Kijak, GH and Sanders-Buell, E and Wolfe, ND and Mpoudi-Ngole, E and Kim, B and Brown, B and Robb, ML and Birx, DL and Burke, DS and Carr, JK and McCutchan, FE
(2004)
Development and application of a high-throughput HIV type 1 genotyping assay to identify CRF02_AG in West/West Central Africa.
AIDS Research and Human Retroviruses, 20 (5).
521 - 530.
ISSN 0889-2229
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Abstract
In West/West Central Africa, CRF02_AG is the most prevalent HIV-1 strain and circulates in the milieu of rare subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs). The molecular complexity of HIV-1 epidemics in this region and the need to extensively sample large populations, such as in the case of vaccine trials, pose seemingly conflicting requirements between full-genome sequencing and high-throughput low-resolution assays. Here we describe the development and evaluation of a multiregion hybridization assay (MHAcrf02) for the efficient genotyping of CRF02_AG in West/West Central Africa. Subtype A, G, and CRF02_AG-specific fluorescent probes were designed flanking five recombination breakpoints in CRF02_AG and were used in real-time PCRs. A panel representing West/West Central African HIV-1 genetic diversity was evaluated by MHAcrf02. The sample set, previously characterized by full-genome sequencing, included CRF02_AG and CRF02_AG-containing recombinants (n = 28), other subtypes, CRFs, and URFs (n = 34). DNA from peripheral blood mononuclear cells, cocultures, and plasmids was used as template. When the patterns of probe reactivity were evaluated. CRF02_AG was identified with a 100% specificity and sensitivity. In conclusion, MHAcrf02 will permit more efficient characterization of HIV-1 in West/West Central Africa, where CRF02_AG is an important strain. Together with other regional genotyping assays MHAcrf02 will contribute to the development of a global picture of HIV-1 diversity and geographic distribution, providing a strong foundation for intervention, including vaccine development.
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| Item Type: |
Article
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| Status: |
Published |
| Creators/Authors: |
| Creators | Email | Pitt Username | ORCID  |
|---|
| Kijak, GH | | | | | Sanders-Buell, E | | | | | Wolfe, ND | | | | | Mpoudi-Ngole, E | | | | | Kim, B | | | | | Brown, B | | | | | Robb, ML | | | | | Birx, DL | | | | | Burke, DS | donburke@pitt.edu | DONBURKE | | | Carr, JK | | | | | McCutchan, FE | | | |
|
| Centers: |
Other Centers, Institutes, Offices, or Units > Center for Vaccine Research |
| Date: |
1 January 2004 |
| Date Type: |
Publication |
| Access Restriction: |
No restriction; Release the ETD for access worldwide immediately. |
| Journal or Publication Title: |
AIDS Research and Human Retroviruses |
| Volume: |
20 |
| Number: |
5 |
| Page Range: |
521 - 530 |
| DOI or Unique Handle: |
10.1089/088922204323087778 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Graduate School of Public Health > Epidemiology |
| Refereed: |
Yes |
| ISSN: |
0889-2229 |
| Date Deposited: |
30 Jul 2015 17:36 |
| Last Modified: |
06 Jan 2018 14:55 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/24371 |
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