Virology

Detection of Simian Immunodeficiency Virus in Diverse Species and of Human Immunodeficiency Virus Type 2 by Using Consensus Primers within the pol Region

Silvina Masciotra, Chunfu Yang, Danuta Pieniazek, Chanda Thomas, Sherry M. Owen, Harold M. McClure, Renu B. Lal
DOI: 10.1128/JCM.40.9.3167-3171.2002

Article Figures & Data

Figures

  • FIG. 1.
    FIG. 1.

    Detection of HIV-2, SIVcpz, and diverse HIV-1 molecular clones by using intHIV-2/SIV primers. Known copy numbers (100, 50, and 25 copies per PCR) of reference clones of HIV-2 (GB122), SIVcpz, and HIV-1 subtypes A (92UG037), B (BCSG3), C (92BR026), D (94UG114), F (93BR020), H (90CR056), AC (92RW009), CRF01-AE (93TH233), CRF02-AG (92NG083), and B/F (93BR029) were amplified by using intHIV-2/SIV primers.

  • FIG. 2.
    FIG. 2.

    Phylogenetic positions of HIV-2 sequences from this study (boldface and underlined) and reference HIV-2 and SIV sequences in the integrase region. Trees were derived from nucleotide sequence alignment of 413 bp by using the neighbor-joining method. Numbers at the nodes represent the percentages of bootstrap values (only values >70 are shown).

  • FIG. 3.
    FIG. 3.

    Phylogenetic position of HIV-1 sequences from this study (boldface and underlined) and previously reported HIV-1 and SIVcpz strains in integrase regions. The topology shows an overall branching order consistent with previously reported phylogenies for full-length sequences. Trees were derived from nucleotide sequence alignments (consensus lengths of 412 bp) using the neighbor-joining method. Horizontal branch lengths are drawn to scale, with the bar indicating 0.10 nucleotide substitution per site. Numbers at the nodes indicate the percentages of bootstrap values (out of 500) in which the cluster to the right is supported (only values 70% or above are shown).

Tables

  • TABLE 1.

    Amplification of HIV-2 and HIV-1 isolates with intHIV-2/SIV primers

    Reference clone or isolateCountry of originSubtypeMaterial testedPCR amplification
    HIV-2
        A1958SenegalADNA+
        60415KSenegalADNA+
        A2270SenegalADNA+
        7924AGuinea-BissauADNA+
        SLRHCGuinea-BissauADNA+
        GB87Guinea-BissauADNA+
        GB122Guinea-BissauARNA+
        310248Ivory CoastADNA+
        77618Ivory CoastARNA+
        7312AIvory CoastA/BaDNA+
        310072Ivory CoastBDNA+
        310319Ivory CoastBDNA+
    HIV-1
        92UG037UgandaADNA+
        93TH233ThailandCRF01-AEDNA+
        92RW009RwandaACDNA+
        92NG083NigeriaCRF02-AGDNA+
        BCSG3United StatesBDNA+
        93BR029BrazilBFDNA+
        92BR026BrazilCDNA−
        94UG114UgandaDDNA+
        93BR020BrazilFDNA+
        90CR056CARbHDNA+
        YBF30CameroonGroup NRNA+

    • ↵ a A/B recombinant (based on full-length genome sequence).

    • ↵ b CAR, Central African Republic.

  • TABLE 2.

    Comparative sensitivities of intHIV-2/SIV and intM-Z primers for PBMC DNA and plasma RNA detection

    SpecimenTypeNo. testedNo. positive (%) with:
    intHIV-2/SIVintM-Z
    HIV-2aPBMC DNA108 (80)0 (0)
    Plasma145 (36)0 (0)
    HIV-1Plasmab3419 (55)34 (100)

    • ↵ a Represents DNA derived from primary lymphocytes or plasma specimens from HIV-2-infected donors from Ivory Coast.

    • ↵ b Represents plasma specimens from HIV-1-infected persons, including 10 subtype A specimens (Ghana and Ivory Coast), 6 subtype B specimens (Argentina, Canada, China, Ghana, and United States), 7 subtype C specimens (Mozambique and Zimbabawe), 5 subtype D specimens (Uganda), 3 subtype E specimens (Thailand), and 3 subtype G specimens (Ghana and Ivory Coast).

  • TABLE 3.

    Detection of diverse SIV isolates with intHIV-2/SIV primers

    SIV lineageIsolate sourceMaterial testedPCR amplification
    Sooty mangabey and macaque
        SIVsmm3Sooty mangabeyRNA+
        SIVsmm9Sooty mangabeyRNA+
        SIVsmm21Sooty mangabeyRNA+
        SIVsmm54Sooty mangabeyRNA+
        SIVsmm55Sooty mangabeyRNA+
        SIVsmm74Sooty mangabeyRNA+
        SIVsmm156Sooty mangabeyRNA+
        SIVrcmRed-capped mangabeyDNA+
        SIVstmStump-tailed macaqueRNA+
    African green monkey
        SIVagmTY01African green monkeyRNA+
        SIVagmtan1African green monkeyRNA+
        SIVagmKenyaAfrican green monkeyRNA+
        SIVagm1584African green monkeyRNA+
    Mandrill
        SIVmndBK12MandrillRNA+
    Sykes monkey
        SIVsykSykes monkeyDNA+
    Chimpanzee
        SIVcpzChimpanzeeDNA+
        SIVhuHumanRNA+
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KEYWORDS

Gene Products, pol
HIV-2
Simian Immunodeficiency Virus

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