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doi: 10.1097/QAD.0000000000000216

The arrival of untreatable multidrug-resistant HIV-1 in sub-Saharan Africa

Magambo, Briana; Nazziwa, Jamiraha; Bbosa, Nicholasb; Gupta, Ravindra K.c; Kaleebu, Pontianoa; Parry, Chris M.a,c

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aMRC/UVRI Research Unit on AIDS

bUganda Virus Research Institute, Entebbe

cDepartment of Infection, UCL, London, UK.

Correspondence to Chris M. Parry, PhD, MRC/UVRI Uganda Research Unit on AIDS, PO Box 49, Entebbe, Uganda. Tel: +256 417 704 000; e-mail:

Received 9 January, 2014

Revised 20 January, 2014

Accepted 20 January, 2014

Antiretroviral therapy (ART) rollout has resulted in over eight million individuals being treated by the end of 2011 [1]. Treatment failure guided largely by clinical criteria, and sometimes CD4+ cell counts, can result in prolonged viral failure in certain individuals with higher prevalence of resistance, potentially compromising second-line protease inhibitor based regimens [2–7]. Third-line combinations including second-generation protease inhibitors, integrase inhibitors and CCR5 antagonists are unlikely to be available in the developing world for at least 5 years. Although cases of second-line treatment failure with extensive resistance are expected and have been reported [8,9], resistance to all available second-line drugs from the three drug classes has not been formally reported until now.

The Uganda Virus Research Institute (UVRI) hosts a WHO accredited Regional HIV Drug Resistance laboratory that receives samples from Uganda and other countries in sub-Saharan Africa. We received a patient sample for HIV drug resistance testing from Arua, northern Uganda, with second-line ART virological failure. The patient's first HIV positive serology test was in August 2004 (age 32 years) when she was classified as in WHO stage 3. Follow-up visits in the next few months indicated greater than 10% weight loss, oral candidiasis and bacterial pneumonia; first-line ART of lamivudine, stavudine and nevirapine was initiated in October 2004 after a CD4+ cell count of 26 cells/μl.

The patient responded well to first-line ART regaining weight with an improving CD4+ cell count and no clinical complications until April 2009 when she was diagnosed with pulmonary tuberculosis. This was successfully treated from April 2009 to March 2010 and coincided with first-line failure; the CD4+ cell count was 49 cells/μl with a viral load of 332 953 copies/ml. In June 2009, the patient was switched to second-line ART of abacavir, didanosine and ritonavir-boosted lopinavir, at that time the only available second line, this was soon after the treatment for tuberculosis was started. CD4+ cell count again improved reaching a peak of 364 cells/μl in July 2010. There were no other clinical complications reported. The patient's most recent viral load was 168 157 copies/ml in January 2012 and in February 2013 her CD4+ cell count was 167 cells/μl. An HIV drug resistance test was requested in July 2013 and carried out at the UVRI laboratory. The patient's virus was found to have M46I, I54V and V82A major as well as L10F, K43KT, A71T and N83D minor protease inhibitor resistance mutations. Nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations detected were M41L, D67G, T69D, V75I, L210W and T215Y, which includes four thymidine analogue mutations that affect all drugs in this class. Despite not having received any nonnucleoside reverse transcriptase inhibitor (NNRTI) drugs in 4 years, since 2009, the Y181C mutation was still present further confirming the stability of NNRTI mutations.

The Stanford HIV drug resistance database indicated that the virus was subtype A, one of the circulating strains in East Africa. The HIV drug resistance interpretation from the Stanford HIV drug resistance database (Table 1) indicates that the patient virus is only fully susceptible to the protease inhibitor darunavir [10]. There is intermediate resistance to tipranavir and high-level resistance to all other protease inhibitors. Neither of these second-generation protease inhibitors (darunavir and tipranavir) are currently available in sub-Saharan Africa as part of public ART programmes. The results also indicate that this virus isolate is not susceptible to any reverse transcriptase inhibitors. Although the lamivudine resistance mutation M184V/I is absent from the majority viral population, this is likely due to the lack of lamivudine in the failing second-line regimen, with the mutation likely preserved at very low levels in the proviral reservoir in lymphocytes. However, no samples or resistance data were available from earlier time points to explore this further, and, unfortunately, the patient subsequently died. To our knowledge, this is the first reported case of multiclass multidrug resistant HIV from sub-Saharan Africa with no fully active drug available in the public health setting.

Table 1
Table 1
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The recently updated WHO guidelines recommend viral load monitoring to identify virological ART failure as early as possible and to maximize activity of second-line regimens [11]. In sub-Saharan Africa, viral load monitoring is not routinely performed, the exception being South Africa. The contribution of this monitoring strategy to the accumulated resistance observed in this patient cannot be ascertained. However, the population prevalence of such resistance is likely to increase under current programmatic conditions. In light of recent data reporting a rise of drug resistance in untreated HIV-infected individuals in sub-Saharan Africa since ART rollout [12], perhaps the greatest concern is transmission of multidrug resistance. Surveillance activities should therefore be strengthened whilst implementing strategies for third-line therapy in sub-Saharan Africa.

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We thank Dr Robert Downing for his assistance in this work and for reviewing the manuscript. The work was partly funded by the UK Medical Research Council (MRC) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement and was supported in part by Training Health Researchers into Vocational Excellence (THRiVE) in East Africa (grant number 087540), funded by Wellcome Trust. R.K.G. is funded by a Wellcome Trust Fellowship (grant number WT093722MA).

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Conflicts of interest

There are no conflicts of interest.

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