title: HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya.
abstract: BACKGROUND
  Antiretroviral resistance leads to treatment failure and resistance transmission. Resistance data in western Kenya are limited. Collection of non-plasma analytes may provide additional resistance information.
  
  
  METHODS
  We assessed HIV diversity using the REGA tool, transmitted resistance by the WHO mutation list and acquired resistance upon first-line failure by the IAS-USA mutation list, at the Academic Model Providing Access to Healthcare (AMPATH), a major treatment programme in western Kenya. Plasma and four non-plasma analytes, dried blood-spots (DBS), dried plasma-spots (DPS), ViveST(TM)-plasma (STP) and ViveST-blood (STB), were compared to identify diversity and evaluate sequence concordance.
  
  
  RESULTS
  Among 122 patients, 62 were treatment-naïve and 60 treatment-experienced; 61% were female, median age 35 years, median CD4 182 cells/µL, median viral-load 4.6 log10 copies/mL. One hundred and ninety-six sequences were available for 107/122 (88%) patients, 58/62 (94%) treatment-naïve and 49/60 (82%) treated; 100/122 (82%) plasma, 37/78 (47%) attempted DBS, 16/45 (36%) attempted DPS, 14/44 (32%) attempted STP from fresh plasma and 23/34 (68%) from frozen plasma, and 5/42 (12%) attempted STB. Plasma and DBS genotyping success increased at higher VL and shorter shipment-to-genotyping time. Main subtypes were A (62%), D (15%) and C (6%). Transmitted resistance was found in 1.8% of plasma sequences, and 7% combining analytes. Plasma resistance mutations were identified in 91% of treated patients, 76% NRTI, 91% NNRTI; 76% dual-class; 60% with intermediate-high predicted resistance to future treatment options; with novel mutation co-occurrence patterns. Nearly 88% of plasma mutations were identified in DBS, 89% in DPS and 94% in STP. Of 23 discordant mutations, 92% in plasma and 60% in non-plasma analytes were mixtures. Mean whole-sequence discordance from frozen plasma reference was 1.1% for plasma-DBS, 1.2% plasma-DPS, 2.0% plasma-STP and 2.3% plasma-STB. Of 23 plasma-STP discordances, one mutation was identified in plasma and 22 in STP (p<0.05). Discordance was inversely significantly related to VL for DBS.
  
  
  CONCLUSIONS
  In a large treatment programme in western Kenya, we report high HIV-1 subtype diversity; low plasma transmitted resistance, increasing when multiple analytes were combined; and high-acquired resistance with unique mutation patterns. Resistance surveillance may be augmented by using non-plasma analytes for lower-cost genotyping in resource-limited settings.
authors.affiliation: Division of Infectious Diseases, Alpert Medical School, Brown University, Providence, RI, USA; rkantor@brown.edu.
authors.forename: Rami
authors.initials: R
authors.lastname: Kantor
authors.affiliation: Center for Statistical Sciences, Brown University, Providence, RI, USA.
authors.forename: Allison
authors.initials: A
authors.lastname: DeLong
authors.affiliation: Division of Infectious Diseases, Alpert Medical School, Brown University, Providence, RI, USA; Division of Infectious Diseases, Stanford University, Stanford, CA, USA.
authors.forename: Maya
authors.initials: M
authors.lastname: Balamane
authors.affiliation: Division of Infectious Diseases, Alpert Medical School, Brown University, Providence, RI, USA.
authors.forename: Leeann
authors.initials: L
authors.lastname: Schreier
authors.affiliation: Research Think Tank, Inc., Buford, GA, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Lloyd
authors.affiliation: Department of Medicine, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; Academic Model Providing Access To Health Care (AMPATH), Eldoret, Kenya.
authors.forename: Wilfred
authors.initials: W
authors.lastname: Injera
authors.affiliation: Department of Medicine, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; Academic Model Providing Access To Health Care (AMPATH), Eldoret, Kenya.
authors.forename: Lydia
authors.initials: L
authors.lastname: Kamle
authors.affiliation: Department of Medicine, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; Academic Model Providing Access To Health Care (AMPATH), Eldoret, Kenya.
authors.forename: Fidelis
authors.initials: F
authors.lastname: Mambo
authors.affiliation: Department of Medicine, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; Academic Model Providing Access To Health Care (AMPATH), Eldoret, Kenya.
authors.forename: Sarah
authors.initials: S
authors.lastname: Muyonga
authors.affiliation: Division of Infectious Diseases, Stanford University, Stanford, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Katzenstein
authors.affiliation: Center for Statistical Sciences, Brown University, Providence, RI, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Hogan
authors.affiliation: Department of Medicine, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; Department of Hematology and Blood Transfusion, College of Health Sciences, Moi University, Eldoret, Kenya.
authors.forename: Nathan
authors.initials: N
authors.lastname: Buziba
authors.affiliation: Department of Medicine, School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya; Academic Model Providing Access To Health Care (AMPATH), Eldoret, Kenya.
authors.forename: Lameck
authors.initials: L
authors.lastname: Diero
mesh_terms: D000328:Adult; D000368:Aged; D044966:Anti-Retroviral Agents / Q000494:pharmacology*; D001769:Blood / Q000821:virology*; D024882:Drug Resistance, Viral; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D007630:Kenya; D008297:Male; D008826:Microbial Sensitivity Tests / Q000379:methods; D008875:Middle Aged; D013048:Specimen Handling / Q000379:methods; D055815:Young Adult
chemical_list: D044966:Anti-Retroviral Agents
keywords: AMPATH; HIV; Kenya; analyte; diversity; drug resistance; subtype