Estimating HIV incidence is an important challenge for public health. An assay that could reliably distinguish incident (new) HIV infections from chronic ones would be invaluable. Initial approaches to this problem have focused on the qualities of the host's humoral response to the virus. Unfortunately, assays based on this principle have been technically difficult and there are concerns about their accuracy. An alternative strategy is to measure the genetic diversity of a patient's virus, with diversity expected to be low in new HIV infections. Directly sequencing viral samples is expensive;measuring sequence diversity through high-resolution melting curves is more affordable, but it is only a qualitative method, and it may be misleading in patients with multiple founder viruses. Here, we propose to adapt a low-cost assay based on DNA hybridization kinetics, called AmpliCot, to the measurement of HIV gene complexity.
The first aim of the project is to adapt and simplify the existing method (used to measure T cell receptor gene complexity) to viral envelope genes. This will require the synthesis of new measurement standards and the validation of new experimental conditions.
The second aim i s to determine how well AmpliCot measurements correlate with viral sequence complexity, sequence diversity, and Shannon entropy (a measure of sequence complexity weighted for relative abundance), with comparison to deep sequencing as a gold standard.
The third aim i s to test the predictive power of AmpliCot, high-resolution melting, or a combination of the two methods, against a test panel of plasma samples from subjects with new and chronic HIV infections. Serial samples from newly-infected HIV patients can be used to test whether the assay can detect an increase in viral genetic diversity over time. The reagents, methods and preliminary data from this pilot project will be used to support an R01 application for more extensive validation of this method.

Public Health Relevance

This project will develop new molecular genetic technology for a blood test that would distinguish newly acquired HIV infections from long-standing infections. A reliable, inexpensive, and high-throughput test for newly acquired HIV infections would help public health officials plan for future demands on the health care system due to HIV and would help in the evaluation of HIV prevention efforts.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21AI102791-02
Application #
8717846
Study Section
AIDS Molecular and Cellular Biology Study Section (AMCB)
Program Officer
Sharma, Usha K
Project Start
2013-01-18
Project End
2014-12-31
Budget Start
2014-01-01
Budget End
2014-12-31
Support Year
2
Fiscal Year
2014
Total Cost
$159,518
Indirect Cost
$47,018
Name
Blood Systems Research Institute
Department
Type
DUNS #
006902498
City
San Francisco
State
CA
Country
United States
Zip Code
94118