title: Development of an env gp41-based heteroduplex mobility assay for rapid human immunodeficiency virus type 1 subtyping.
abstract: The gp120 region of the human immunodeficiency virus type 1 (HIV-1) envelope (env) gene exhibits a high level of genetic heterogeneity across the group M subtypes. The heteroduplex mobility assay (HMA) has successfully been used to assign subtype classifications, but C2V5 primers often fail to amplify African strains. We developed an env gp41-based HMA for which the target sequence is amplified with highly conserved gp41 primers, known to efficiently amplify nucleic acids from HIV-1 group M, N, and O viruses. By using gp41 from a new panel of reference strains, the subtype assignments made by our modified HMA were concordant with those obtained by sequencing and phylogenetic analysis of 34 field strains from 10 countries representing subtypes A to G. Testing of field strains from Nigeria further demonstrated the utility of this modified assay. Of 28 samples, all could be amplified with gp41 primers but only 17 (60.7%) could be amplified with the standard C2V5 primers. Therefore, gp41-based HMA can be a useful tool for the rapid monitoring of prevalent subtypes in countries with divergent strains of circulating HIV-1.
authors.affiliation: Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA.
authors.forename: S M
authors.initials: SM
authors.lastname: Agwale
authors.forename: K E
authors.initials: KE
authors.lastname: Robbins
authors.forename: L
authors.initials: L
authors.lastname: Odama
authors.forename: A
authors.initials: A
authors.lastname: Saekhou
authors.forename: C
authors.initials: C
authors.lastname: Zeh
authors.forename: A
authors.initials: A
authors.lastname: Edubio
authors.forename: O M
authors.initials: OM
authors.lastname: Njoku
authors.forename: N
authors.initials: N
authors.lastname: Sani-Gwarzo
authors.forename: M F
authors.initials: MF
authors.lastname: Gboun
authors.forename: F
authors.initials: F
authors.lastname: Gao
authors.forename: M
authors.initials: M
authors.lastname: Reitz
authors.forename: D
authors.initials: D
authors.lastname: Hone
authors.forename: T M
authors.initials: TM
authors.lastname: Folks
authors.forename: D
authors.initials: D
authors.lastname: Pieniazek
authors.forename: C
authors.initials: C
authors.lastname: Wambebe
authors.forename: M L
authors.initials: ML
authors.lastname: Kalish
mesh_terms: D004279:DNA, Viral / Q000032:analysis* / Q000235:genetics; D005814:Genes, Viral; D015700:HIV Envelope Protein gp41 / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D020180:Heteroduplex Analysis / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D004279:DNA, Viral; D015700:HIV Envelope Protein gp41