ABSTRACT
A prototype assay was used to genotype integrase (IN) from 120 HIV-1- infected IN inhibitor-naive adults from Argentina, Brazil, Cameroon, South Africa, Thailand, and Uganda. Subtype designations based on analysis of pol IN sequences were A (14), B (15), C (12), D (11), F (12), G (7), H (1), CRF01_AE (9), CRF02_AG (34), CRF22_01A1 (4), and CRF37_cpx (1). Ten (8.3%) of 120 samples had mutations associated with reduced susceptibility to the IN inhibitors, raltegravir and elvitegravir. Two samples had E92Q (both subtype B) and eight had E157Q (2A, 1C, 1D, 1F, 3 CRF02_AG). Some samples had other mutations selected by these drugs including T97A, and some had amino acid polymorphisms at positions associated with raltegravir and elvitegravir resistance. Mutations associated with other investigational HIV IN inhibitors were also identified. This suggests that HIV strains may vary in their natural susceptibility to HIV IN inhibitors.
Subject(s)
HIV Infections/virology , HIV Integrase/genetics , HIV-1/classification , HIV-1/genetics , Argentina , Brazil , Cameroon , Cluster Analysis , Drug Resistance, Viral , Genotype , HIV Integrase Inhibitors/pharmacology , Humans , Molecular Sequence Data , Mutation, Missense , Phylogeny , Sequence Analysis, DNA , Sequence Homology , South Africa , Thailand , UgandaABSTRACT
In the Brazilian HIV-1 epidemic subtypes B, C, and F1 are cocirculating in the high risk population groups, and there is a high prevalence of intersubtype recombinant forms. The dynamic nature of the HIV epidemic in Brazil led us to study HIV-1 subtypes present in HIV-infected blood donations collected from 2001 to 2003. Donations from 91 seropositive donors were evaluated. Genetic subtype was obtained for 88 specimens based on sequence analysis of gag p24, pol IN, and env gp41 IDR. HIV-1 subtype B was the predominant strain present in the donor population (73.9%). A significant prevalence of intersubtype recombinants of subtypes B and F1 was found (22.7%). Subtype C (1.1%) and F1 (2.3%) were rare. None of the B/F1 recombinants is CRF28_BF or CRF29_BF. The high level of unique B/F1 recombinant strains in this population demonstrates the dynamic and complex nature of the HIV epidemic in Brazil.
Subject(s)
HIV Infections/virology , HIV-1/classification , HIV-1/genetics , Blood Donors , Brazil/epidemiology , Genotype , HIV Core Protein p24/genetics , HIV Envelope Protein gp41/genetics , HIV-1/isolation & purification , Humans , Molecular Sequence Data , Phylogeny , RNA, Viral/genetics , Recombination, Genetic , Sequence Analysis, DNA , Sequence Homology, Amino Acid , pol Gene Products, Human Immunodeficiency Virus/geneticsABSTRACT
The high level of HIV genetic diversity has important implications for screening, diagnostic testing and patient monitoring. Continued diversification and global redistribution of HIV groups, subtypes and recombinants make it imperative that serological and molecular assays be designed and evaluated to ensure reliable performance on all HIV infections. Recognizing the importance of this issue, we initiated a comprehensive program to monitor global diversification of HIV, search for newly emerging variants, assemble large-volume panels of genetically and geographically diverse strains, and develop strategies to determine the impact of HIV diversity on assays used for detecting and monitoring HIV infection. Efforts to identify and characterize rare and emerging HIV strains have lead to the identification of HIV-1 group O, group N, and dual infections of groups M and O. A panel of plasma specimens was established that includes specimens collected from 12 countries in Africa, Asia, Europe, and South America; the panel comprises infections due to HIV-1 group M subtypes A, B, C, D, F, and G, as well as CRF01, CRF02, and unique recombinant forms, group N, and group O. Serological and molecular characterization of this unique panel has provided vital sequence data to support assay development and an invaluable source of well-defined specimens to evaluate and compare assay performance. The ability to address the challenge posed by ongoing evolution of HIV and the emergence of new variants requires continued surveillance of global HIV strain diversity, a sound scientific foundation for assay development, and suitable panels to evaluate and validate assay performance.
Subject(s)
Genetic Variation , HIV Infections/virology , HIV-1/genetics , HIV-2/genetics , Africa , Asia , Biological Assay , Europe , Evolution, Molecular , HIV Infections/diagnosis , HIV Infections/epidemiology , HIV-1/classification , HIV-1/immunology , HIV-1/isolation & purification , HIV-2/classification , Humans , Molecular Epidemiology , Reagent Kits, Diagnostic/virology , Sensitivity and Specificity , South AmericaABSTRACT
The combination of automated sample preparation and real-time RT-PCR for measurement of HIV-1 viral load has the potential to significantly enhance throughput, reduce operator-associated error, and increase assay sensitivity and dynamic range. In this study, RNA was extracted from the plasma of 91 HIV-1 seropositive Brazilian blood donors using the Abbott m2000sp automated sample preparation system. Viral loads measured using the RealTime HIV-1 (RealTime HIV-1) assay and the Abbott m2000rt instrument were compared to values obtained in the LCx HIV RNA quantitative assay. Subtype was determined for 89 of 91 specimens by sequence/phylogenetic analysis of three genomic regions: gag p24, pol integrase, and env gp41. The panel included 69 subtype B, 1 C, 2 F, and 17 recombinant strains. Eighty-seven specimens were quantified by both assays. Two specimens were quantified only in RealTime HIV-1. Two additional specimens below the detection limit of both assays were also negative on PCR amplification. Viral load results were highly correlated, and good agreement was observed between assays with 90% of values within 0.5 log(10)copies/ml. The RealTime HIV-1 assay and m2000 system offer the advantages of automation while providing reliable quantification of diverse HIV strains.