title: Genetic diversity and phenotypic characterization of HIV-1 circulating recombinant forms (CRFs) among drug-naive and -exposed patients in Burkina Faso
creator: Sathiandee, Kanokporn
subject: 570
subject: 570 Life sciences
description: The genotypic and phenotypic characteristics of HIV-1 CRF02_AG strains from infected patients in Burkina Faso were determined in order to understand about resistance development and susceptibility to antiretroviral drugs of HIV-1 non-subtype B. Drug resistance studies among Nevirapine (NVP) naïve and exposed women from Nouna, and HAART-exposed HIV patients attending the University Hospital in Ouagadougou, Burkina Faso were performed. The diversity and evolution of HIV-1 reverse transcriptase (RT) quasispecies in paired plasma, breast milk whey and/or breast milk cells from seventeen HIV-infected NVP-naïve and exposed women were determined by direct sequencing and clonal analysis. NVP resistance mutations were detected in 8% of infected mothers by direct sequencing. By using clonal analysis, the detection rate increased to 46% which indicates the high sensitivity of clonal analysis in detecting low proportion of drug resistance variants. To analyze compartmentalization of virus population in different anatomic compartments, phylogenetic analysis comparing virus populations of plasma, breast milk and/or breast milk cells from individual patients at both single and multiple time points was performed and the circulation of both compartmentalized (50%) and non-compartmentalized (45.5%) variants were found. These results suggest that in some individuals, viruses in breast milk whey may be evolving separately from plasma viruses. In most cases, breast milk whey variants were completely different from those of breast milk cells suggesting that free HIV virions in breast milk do not originate from infected breast milk cells. Different resistance mutation patterns were observed between viruses in plasma, breast milk and breast milk cells which suggest that transmission of HIV-1 from mother-to-child via breastfeeding may involve variants harbouring resistance mutations which cannot be predicted from variants present in plasma.  To determine possible influences of genetic background on drug susceptibility of virus, a new CRF02_AG proviral plasmid (pBD6TB9RI) and the derivative CRF02_AG/subtype B chimera containing PR-RT fragment of pNL4-3 were generated. By testing drug susceptibility against 5 protease inhibitors (PIs), 6 nucleoside reverse transcriptase inhibitors (NRTIs), and 3 non-nucleoside reverse transcriptase inhibitors (NNRTIs), the CRF02_AG virus showed similar phenotypic results like the CRF02_AG/subtype B chimera. To further evaluate the CRF02_AG plasmid backbone, PR-RT amplified fragments derived from HAART-experienced HIV patients were cloned into the pBD6TB9RI plasmid and transfection derived viruses were tested against the panel of antiretroviral drugs. The phenotypic results for both NRTIs and NNRTIs strongly correlated with the predicted genotypic resistance patterns. However, there were minor discordances with some PIs. This suggests that the novel recombinant viral assay should be useful in assessing the drug susceptibility of CRF02_AG and other non-B strains which are widely distributed in West and Central Africa. 
date: 2009
type: Dissertation
type: info:eu-repo/semantics/doctoralThesis
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/10109/1/Sathiandee_27.11.09.pdf
identifier: DOI:10.11588/heidok.00010109
identifier: urn:nbn:de:bsz:16-opus-101091
identifier:   Sathiandee, Kanokporn  (2009) Genetic diversity and phenotypic characterization of HIV-1 circulating recombinant forms (CRFs) among drug-naive and -exposed patients in Burkina Faso.  [Dissertation]     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/10109/
rights: info:eu-repo/semantics/openAccess
rights: http://archiv.ub.uni-heidelberg.de/volltextserver/help/license_urhg.html
language: eng