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Development and application of a high-throughput HIV type 1 genotyping assay to identify CRF02_AG in West/West Central Africa

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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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Kijak, GH
Sanders-Buell, E
Wolfe, ND
Mpoudi-Ngole, E
Kim, B
Brown, B
Robb, ML
Birx, DL
Burke, DSdonburke@pitt.eduDONBURKE
Carr, JK
McCutchan, FE
Centers: Other Centers, Institutes, 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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