Short Communication: High Viral Load and Multidrug Resistance Due to Late Switch to Second-Line Regimens Could Be a Major Obstacle to Reach the 90-90-90 UNAIDS Objectives in Sub-Saharan Africa

Abstract

In the context of lifelong antiretroviral treatment (ART) as early as possible and to end the HIV/AIDS epidemic as a public health treat by 2030, it is important to evaluate the potential risk of transmission of HIV-1 drug resistance (HIVDR) in resource-limited countries (RLCs). Since HIV transmission is driven by HIV-1 RNA viral load (VL), we studied the association between plasma VL and HIVDR profiles in 451 adults failing first-line ART from the 2LADY-ANRS12169/EDCTP trial in Burkina Faso, Cameroon, and Senegal. Median duration on first-line ART was 49 months (IQR: 33–69) and 91% patients were asymptomatic. Genotypic drug resistance testing was successful for 446 patients and 98.7% of them were resistant to at least one of the first-line drugs; 40.6% and 55.8% were resistant to two or three drugs of their ongoing first-line ART, respectively. The median VL was higher in patients with HIVDR to all ongoing first-line drugs than in those still susceptible to at least one drug; 4.7 log₁₀ copies/ml (IQR: 4.3–5.2) versus 4.2 log₁₀ copies/ml (IQR: 3.7–4.7), respectively (p < .001). The proportion of patients with HIVDR to all ongoing first-line drugs was highest (77.9% [95/122]) in patients with VL >5.0 log₁₀ copies/ml. High rates of cross-resistance to other nucleoside reverse-transcriptase inhibitors were observed and were also highest in patients with high VL. Without improvement of patient monitoring to avoid late switch to second-line regimens, a potential new epidemic caused by HIVDR strains could emerge in sub-Saharan Africa and compromise all efforts to reach 90-90-90 UNAIDS objective by 2020.

The major goal of the Joint United Nations AIDS Programme (UNAIDS) is to end the HIV/AIDS epidemic as a public health threat by 2030. To achieve this, HIV transmission has to be reduced significantly, and it should be ensured that by 2020, 90% of people living with HIV should know their HIV status and 90% of them should receive anti-retroviral treatment (ART), intending to achieve viral suppression.¹ Therefore, WHO recommends now that all adults diagnosed with HIV should initiate ART, regardless of clinical stage or CD4 counts.²

ART scale-up in resource-limited countries (RLCs) has been possible because countries adopted the WHO public health approach based on standardized and simplified first-line ART protocols with limited laboratory monitoring. However, in the absence of HIV-1 RNA viral load (VL) monitoring, virological failure (VF) is not timely detected and switch to second-line regimens is delayed. People continue thus on failing ART and accumulate drug resistance mutations, which can compromise efficacy of second-line ART and can also be transmitted. Indeed, rates of transmitted HIV-1 drug resistance (HIVDR) tend to increase over time and with wider ART coverage in RLCs.³ Although the public health approach has been implemented with success in certain countries, high rates (>20%) of VF and HIVDR have been observed in others.⁴ Moreover, in certain settings in sub-Saharan Africa, an alarming proportion of these VFs is due to HIVDR.⁵ In the context of access to effective lifelong ART as early as possible, it is thus important to evaluate the potential risk of transmission of HIVDR in RLCs.

Although VL in genital secretions drives HIV transmission, plasma VL predicts the risk of heterosexual transmission of HIV-1.^6,7 In this study, we studied the association between plasma VL and HIVDR profiles to evaluate the potential transmissibility of drug-resistant HIV strains. The study was conducted in 451 adults failing first-line ART included in the 2LADY-ANRS12169/EDCTP trial, conducted in Burkina Faso (n = 90), Cameroon (n = 302), and Senegal (n = 59), between January 2010 and September 2012.⁸ Treatment failure was defined as confirmed plasma VL >1,000 copies/ml (m2000 RealTime HIV-1 test; Abbott) repeated after at least 1 month adherence support. After adherence support, 13.8% (81/584) of patients had VL below 1,000 copies/ml. For the 451 patients who had still VL >1, 000 copies/ml, the median duration on first-line ART was 49 months (IQR: 33–69) and the first-line ART drugs were 3TC (lamivudine) for all, AZT (zidovudine) or d4T (stavudine) for 85% and 15%, respectively, and EFV (efavirenz) or NVP (nevirapine) for 29% and 71%, respectively. At diagnosis of VF and subsequent switch to second-line ART, 411 (91%) patients were asymptomatic despite median CD4 count of 183 cells/mm³ (IQR: 87–290) and median VL of 4.5 log₁₀ copies/ml (IQR: 4.0–5.1).

Protease and partial reverse transcriptase sequences from patients with VF were obtained as previously described and with the ANRS protocol (www.hivfrenchresistance.org/ANRS-procedures.pdf).⁸ The ANRS-v25 algorithm (www.hivfrenchresistance.org/2015/Algo2015-hiv1.pdf) was used to predict drug resistance to the different ARV drugs. Protease and reverse transcriptase regions were successfully amplified and sequenced for 446/451 patients and 98.7% (n = 440) were resistant to at least one of the first-line drugs; 97.7% (85/87) in Burkina Faso, 99.0% (299/302) in Cameroon, and 98.2% (56/57) in Senegal. Overall, 97.1% (n = 433) were resistant to nonnucleoside reverse transcriptase inhibitors (NNRTIs) (412 to EFV and NVP, 21 to NVP only).

Concerning nucleoside reverse transcriptase inhibitors (NRTIs), 97.3% (n = 434) were resistant to 3TC and 55.8% (n = 249) to AZT and d4T. In practice, 2.2% (n = 10), 40.6% (n = 181), and 55.8% (n = 249) patients were thus predicted to be resistant (i.e., scored as resistant and not as intermediate resistance) to one, two, or three drugs of their ongoing first-line ART, respectively. In addition, 8.5% (n = 38) patients were not yet predicted resistant to AZT and d4T, but harbored already one (n = 22) or two (n = 16) thymidine analogue mutations (TAMs): M41L (n = 5), D67N (n = 6), K70R (n = 32), or K219Q/E/N (n = 11).

The median VL was higher in patients with HIVDR to all ongoing first-line drugs than in those still susceptible to at least one drug; 4.7 log₁₀ copies/ml (IQR: 4.3–5.2) versus 4.2 log₁₀ copies/ml (IQR: 3.7–4.7), respectively (p < .001, Mann-Whitney U test). The proportion of patients with HIVDR to all ongoing first-line drugs was higher in patients with high plasma VL; that is, 25.5% (27/106), 58.3% (127/218), and 77.9% (95/122) when VL was from >3.0 to ≤4.0 log₁₀ and >4.0 to ≤5.0 log₁₀ to >5.0 log₁₀ copies/ml, respectively (p < .01, multinomial logistic regression, adjusted on patient characteristics [study site, gender, WHO clinical stage, CD4 counts, and time on ART]) (Fig. 1A).

FIG. 1.

HIV-1 drug resistance (HIVDR) to first-line drugs (A) and cross-resistance (B) in patients with virological failure and successful genotyping according to plasma HIV viral load. Proportion of mutations from the IAS–2015 list associated with clinical resistance to reverse transcriptase inhibitors (C); mutations associated with resistance from the ANRS algorithm were documented at positions indicated by asterisk: V179I/M (7.8%), L74I (2.0%), V75A/M/T (1.3%), K101R (1.6%), G190Q/V (0.7%), T215A/I/S/V (2.0%), and K103H (0.2%) (n = 446).

Among the 249 patients resistant to AZT and d4T, 75.5% (n = 188) accumulated NRTI mutations and harbored ≥2 TAMs in addition to M184IV. Moreover, 20.9% (52/249) patients accumulated ≥5 TAMs and have a longer median ART duration, that is, 63 months (IQR: 44–76). As a consequence, high rates of cross-resistance to other NRTIs were observed: 37.7% (n = 168) to ABC (abacavir); 11.2% (n = 50) to TDF (tenofovir), and 7.4% (n = 33) to DDI (didanosine). Intermediate HIVDR to ABC and TDF was also predicted in 59.6% (n = 266) and 10.8% (n = 48) patients, respectively.

The proportion of patients with NRTI cross-resistance was also higher in patients with high plasma VL; that is, 35.8% (n = 78/218), 8.3% (n = 18/218), and 4.1% (n = 9/218) when VL was >4.0 to ≤5.0 log₁₀ copies/ml, were resistant to ABC, TDF, and DDI, respectively, versus 64.8% (n = 79/122), 23.4% (n = 29/122), and 18.0% (n = 22/122) with VL >5.0 log₁₀ copies/ml (p < .01, multinomial logistic regression, adjusted on patient characteristics as mentioned above) (Fig. 1B). Cross-resistance to other NNRTIs like RPV (rilpivirine) and ETR (etravirine) was observed in 56.1% (n = 250) and 35.9% (n = 160) patients, respectively; 15.9% (n = 71) had also intermediate resistance to ETR.

NNRTI cross-resistance was not associated with VL and was not always related to accumulation of mutations because the presence of certain mutations was sufficient (ex. K101E/P [EFV, NVP, RPV], E138A/G/K/Q/R/S [RPV], Y181C/I/V [EFV, NVP, RPV, ETR] or H221Y [ETR/RPV]), according to the latest version of the ANRS algorithm. However, in our study, all these mutations were observed in combination with other NNRTI mutations, except Y181C in 3.8% of patients only. The frequency of the different NRTI and NNRTI mutations is shown in Figure 1C.

VL is the main predictor of sexual transmission of HIV-1 and in general, transmission is low among persons with VL below 1,500 copies/ml, but above this value, transmission increases with increasing VL.⁷ In this study, we showed that in sub-Saharan Africa, high VL in patients on ART can also be associated with multidrug resistance and not only to nonadherence. Importantly, most of the failing patients (98.7%) have mutations conferring resistance to at least one of the first-line drugs, but 90% were still asymptomatic and would have continued on failing ART based on clinical monitoring only. Consequently, the proportion of patients who are unaware of their VF status could contribute to the spread of HIVDR strains and reduce efforts of ART scale-up to prevent new HIV infections.

If ART scale-up continues without optimal patient monitoring and with use of antiretroviral drugs with a low genetic barrier in first-line ART, it can be expected that in certain RLCs, a significant proportion of patients on long-term first-line ART will have high VL and harbor multidrug-resistant strains. For example, assuming that the ART-naive population is infected with wild-type HIV-1 variants, our observations point out to a prevalence of drug resistance ranging from 2.1% to 3.8% of all viremic individuals in 2012 for the studied countries.^1,4 The proportion of viremic patients will be considerably lower in the context of ART coverage of 90% and as a consequence, the overall likelihood to become infected will also be lower. However, the prevalence of drug resistance will increase among them and the chance to become infected with drug-resistant HIV strains will be higher, especially with a continued use of clinical and/or immunological patient monitoring in ART programs. Despite the longer and broader ART coverage, the proportion of new infections with HIVDR strains could thus be higher in RLCs than in Europe or US where patients switch to second-line regimens before high VLs are reached.⁹

At present, transmitted HIVDR in RLCs concerns mainly resistance to NNRTIs, but it is likely that transmission of NRTI mutations will increase.^3,10 Furthermore, the accumulation of HIVDR mutations and high VL due to late switch to second-line regimens not only boosts widespread transmission with HIVDR strains but also compromises efficacy of second-line drugs, for example, several studies showed higher probability of early failure of second-line regimens in patients with high VL at switch.^8,11 WHO recommends VL monitoring since 2013, but despite efforts to increase VL capacity, today access to VL testing remains largely insufficient.

With the new WHO recommendations, it is estimated that around 15 million additional individuals will need lifelong ART in the next 5 years in sub-Saharan Africa. In addition to provide rapidly wide access to VL monitoring, more robust first-line regimens, based on new protease or integrase inhibitors, should also be recommended in RLCs. Scaling-up of VL monitoring needs also to be accompanied by training on optimal use of VL results for clinical decisions. Without such efforts, people on failing ART represent a potential source for an epidemic with multidrug-resistant strains that could delay the 90-90-90 UNAIDS objectives and overall worldwide HIV control.

Sequence Data

Sequences are submitted to Genbank under the following accession numbers: KU684667 to KU685112.

Footnotes

Acknowledgments

This work was supported by the Agence National de Recherche sur le SIDA—Inserm ANRS—(Grant number 12169) and by European and Developing Countries Clinical Trials Partnership (EDCTP) (grant number IP.2007.33011.004). C.J.V.A. was supported by a fellowship from the Labex EpiGenMed, by the National Research Agency, Program for Future Investment “ANR-10-LABX-12-01,” and the University of Montpellier, France.

We thank the 2LADY Study Group: Protocol Steering Committee: E. Delaporte, S. Koulla-Shiro, C.T. Ndour, A. Sawadogo, V. Le Moing, J. Reynes, A. Calmy, L. Ciaffi, P.M. Girard, S. Eholie, M.L. Chaix, C. Kouanfack, I. Tita, B. Bazin, P. Garcia, and J.B. Guiard-Schmid. Project Team: V. Le Moing, S. Izard, S. Eymard-Duvernay, L. Ciaffi, M. Peeters, L. Serrano, A. Cournil, I. Diallo, and E. Delaporte. Site Investigators: J.M. Mben, R. Toby, N. Manga, L. Ayangma, B. Taman, F.N. Kabore, E. Kamboule, J. Zoungrana, A. Diouf, M. Diallo, L. Fortes, N.F. Ngom Gueye, and G. Batista. Site Staff: A. Aghokeng, E. Guichet, H. Abessolo, C. Essomba, G. Manirakiza, F. Essomba, T. Mbarga, S. Epanda, A. Bikie, T. Nke, N. Massaha, E. Nke, M. Ngolle, D. Bikobo, L. Abologo, O. Elat, G. Laborde-Balen, A. Diouf, A. Diop, B. Diouf, N. Bara, M.B. Koita Fall, C. Toure-Kane, F.B. Seck, S. Ba, P. Njantou, A. Ndyaye, A. Hema, P. Fao, P. Ouedrago, R. Traore, Y. Sanou, G. Bado, M. Coulibaly, E. Some, J. Some, A. Kambou, A. Tapsoba, D. Sombie, S. Sanou, and B. Traore. Data and Safety Monitoring Board: P. Flandre, C. Michon, J. Drabo, and F. Simon.

Author Disclosure Statement

E.D. had travel grant from Gilead outside the submitted work; L.C. had travel grant from Gilead and Janssen outside the submitted work. For the remaining authors, none were declared.

References

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Guideline on when to start antiretroviral therapy and on pre-exposure prophylaxis for HIV WHO. September, 2015. Available at www.who.int/entity/hiv/pub/guidelines/earlyrelease-arv/en/, accessed January 4, 2016 .

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