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Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis

Barbara A Rath128*, Max von Kleist3, Maria E Castillo49, Lenka Kolevic4, Patricia Caballero5, Giselle Soto-Castellares6, Angela M Amedee7, James E Robinson2, David K Katzenstein8, Russell B Van Dyke2 and Richard A Oberhelman2

Author Affiliations

1 Department of Pediatrics, Division of Pneumonology-Immunology, Charité University Medical Center, Berlin, Germany

2 Department of Pediatrics, Division of Infectious Diseases, Tulane University Health Sciences Center, New Orleans, Louisiana, USA

3 Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany

4 Infectious Diseases Service, Instituto Nacional de Salud del Niño Lima, Peru

5 Executive Directorate of Research, National Institute of Health, Lima, Peru

6 Asociación Benéfica PRISMA, Lima, Peru

7 Department of Microbiology, Immunology & Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA

8 Center for AIDS Research, Stanford University, Stanford, Palo Alto, USA

9 Department of Pediatrics, Universidad Peruana Cayetano Heredia, Lima, Peru

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BMC Infectious Diseases 2013, 13:1  doi:10.1186/1471-2334-13-1

Published: 2 January 2013



The impact of extended use of ART in developing countries has been enormous. A thorough understanding of all factors contributing to the success of antiretroviral therapy is required. The current study aims to investigate the value of cross-sectional drug resistance monitoring using DNA and RNA oligonucleotide ligation assays (OLA) in treatment cohorts in low-resource settings. The study was conducted in the first cohort of children gaining access to structured ART in Peru.


Between 2002–5, 46 eligible children started the standard regimen of AZT, 3TC and NFV Patients had a median age of 5.6 years (range: 0.7-14y), a median viral load of 1.7·105 RNA/ml (range: 2.1·103 – 1.2·106), and a median CD4-count of 232 cells/μL (range: 1–1591). Of these, 20 patients were classified as CDC clinical category C and 31/46 as CDC immune category 3. At the time of cross-sectional analysis in 2005, adherence questionnaires were administered. DNA OLAs and RNA OLAs were performed from frozen PBMC and plasma, RNA genotyping from dried blood spots.


During the first year of ART, 44% of children experienced virologic failure, with an additional 9% failing by the end of the second year. Virologic failure was significantly associated with the number of resistance mutations detected by DNA-OLA (p < 0.001) during cross-sectional analysis, but also with low immunologic CDC-scores at baseline (p < 0.001). Children who had been exposed to unsupervised short-term antiretrovirals before starting structured ART showed significantly higher numbers of resistance mutations by DNA-OLA (p = 0.01). Detection of M184V (3TC resistance) by RNA-OLA and DNA-OLA demonstrated a sensitivity of 0.93 and 0.86 and specificity of 0.67 and 0.7, respectively, for the identification of virologic failure. The RT mutations N88D and L90M (NFV resistance) detected by DNA-OLA correlated with virologic failure, whereas mutations at RT position 215 (AZT resistance) were not associated with virologic failure.


Advanced immunosuppression at baseline and previous exposures to unsupervised brief cycles of ART significantly impaired treatment outcomes at a time when structured ART was finally introduced in his cohort. Brief maternal exposures to with AZT +/− NVP for the prevention of mother-to-child transmission did not affect treatment outcomes in this group of children. DNA-OLA from frozen PBMC provided a highly specific tool to detect archived drug resistance. RNA consensus genotyping from dried blood spots and RNA-OLA from plasma consistently detected drug resistance mutations, but merely in association with virologic failure.