Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality

PLoS Pathogens

Katherine M. Bruner¹  Sarah B. Laskey¹  Robert F. Siliciano¹  Christopher W. Pohlmeyer¹ 

[1] Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America

关键词: Sequence alignment;    HIV-1;    Sequence analysis;    Viral genome;    Phylogenetic analysis;    Polymerase chain reaction;    DNA sequence analysis;    Viral genomics;   

DOI  :  10.1371/journal.ppat.1005689

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings.

【 授权许可】

CC BY