EPIDEMIOLOGY Isolation and Biological Characterization of Non-B HIV Type 1 from Kenya Joseph K. Muriuki, 1,2 Joseph N. Ngeranwa, 2 Joseph Mwangi, 1 George Orinda, 2 Raphael Lwembe, 1 and Samuel Khamadi 1 Abstract The isolation and characterization of primary strains of human immunodeficiency virus (HIV) is a vital tool for assessing properties of viruses replicating in HIV-infected subjects. HIV-1 isolation was carried out from 30 HIV-1-infected patients from a Comprehensive Care Clinic (CCC) after informed consent. Virus was successfully isolated from 9 out of the 30 samples investigated. Seven of the isolates were from drug-naive patients while two were from patients on antiretroviral drugs. The isolates were biologically phenotyped through measurement of the syncytium-inducing capacity in MT2 cells. Six of the isolates exhibited syncytia induction (SI) associated with CXCR4 coreceptor usage while three of the isolates were non-syncytia-inducing (NSI) isolates associated with CCR5 coreceptor usage. In addition, the replication capacity of the isolates was further determined in established cell line CD4 + C8166. Indirect immunofluorescence assay was used to check the antigen expression on the cells as a supplementary test. HIV-1 isolation success was 70% (7/10) and 20% (2/20) in naive and drug-experienced patients, respectively. The majority of the viral isolates obtained (6/9) were of the SI phenotype, though SI virus strains are rare among non-B subtypes. A significant correlation between virus isolation success and viral load was established. Coreceptor use data for heavily treatment-experienced patients with limited treatment options are scanty and this is the group with perhaps the most urgent need of novel antiretroviral agents. Introduction H IV/AIDS continues to be a major health and devel- opment problem globally. In Kenya the national HIV prevalence is currently at 7.1% and it is estimated that over 1 million people have died and over 1.5 million are living with HIV. 1 In Kenya the major circulating HIV-1 is subtype A. 2 However, ongoing studies have shown the circulation of other subtypes, namely C, D, and the circulating recombi- nant forms (CRFs). This virus diversity has been attributed partly to cross-boarder interactions such as in northern Kenya. 3 The broad viral diversity makes it necessary to bi- ologically characterize the local isolates and this has not been done. For this to take place, primary isolates of HIV-1 have to be generated. HIV coreceptor usage and switching have been analyzed most extensively for clade B isolates, which predominate in North America and western Europe. 4,5 The biological and molecular properties of non-clade B viruses, which now cause the majority of new HIV-1 infections worldwide, re- main largely unknown. The coreceptor specificity of non- clade B HIV-1 isolates is only beginning to be character- ized. 6,7 Available data suggest that clade C isolates, which predominate in sub-Saharan Africa and Asia, are by and large R5, even when derived from patients with advanced AIDS. 8,9 The MT2 cell line expresses CD4 and the CXCR4 cor- eceptor, but no CCR5; the X4 but not R5 strains infect these cells. The cell line can be useful for differentiating the CXCR4-using or syncytia-inducing (SI) strains from the CCR5-using or non-syncytia-inducing (NSI) strains. The method may be more useful for obtaining prior knowledge of preferential coreceptor usage in viruses from patients before starting therapy with chemokine inhibitors, especially with CCR5 antagonists, in order to exclude the presence of X4 viruses. These variants could be present at cellular res- ervoirs and therefore are being missed by testing plasma, a limitation that probably also applies to other methods based on viral isolates derived from peripheral blood mononuclear cells (PBMCs). 10 Virologic features of HIV-1 isolates and plasma viral bur- den have been reported to play an important role in disease 1 Centre of Virus Research, Kenya Medical Research Institute, Nairobi, Kenya. 2 Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya. AIDS RESEARCH AND HUMAN RETROVIRUSES Volume 28, Number 7, 2012 ª Mary Ann Liebert, Inc. DOI: 10.1089/aid.2010.0095 660