Quantitation of Non-B Clade HIV


Synopsis: RT-PCR and bDNA assays for HIV-1 yielded different results in a young woman from Cameroon, suggesting she has a non-B clade virus.

A previously untreated HIV-infected patient of mine was recently screened for inclusion in a research protocol. Despite multiple detectable viral loads during the previous year varying from 578 to 10,230 particles per mL of plasma as determined by the Chiron HIV-1 RNA 2.0 bDNA assay, two sequential screening tests using the RT-PCR assay were negative. This discrepancy points out an important difference between these two assays and their ability to detect non-B clade HIV-1 variants.

This 32-year-old woman had migrated from Cameroon about six years earlier, and was found to be HIV-positive on routine ELISA screening in the United States about two years ago. Because of high CD4 cell counts and low viral load test results, she had previously chosen to defer initiation of antiretroviral therapy. Based on the discrepant results between the two assays, she is likely infected with a non-B clade HIV virus. Her virus is presently being sequenced and phenotyped.

At least 10 genetically distinct HIV-1 subtypes have been recognized; it is likely that other unidentified subtypes exist. Group M contains A through J, while Group O (outliers) contains a number of closely related viruses. While subtype B is common in western Europe and in the United States, non-B subtypes were previously fairly well localized to Africa and Asia. The epidemiology of these viruses is, however, being altered by an increase in migration, foreign travel, and "sex tourism." Recent surveys suggest that non-B clade virus is now found in 16-20% of patients in London and in France. At least four different subtypes (B, C, D, and F) have been identified in Rio de Janeiro, Brazil, creating an environment resulting in both dual and recombinant mosaic infections in 11.4% of the city’s HIV-infected population .1

RT-PCR assay uses only two relatively short target sequences for its probes, making it highly susceptible to any mutational changes affecting those genetic regions. In contrast, the bDNA assay uses a total of 98 probes directed at a larger span of the pol gene. Any genetic variation in one or several of the targeted zones would, therefore, be less likely to limit the sensitivity of this assay. Quantitation of viremia due to non-B clade HIV-1 subtypes using the bDNA assay may yield viral load measurements 2 to 3 logs higher when compared with either the standard or ultrasensitive Roche RT-PCR assay. In our case, the low levels of circulating virus detected by the bDNA assay were completely missed by the ultrasensitive RT-PCR assay.

In addition to the potential for eluding amplification by PCR, detection of subtype O strains can pose other difficulties. HIV-1 O subtypes are prevalent in west central Africa, especially in Cameroon, equatorial Guinea, and Gabon, where genetic studies suggest they may have more recently been introduced into the population. Detection of antibodies to subtype O strains using unmodified ELISA assays can result in false-negative tests, and some O subtypes can cause false-negative immunoblots.2

Not only will the increasing prevalence of non-B clade virus and genetically mosaic variants interfere with ongoing efforts to develop a broadly effective anti-HIV-1 vaccine, clinicians should be aware of the potential for discrepant or falsely negative test results when assessing a patient with non-B clade virus. One should consider the likely origin of a patient’s HIV infection before ordering quantitative studies using the current RT-PCR assays.


    1. Kemper CA. Infect Dis Alert 1999;18:136.

    2. Gurtler LG, et al. Arch Virol Suppl 1996;11:195-202.

Potential differences between current bDNA and RT-PCR assays for quantifying HIV include:

    a. bDNA may be more sensitive in detecting non-B clade HIV.
    b. Current RT-PCR assays yield viral loads 2-3 times higher than bDNA.
    c. Non-b clade HIV is present in about 20% of patients in parts of Europe.
    d. Non-b clade virus is rare in the United States.
    e. a and c