Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries

Abstract

BackgroundThymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country.MethodsWe examined the drug resistance genotypes by Sanger sequencing of 262 HIV-infected patients failing a first line combined antiretroviral treatment containing either AZT or d4T, which represents approximately 5% of the patients at the Joint Clinical Research Center receiving a AZT or d4T containing treatment. Next generation sequencing (DEEPGEN™HIV) and multiplex oligonucleotide ligation assays (AfriPOLA) were then performed on a subset of patient samples to detect low frequency drug resistant mutations. CD4 cell counts, viral RNA loads, and treatment changes were analyzed in a cohort of treatment success and failures.ResultsOver 80% of patients failing first line AZT/d4T-containing cART had predicted drug resistance to 3TC (Lamivudine) and non-nucleoside RT inhibitors (NNRTIs) in the treatment regimen but only 45% had resistance AZT/d4T associated resistance mutations (TAMs). TAMs were however detected at low frequency within the patients HIV quasispecies (1–20%) in 21 of 34 individuals who were failing first-line AZT-containing cART and lacked TAMs by Sanger. Due to lack of TAMs by Sanger, AZT was typically maintained in second-line therapies and these patients had a low frequency of subsequent virologic success.ConclusionsOur findings suggest that continued use of AZT and d4T in first-line treatment in low-to-middle income countries may lead to misdiagnosis of HIV-1 drug resistance and possibly enhance a succession of second- and third-line treatment failures.Electronic supplementary materialThe online version of this article (doi: 10.1186/s40249-017-0377-0) contains supplementary material, which is available to authorized users.

Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay

“…Similar to previous studies [ 19 , 41 , 49 , 61 ], DEEPGEN™ detected all the drug resistance mutations, in all 109 patients, originally identified in each laboratory using Sanger sequencing. More importantly, a total of 280 additional drug resistance mutations were identified in both cohorts of HIV-infected individuals, i.e., mutations below the limit of detection of Sanger sequencing (~ 20%) [ 14 – 18 ] and only detectable using deep sequencing, therefore modifying the Sanger-based HIVdb scores and overall resistance interpretation.…”

“…A few minority INSTI-resistance mutations were observed in the 109 HIV-infected individuals, reflecting the limited number of patients being treated with INSTIs at the time of the study (23/109). Most of these mutations have also been detected as minority variants in cohorts of patients failing first- or second-line cART [ 10 , 40 , 41 , 49 , 55 , 61 – 64 ] or in antiretroviral-naïve patients [ 10 , 65 – 69 ], including a study from the U.K. [ 3 ]. As expected, drug resistance profiles based on Sanger sequencing correlated significantly with cART history; however, the correlation was stronger when minority mutations were included in the analysis, suggesting that the presence of drug resistant minority variants as part of the HIV-1 quasispecies is a direct consequence of the antiretroviral drug pressure.…”

“…As described above, a number of studies -including some from the U.K.—have shown that deep sequencing assays are excellent tools to increase the detection of drug resistance mutations [ 19 , 34 , 40 , 41 , 62 , 63 , 65 , 67 ], monitor transmission of HIV-1 drug resistance [ 3 , 19 , 33 , 41 , 49 , 61 , 63 , 65 , 68 , 69 , 77 – 82 ], and potentially determine the relevance of detecting minority drug resistance mutations in the clinical setting [ 10 , 11 , 31 , 40 , 55 , 83 , 84 ]. Are these minority drug resistant HIV-1 variants going to be selected as majority members of the quasispecies, eventually contributing to elevated plasma viremia and leading to virologic failure?…”

Risk factors for Blastocystis infection in HIV/AIDS patients with highly active antiretroviral therapy in Southwest China

“…Despite the expansion of antiretroviral treatment programme several years ago, 940 000 people died from AIDS related illnesses and 1.8 million people became newly infected with HIV/AIDS, it remains a global public health problem [1–4]. Currently, dramatic expansion of the pandemic has brought about a significant change in the prevalent of pathogens all over the world, especially in developing countries [5–7].…”

Synthesis of fluorescent drug molecules for competitive binding assay based on molecularly imprinted polymers

“…5 Zidovudine has been approved for the treatment of HIV-1, and even helping with prevention of maternal-fetal HIV-1 transmission. 6 Lamivudine is a potent and effective anti-retroviral drug, which is prescribed in the human immune virus (HIV) therapy. It is a water-soluble nucleoside analog and plays a vital role to inhibit reverse transcriptase.…”