mAb) is shown in black and the infectivity control shown in grey. The optimum concentration for viral inhibition by HP2/1 is 0.275 nM and Act-1 is 2.2 pM, while the viral replication is significantly upregulated at 30 nM in both cases. These results are representative of five independent experiments using 3 donors, with error bars indicating the SEM and points, the mean of three replicates.

Additional file 5:^{(763K, pdf)}

α4β7 mediated virus capture inhibition assay for all 60 IECs. Virus growth kinetic curves of CAP8, 88, 177, 200, 206, 210, 225, 239, 244, 255 and 256 viruses done in triplicate; in the presence or absence of HP2/1 mAb (red), Act-1 mAb (blue) or CD4 mAb (grey) demonstrate their inhibitory effect on the replication of T/F, early and chronic clones. Data are representative of two independent experiments, with the curves representative of the mean p24 readings and error bars indicating the SEM. The longitudinal samples including a T/F from the 3 individuals included in Figure 2 are indicated by an asterisk.

Additional file 6:^{(17K, xlsx)}

Characteristics of IECs used in this study.

Additional file 7:^{(1.0M, pdf)}

gp160 sequence alignment of matched T/F and acute virus pairs. Changes between the T/F and acute (2-6 month) viruses for 3 pairs (CAP88, CAP200, CAP206) are indicated. Important functional and structural regions of gp160 are highlighted. Predicted N-linked glycans are shown in CAPS and red.

Additional file 8:^{(671K, pdf)}

The impact of HIV glycans on α4β7 reactivity. (A) Correlations between the glycan density, the length of V1/V2, V3, C3/V4, V5 and dependence on α4β7 (Act-1) for replication of 60 IEC. Blocks shaded in grey are those which were significant in a linear mixed model corrected for repeated measures. Beta coefficients and p values are shown below the respective blocks. (B) Frequency of predicted N-linked glycans in the conserved regions of gp120 relative to the percentage of viruses that showed high (green, n = 33) or low (blue, n = 27) dependency on α4β7. Significance was determined by the Fisher exact test where PNG234 (**p = 0.009) and PNG334 (**p = 0.006) were more frequent in viruses with high α4β7 dependence andPNG332 was more frequent in viruses with low α4β7 dependence(*p = 0.026).

Additional file 9:^{(11K, xlsx)}

Univariate correlations between α4β7 dependence for replication and cytokine levels in CVL and plasma at transmission.

 

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Simone I Richardson, Email: az.ca.dcin@renomis.

Elin S Gray, Email: ua.ude.uce@yarg.e.

Nonhlanhla N Mkhize, Email: az.ca.dcin@monon.

Daniel J Sheward, Email: az.ca.tcu@drawehs.leinad.

Bronwen E Lambson, Email: az.ca.dcin@lnewnorb.

Constantinos Kurt Wibmer, Email: az.ca.dcin@wtruk.

Lindi Masson, Email: moc.liamg@nossam.idnil.

Lise Werner, Email: gro.asirpac@renreW.esiL.

Nigel Garrett, Email: gro.asirpac@tterraG.legiN.

Jo-Ann S Passmore, Email: az.ca.tcu@eromssap.nna-oj.

Quarraisha Abdool Karim, Email: gro.asirpac@miraKloodbA.ahsiarrauQ.

Salim S Abdool Karim, Email: gro.asipac@miraKloodbA.milaS.

Carolyn Williamson, Email: az.ca.tcu@nosmailliw.nyloraC.

Penny L Moore, Email: az.ca.dcin@mynnep.

Lynn Morris, Email: az.ca.dcin@mnnyl.

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References

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