title: Partial HIV C2V3 envelope sequence analysis reveals association of coreceptor tropism, envelope glycosylation and viral genotypic variability among Kenyan patients on HAART.
abstract: HIV-1 is highly variable genetically and at protein level, a property it uses to subvert antiviral immunity and treatment. The aim of this study was to assess if HIV subtype differences were associated with variations in glycosylation patterns and co-receptor tropism among HAART patients experiencing different virologic treatment outcomes.
  
  
  
  A total of 118 HIV env C2V3 sequence isolates generated previously from 59 Kenyan patients receiving highly active antiretroviral therapy (HAART) were examined for tropism and glycosylation patterns. For analysis of Potential N-linked glycosylation sites (PNGs), amino acid sequences generated by the NCBI's Translate tool were applied to the HIVAlign and the N-glycosite tool within the Los Alamos Database. Viral tropism was assessed using Geno2Pheno (G2P), WebPSSM and Phenoseq platforms as well as using Raymond's and Esbjörnsson's rules. Chi square test was used to determine independent variables association and ANOVA applied on scale variables.
  
  
  
  At respective False Positive Rate (FPR) cut-offs of 5% (p = 0.045), 10% (p = 0.016) and 20% (p = 0.005) for CXCR4 usage within the Geno2Pheno platform, HIV-1 subtype and viral tropism were significantly associated in a chi square test. Raymond's rule (p = 0.024) and WebPSSM (p = 0.05), but not Phenoseq or Esbjörnsson showed significant associations between subtype and tropism. Relative to other platforms used, Raymond's and Esbjörnsson's rules showed higher proportions of X4 variants, while WebPSSM resulted in lower proportions of X4 variants across subtypes. The mean glycosylation density differed significantly between subtypes at positions, N277 (p = 0.034), N296 (p = 0.036), N302 (p = 0.034) and N366 (p = 0.004), with HIV-1D most heavily glycosylated of the subtypes. R5 isolates had fewer PNGs than X4 isolates, but these differences were not significant except at position N262 (p = 0.040). Cell-associated isolates from virologic treatment success subjects were more glycosylated than cell-free isolates from virologic treatment failures both for the NXT (p = 0.016), and for all the patterns (p = 0.011).
  
  
  
  These data reveal significant associations of HIV-1 subtype diversity, viral co-receptor tropism, viral suppression and envelope glycosylation. These associations have important implications for designing therapy and vaccines against HIV. Heavy glycosylation and preference for CXCR4 usage of HIV-1D may explain rapid disease progression in patients infected with these strains.
authors.affiliation: Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.|Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000 -00200, Nairobi, Kenya.
authors.forename: Rose C
authors.initials: RC
authors.lastname: Kitawi
authors.affiliation: Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.|South Eastern Kenya University, P.O Box 170-90200, Kitui, Kenya.
authors.forename: Carol W
authors.initials: CW
authors.lastname: Hunja
authors.affiliation: Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.|African Center for Clinical Trials, P.O. Box 2288-00202, Nairobi, Kenya.|Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya.
authors.forename: Rashid
authors.initials: R
authors.lastname: Aman
authors.affiliation: Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.|Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.|Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya.
authors.forename: Bernhards R
authors.initials: BR
authors.lastname: Ogutu
authors.affiliation: Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000 -00200, Nairobi, Kenya.
authors.forename: Anne W T
authors.initials: AW
authors.lastname: Muigai
authors.affiliation: Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
authors.forename: Gilbert O
authors.initials: GO
authors.lastname: Kokwaro
authors.affiliation: Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya. ochiengwashingtone@gmail.com.|Institute of Healthcare Management, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya. ochiengwashingtone@gmail.com.|Kenya Medical Research Institute, P.O. Box 54840-00200, Nairobi, Kenya. ochiengwashingtone@gmail.com.|Immunology and Infectious Diseases Dept, Harvard School of Public Health, Boston, MA, USA. ochiengwashingtone@gmail.com.
authors.forename: Washingtone
authors.identifier: 0000-0002-9035-4405
authors.initials: W
authors.lastname: Ochieng
mesh_terms: D023241:Antiretroviral Therapy, Highly Active; D019295:Computational Biology; D014644:Genetic Variation; D006031:Glycosylation; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D006801:Humans; D007630:Kenya; D017421:Sequence Analysis; D056189:Viral Tropism; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics* / Q000378:metabolism*
chemical_list: D054299:env Gene Products, Human Immunodeficiency Virus
keywords: Africa; HIV-1; Kenya; Potential N-linked glycosylation; Subtype; Treatment; Tropism