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Identification and characterization of a new BF intersubtype circulating recombinant form (CRF44_BF) in Chile
E. Delgado1, M. Rios2, J. Fernandez2, L. Perez-Alvarez1, M. Thomson1
1Instituto de Salud Carlos III, Majadahonda, Madrid, Spain, 2Instituto de Salud Pública de Chile, Santiago, Chile
Background: HIV-1 BF intersubtype recombinant forms are common in South America, particularly in Argentina, Uruguay, and Brazil. To date, 8 CRFs comprising subtypes B and F have been reported: CRF12_BF, CRF17_BF, CRF28_BF, CRF29_BF, CRF38_BF, CRF39_BF, CRF40_BF and CRF42_BF.In a previous survey based on protease-reverse transcriptase sequences from 136 Chilean HIV-1-infected persons we detected a phylogenetic cluster of 10 individuals harbouring BF recombinant viruses sharing three breakpoints, suggesting the existence of a new CRF. Previously, we had described the near full-length genome sequence of one virus of this cluster (CH12).
Methods: Near full-length genome of a second virus of this cluster (CH80), with no epidemiological links to CH12, was amplified and sequenced in four overlapping fragments.using DNA from patient's PBMCs. Recombinant structures were analyzed by bootscanning using Simplot. Phylogenetic analyses were performed via maximum likelihood.
Results: CH12 and CH80 shared identical mosaic structures consisting of a predominantly subtype F1 genome with 3 fragments of subtype B in HXB2 positions 2470 to 2725, 2935 to 3696, and 6342 to 6447. Two breakpoints (at 2470 and 3697 positions) are coincident with CRF12_BF, CRF17_BF and CRF38_BF.In phylogenetic trees of full-length genomes, CH12 and CH80 clustered together, and both grouped in a cluster with CH12_BF, CH17_BF and CRF38_BF, with the Chilean viruses forming a separate subcluster.All 10 infections with the newly identified CRF (designated CRF44_BF) were from North and Central Chile. Six patients were children infected from their mothers; two were the mothers of two of the children, and two men had acquired infection through homosexual intercourse.
Conclusions: We have identified a new HIV-1 CRF in Chile, designated CRF44_BF. It is the eighth BF intersubtype CRF identified in South America. Coincident breakpoints and phylogenetic clustering support a common origin of different BF CRFs identified in Argentina, Uruguay, and Chile.
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