title: An affordable HIV-1 drug resistance monitoring method for resource limited settings.
abstract: HIV-1 drug resistance has the potential to seriously compromise the effectiveness and impact of antiretroviral therapy (ART). As ART programs in sub-Saharan Africa continue to expand, individuals on ART should be closely monitored for the emergence of drug resistance. Surveillance of transmitted drug resistance to track transmission of viral strains already resistant to ART is also critical. Unfortunately, drug resistance testing is still not readily accessible in resource limited settings, because genotyping is expensive and requires sophisticated laboratory and data management infrastructure. An open access genotypic drug resistance monitoring method to manage individuals and assess transmitted drug resistance is described. The method uses free open source software for the interpretation of drug resistance patterns and the generation of individual patient reports. The genotyping protocol has an amplification rate of greater than 95% for plasma samples with a viral load >1,000 HIV-1 RNA copies/ml. The sensitivity decreases significantly for viral loads <1,000 HIV-1 RNA copies/ml. The method described here was validated against a method of HIV-1 drug resistance testing approved by the United States Food and Drug Administration (FDA), the Viroseq genotyping method. Limitations of the method described here include the fact that it is not automated and that it also failed to amplify the circulating recombinant form CRF02_AG from a validation panel of samples, although it amplified subtypes A and B from the same panel.
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Justen
authors.initials: J
authors.lastname: Manasa
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Siva
authors.initials: S
authors.lastname: Danaviah
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Sureshnee
authors.initials: S
authors.lastname: Pillay
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Prevashinee
authors.initials: P
authors.lastname: Padayachee
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Hloniphile
authors.initials: H
authors.lastname: Mthiyane
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Charity
authors.initials: C
authors.lastname: Mkhize
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Richard John
authors.initials: RJ
authors.lastname: Lessells
authors.affiliation: Unit D11, Jembi Health Systems.
authors.forename: Christopher
authors.initials: C
authors.lastname: Seebregts
authors.affiliation: Academic Medical Center, Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), University of Amsterdam.
authors.forename: Tobias F Rinke
authors.initials: TF
authors.lastname: de Wit
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Johannes
authors.initials: J
authors.lastname: Viljoen
authors.affiliation: Division of Infectious Diseases and Geographic Medicine, Centre for AIDS Research, Stanford Medical School.
authors.forename: David
authors.initials: D
authors.lastname: Katzenstein
authors.affiliation: Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; tdeoliveira@africacentre.ac.za.
authors.forename: Tulio
authors.initials: T
authors.lastname: De Oliveira
mesh_terms: D044966:Anti-Retroviral Agents / Q000494:pharmacology*; D019295:Computational Biology; D024882:Drug Resistance, Viral / Q000235:genetics; D060005:Genotyping Techniques / Q000379:methods; D015658:HIV Infections / Q000097:blood / Q000188:drug therapy* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D012367:RNA, Viral / Q000032:analysis* / Q000097:blood / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D019562:Viral Load
chemical_list: D044966:Anti-Retroviral Agents; D012367:RNA, Viral
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