Designing a genome-based HIV incidence assay with high sensitivity and specificity
- 23 October 2011
- journal article
- research article
- Published by Ovid Technologies (Wolters Kluwer Health) in AIDS
- Vol. 25 (16), F13-F19
- https://doi.org/10.1097/qad.0b013e328349f089
Abstract
Objective: Considerable inaccuracy in estimates of HIV incidence has been a serious obstacle to the development of efficient HIV/AIDS prevention and interventions. Accurately distinguishing recent or incident infections from chronic infections enables one to monitor epidemics and evaluate the impact of HIV prevention/intervention trials. However, serological testing has not been able to realize these promises due to a number of critical limitations. Our study is to design a novel scheme of identifying incident infections in a highly accurate manner, based on the characteristics of HIV gene diversification within an infected individual. Methods: We perform a comprehensive meta-analysis on 5596 full envelope HIV genes generated by single genome amplification-direct sequencing from 182 incident and 43 chronic cases. We devise a binary classification test based on the tail characteristics of the Hamming distance distribution of sequences. Results: We identify a clear signature of incident infections, the presence of closely related strains in the sampled HIV envelope gene sequences in each HIV-infected patient, in both single-variant and multivariant transmissions. The sequence similarity used as a biomarker is found to have high specificity and sensitivity, greater than 95%, and is robust to viral and host-specific factors such as the clade of the viral strain, viral load, and the length and location of sequences in the HIV envelope gene. Conclusion: Because of rapid and continuing improvements in sequencing technology and cost, sequence-based incidence assays hold great promise as a means of quantifying HIV incidence from a single blood test.Keywords
This publication has 24 references indexed in Scilit:
- Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug UsersJournal of Virology, 2010
- High Multiplicity Infection by HIV-1 in Men Who Have Sex with MenPLoS Pathogens, 2010
- Modeling sequence evolution in acute HIV-1 infectionJournal of Theoretical Biology, 2009
- Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted VariantsJournal of Virology, 2009
- Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease ProgressionPLoS Computational Biology, 2008
- Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infectionProceedings of the National Academy of Sciences of the United States of America, 2008
- Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and SequencingJournal of Virology, 2008
- Human Immunodeficiency Virus (HIV) Antibody Avidity Testing To Identify Recent Infection in Newly Diagnosed HIV Type 1 (HIV-1)-Seropositive Persons Infected with Diverse HIV-1 SubtypesJournal of Clinical Microbiology, 2007
- Randomized, Controlled Intervention Trial of Male Circumcision for Reduction of HIV Infection Risk: The ANRS 1265 TrialPLoS Medicine, 2005
- Basic principles of ROC analysisSeminars in Nuclear Medicine, 1978