Over 50% of infants in sub-Saharan Africa who are infected with human immunodeficiency virus type 1 (HIV-1) die before 2 years of age. Fortunately, early diagnosis and treatment of infected infants significantly slows disease progression and improves survival. While access to treatment is improving, currently available infant HIV-1 diagnostics are expensive and require complex equipment and sample processing. Therefore, infant HIV-1 testing is restricted to centralized laboratories, which delays the timely reporting of test results to rural areas. A rapid and easy-to-use infant HIV diagnostic that can be performed at the point of care or in rural clinics closer to the user will reduce turn-around time for testing so treatment can start sooner and significantly improve AIDS-specific child mortality rates in rural areas. The goal of this proposed project is to create an infant HIV-1 diagnostic that can detect the strains of HIV that are circulating worldwide and that requires minimal infrastructure to perform. We have identified a combination of technologies that can meet this goal. An isothermal amplification method, recombinase polymerase amplification (RPA), uses sequence-specific primers and probes to amplify DNA at a constant temperature of ~380C. Amplicons can be detected by either fluorescence, using a simple low-cost reader, or by a lateral flow strip (LFS), reducing the need for any complex equipment. It is the primary aim of this proposal to design a single RPA HIV-1 assay that can diagnose all common HIV-1 subtypes. The same primer and probe(s) sequences may be utilized in either the fluorescence or LFS format adding greater utility for assay use. Because HIV-1 is extraordinarily diverse, conserved regions of the genome will be identified and RPA primers and probes will be designed and tested against a panel of diverse viral templates. The HIV-1 RPA assay will be optimized to tolerate diversity across HIV subtypes with high sensitivity and specificity. Whole blood is routinely utilized to detect HIV-1 DNA. Typically, whole blood dried on filter paper is used to stabilize blood collected for infant diagnostics. This project will determine whether whole blood or dried blood spots (DBS) are compatible with the RPA assay or whether membranes that capture lymphocytes increase assay sensitivity. Existing and novel rapid DNA extraction methods using DBS will be assessed in conjunction with the RPA assay to establish a test protocol that gives optimal sensitivity. In order to remove the requirement for powered incubation equipment, an exothermal compound that heats within the optimal incubation range of RPA has been identified for use with the LFS RPA format. The overall goal of the proposed project is to create an HIV-1 diagnostic based on RPA that can be minimally or entirely non- instrumented;requires minimal sample processing, with amplicon detection via fluorescence or LFS;and can be used at the point of care in a variety of resource-limited settings.

Public Health Relevance

Currently many infants infected with HIV-1 die due to lack of diagnosis and treatment, especially in rural areas that have limited access to testing facilities. Therefore, the rapid diagnosis of HIV-1 is a critical factor for successful disease management of infected infants. This proposal describes several nascent technologies that can be used to develop a rapid and easy-to-use HIV-1 diagnostic tool for use at the point of care in low-resource settings.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI097038-03
Application #
8488405
Study Section
Special Emphasis Panel (ZRG1-AARR-K (90))
Program Officer
Fitzgibbon, Joseph E
Project Start
2011-07-01
Project End
2014-06-30
Budget Start
2013-07-01
Budget End
2014-06-30
Support Year
3
Fiscal Year
2013
Total Cost
$378,624
Indirect Cost
$59,769
Name
Program/Appropriate/Technology/Health
Department
Type
DUNS #
103713624
City
Seattle
State
WA
Country
United States
Zip Code
98121
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Boyle, David S; McNerney, Ruth; Teng Low, Hwee et al. (2014) Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification. PLoS One 9:e103091
Boyle, David S; Lehman, Dara A; Lillis, Lorraine et al. (2013) Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. MBio 4:
Boyle, David S; Hawkins, Kenneth R; Steele, Matthew S et al. (2012) Emerging technologies for point-of-care CD4 T-lymphocyte counting. Trends Biotechnol 30:45-54