Detection of Phylogenetically Diverse Human Immunodeficiency Virus Type 1 Groups M and O from Plasma by Using Highly Sensitive and Specific Generic Primers

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Journal of Clinical Microbiology, August 1999, p. 2581-2586, Vol. 37, No. 8
0095-1137/99/$04.00+0

Detection of Phylogenetically Diverse Human Immunodeficiency Virus Type 1 Groups M and O from Plasma by Using Highly Sensitive and Specific Generic Primers

Chunfu Yang,¹ Danuta Pieniazek,¹ Sherry M. Owen,¹ Carol Fridlund,¹ John Nkengasong,² Timothy D. Mastro,³^,⁴^,⁵ Mark A. Rayfield,⁵ Robert Downing,⁵ Benon Biryawaho,⁵ Amilcar Tanuri,⁶ Leopold Zekeng,⁷ Guido van der Groen,⁸ Feng Gao,⁹ and Renu B. Lal¹^,^*

Project RETRO-CI, Abidjan, Ivory Coast²; HIV/AIDS Collaboration, Nonthaburi, Thailand³; HIV and Retrovirology Branch, Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases,¹ and International Activities Branch, Division of HIV/AIDS Prevention-Surveillance and Epidemiology, National Center for HIV, STD and TB Prevention,⁴ Centers for Disease Control and Prevention, Atlanta, Georgia; Uganda Virus Research Institute, Entebbe, Uganda⁵; Laboratorio de Virologica Molecular, Departmento de Genetica, Rio de Janeiro, Brazil⁶; Center Hospitalier et Universitaire, Université de Yaoundé, Yaoundé, Cameroon⁷; Division of Microbiology, Institute of Tropical Medicine, Antwerp, Belgium⁸; and Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama⁹

Received 5 February 1999/Returned for modification 7 April 1999/Accepted 26 April 1999

The high degree of genetic diversity within human immunodeficiency virus type 1 (HIV-1), which includes two major groups,M (major) and O (outlier), and various env subtypes within groupM (subtypes A to J), has made designing assays that will detectall known HIV-1 strains difficult. We have developed a genericprimer set based on the conserved immunodominant region of transmembraneprotein gp41 that can reliably amplify as few as 10 copies/PCRof viral DNA from near-full-length clones representing group Msubtypes A to H (subtypes I and J were not available). The assayis highly sensitive in detecting plasma viral RNA from HIV-1 strainsof diverse geographic origins representing different subtypesof HIV-1 group M as well as HIV-1 group O. Of the 253 group Mplasma specimens (subtypes A, 68 specimens; B, 71; C, 19; D, 27;E, 23; F, 33; and G, 12), 250 (98.8%) were amplified by usingthe gp41 M/O primer set. More importantly, all 32 (100%) groupO plasma samples were also amplified with these primers. In vitrospiking experiments further revealed that the assay could reliablydetect as few as 25 copies/ml of viral RNA and gave positive signalsin HIV-1-seropositive specimens with plasma copy numbers belowthe limits of detection by all commercially available viral loadassays. In addition, analysis of five seroconversion panels indicatedthat the assay is highly sensitive for early detection of plasmaviremia during the "window period." Thus, the highly sensitiveassay will be useful for early detection of HIV-1 in clinicalspecimens from all known HIV-1 infections, regardless of theirgenotypes and geographicorigins.

^* Corresponding author. Mailing address: HIV and Retrovirology Branch, DASTLR/NCID, Centers for Disease Control and Prevention,Mail Stop D-12, 1600 Clifton Road, Atlanta, GA 30333. Phone: (404)639-1036. Fax: (404) 639-2660. E-mail: rbl3{at}cdc.gov.

Journal of Clinical Microbiology, August 1999, p. 2581-2586, Vol. 37, No. 8
0095-1137/99/$04.00+0

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