Designing a genome-based HIV incidence assay with high sensitivity and specificity - Introduction

A Special Author Introduction
AIDS

ISSN: 0269-9370 • Frequency: 18/year • Subscribe Now • Journal Website

A Roadmap for Developing an HIV-1 Incidence Assay

By Ha Youn Lee

The HIV incidence is the most effective measure to address the changes occurring in the HIV-1 epidemics in a given area. Precise estimates of the incidence rate allow us to trace the trajectory of the epidemics, evaluate the impact of ongoing prevention and intervention trials, and properly distribute HIV-1-related healthcare resources. In 1998, the CDC developed a Serologic Testing algorithm where the magnitude of the HIV-1-specitic antibody responses is a marker designating whether each individual has been recently infected or has had a long-standing infection. However, the serologic assays, including an alternative antibody avidity assay, were found to have a number of critical limitations, resulting in above 10% of the inaccuracy on average.

We set out to design a novel assay which relies on a set of HIV-1 sequences obtained from an infected individual. By analyzing thousands of full envelope genes sampled from hundreds of patients, we identified a measure reflecting the characteristics of HIV-1 sequence diversification and successfully distinguished the incident infections from the chronic infections. Whilst the sequence diversity of early infections can be as high as that of the chronic infections when multiple distinct viruses were transmitted, our measure, the level of sequence similarity, was significantly higher within the group of the incident subjects in compared to the chronic cases. The accuracy of our biomarker in the frame of the binary classification test was measured to be greater than 95%. Our assay was robust to viral and host specific factors such as the clade of the viral strain, the number of founder strains, viral load, and the length and location of the HIV-1 envelope sequence. The sequence-based incidence assay may hold promise for providing reliable and simple estimates for the rate of HIV-1 incidence.

To read the full article, you must be logged in. Click here to login or register.

Follow AIDS on Twitter: @AIDS_Journal

*2010 Journal Citation Reports^® ©Thompson Reuters, 2011