title: A Multiplex PCR Approach for Detecting Dual Infections and Recombinants Involving Major HIV Variants.
abstract: The cocirculation of different HIV types and groups can lead to dual infections and recombinants, which hinder diagnosis and therapeutic management. We designed two multiplex PCRs (mPCRs) coupled with capillary electrophoresis to facilitate the detection of such infections. The first, MMO2, targets three variants (HIV-1/M, HIV-1/O, and HIV-2), and the second, MMO, targets HIV-1/M and HIV-1/O. These mPCRs were validated on DNA and RNA extracts from 19 HIV-1/M, 12 HIV-1/O, and 13 HIV-2 cultures and from mixtures simulating dual infections. They were then assessed with DNA and RNA extracts from samples of 47 clinical monoinfections and HIV-1/M+O dual infections or infections with HIV-1/MO recombinants. Both mPCRs had excellent specificity. Sensitivities ranged from 80 to 100% for in vitro samples and from 58 to 100% for clinical samples, with the results obtained depending on the material used and the region of the genome concerned. Sensitivity was generally lower for DNA than for RNA and for amplifications of the integrase and matrix regions. In terms of global detection (at least one target gene for each strain), both mPCRs yielded a detection rate of 100% for in vitro samples. MMO2 detected 100% of the clinical strains from DNA and 97% from RNA, whereas MMO detected 100% of the strains from both materials. Thus, for in vitro and clinical samples, MMO2 was a useful tool for detecting dual infections with HIV-1 and HIV-2 (referred to as HIV-1+HIV-2) and HIV-1/M+O, and MMO was useful for detecting both MO dual infections and MO mosaic patterns.
authors.affiliation: Laboratoire de Virologie, Associé au Centre National de Référence du VIH, Hôpital Charles Nicolle, CHU de Rouen, Rouen, France GRAM EA2656, Faculté de Médecine-Pharmacie, Normandie Université, Rouen, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Cappy
authors.affiliation: Laboratoire de Virologie, Associé au Centre National de Référence du VIH, Hôpital Charles Nicolle, CHU de Rouen, Rouen, France.
authors.forename: Fabienne
authors.initials: F
authors.lastname: De Oliveira
authors.affiliation: Laboratoire de Virologie, Associé au Centre National de Référence du VIH, Hôpital Charles Nicolle, CHU de Rouen, Rouen, France GRAM EA2656, Faculté de Médecine-Pharmacie, Normandie Université, Rouen, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Gueudin
authors.affiliation: Laboratoire de Virologie, Associé au Centre National de Référence du VIH, Hôpital Charles Nicolle, CHU de Rouen, Rouen, France GRAM EA2656, Faculté de Médecine-Pharmacie, Normandie Université, Rouen, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Alessandri-Gradt
authors.affiliation: Laboratoire de Virologie, Associé au Centre National de Référence du VIH, Hôpital Charles Nicolle, CHU de Rouen, Rouen, France GRAM EA2656, Faculté de Médecine-Pharmacie, Normandie Université, Rouen, France jean-christophe.plantier@univ-rouen.fr.
authors.forename: Jean-Christophe
authors.identifier: 0000-0001-6417-4083
authors.initials: JC
authors.lastname: Plantier
mesh_terms: D060085:Coinfection / Q000175:diagnosis* / Q000821:virology*; D006678:HIV / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D015658:HIV Infections / Q000175:diagnosis* / Q000821:virology*; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity