Challenges for accurate HIV diagnosis: viral genetic diversity and acute infection

Since its discovery 30 years ago, the human immunodeficiency virus (HIV) has posed unique diagnostic and therapeutic challenges worldwide, due to the ability of the virus to rapidly evolve and mutate. The original HIV strain, HIV type 1 (HIV-1), was followed by the discovery of HIV-2 and subsequently by identification of HIV-1 group O. Today HIV-1 is classified into groups, subtypes, and recombinant forms based on the high level of genetic diversity among the different strains.

Most diagnostic test reagents for HIV have been derived from HIV-1 subtype B that is common in the United States, but due to immigration and frequent international travel the regional balance of HIV strains is shifting. The continuing spread of HIV has caused a global pandemic of unprecedented genetic and geographic complexity. We know that five HIV-1 subtypes and two circulating recombinant forms have each established a global prevalence greater than 2.5%, a level that virtually ensures continued presence for decades to come.¹

The United States has seen a slow increase in the prevalence of HIV non-B subtypes during the last 15 years.² The U.S. Centers for Disease Control and Prevention (CDC) has reported that the estimated prevalence of HIV non-B subtypes is about 4%.3 Variant strains of HIV-1 originating in Africa, Asia, and Latin America are being detected throughout the United States, including not only cities and states with large immigrant communities but also rural Midwestern states.² This increase in the prevalence of non-B strains and ongoing geographical redistribution of HIV strains makes it essential that HIV assay sensitivity is not influenced by genetic variation within HIV types, groups, and subtypes.

To assure that HIV assays for patient diagnosis and management and donor blood screening maintain optimal levels of sensitivity and specificity, ongoing global surveillance of HIV is required to track the variability of the virus, identify and characterize newly emerging variant strains, and monitor shifts in the predominant circulating strains. A global surveillance program has been developed to ensure that HIV assays provide reliable, accurate test results worldwide. Acquisition and characterization of HIV-infected specimens from around the world have provided data to guide design of assays and formats and allowed evaluation of assay performance using specimen panels that represent the global diversity of HIV strains.

A recent example of the value of the surveillance program is the identification of a newly emerging HIV-1 group in Cameroon. In a study published in the Journal of Virology in 2011, researchers identified a group P strain in a male hospital patient in Cameroon.⁴ This is only the second group P strain identified and confirms that group P, a virus originating in gorillas, is circulating in humans. The first group P was discovered in a Cameroonian woman living in Paris.⁵

The surveillance program provides global specimen panels to demonstrate that assay performance is not affected by HIV strain diversity. The Ag detection side of one combination HIV antigen (Ag) and antibody (Ab) assay was evaluated using 47 viral strains originating from 21 different countries and representing the major HIV-1 group M subtypes and recombinant forms as well as group O.⁶ For evaluation of antibody detection, a panel of 693 specimens obtained from 13 different countries and representing HIV-1 groups M, N, and O and HIV-2 was used.⁶ In addition, using a diverse panel of HIV-1 virus isolates, it was determined that this assay could detect acute infections once the viral loads exceed 58,000 RNA copies per mL regardless of HIV-1 strain.⁷ It should be noted that commercially available HIV Ag/Ab combination tests vary widely in their analytical sensitivity for HIV Ag, especially across diverse HIV-1 groups and subtypes.⁸

Recent awareness of the role acute HIV infections play in the onward transmission of HIV has highlighted the importance of assays that can detect both acute and chronic HIV infection. Even though very significant progress has been made in HIV prevention and treatment in the last quarter century, the epidemic persists. According to the CDC, in the United States more than 56,000 individuals become infected with HIV every year, and today more than a million people live with HIV.⁹ It is estimated that 10% to 50% of new HIV infections are traceable to acutely or recently infected individuals.^10,11 The recently infected are responsible for many new HIV transmissions, mainly because these individuals are often unaware that they are infected. In addition, the recently infected are highly contagious because of initial high viral loads and the absence of neutralizing antibodies which may lower the transmission risk during the chronic infection phase.^11,12 Therefore, identifying more infected people earlier offers a significant opportunity for counseling, which can reduce high-risk behaviors, and for the initiation of antiretroviral treatment, which has been shown to significantly reduce transmission of HIV.¹³

According to a review published in the New England Journal of Medicine in 2011, fourth-generation HIV testing, “can increase the number of patients with acute HIV-1 infection whose condition is diagnosed at a time when they are most infectious to others.”¹²

New CDC HIV testing guidelines, currently in draft form, and recently published CLSI guidelines propose a testing algorithm that uses a fourth-generation HIV combination assay as the initial screening assay.^14,15 The algorithm gives priority to sensitivity so that acute infections are detected. In addition, it aims to identify HIV-2 infections. The algorithm requires only three tests: an HIV combination assay followed by an antibody differentiation assay and then an HIV-1 RNA assay, if needed. This simplified approach is expected to reduce the time to report a positive result and increase the accuracy of the final result.

Initial evaluations of the algorithm have demonstrated an increase in detection of acute infections.¹⁴ An emergency department in Phoenix, AZ, found 32.4% of 37 newly diagnosed HIV infections were acute infections that would have gone undiagnosed if traditional testing using an HIV antibody-only assay followed by western blot had been performed. The CDC-sponsored STOP study, conducted in New York City, San Francisco, and North Carolina, identified 55 acute HIV infections, increasing the yield of diagnosed HIV infections by 8.3% Even in areas with a low incidence of HIV, where clinicians are unlikely to suspect HIV when seeing a patient with an early-stage infection, testing with a fourth-generation assay provided benefit. A laboratory in Sioux Falls, SD, detected three acute HIV infections.¹⁶ The Florida Department of Health reported a reduction in the time to report a positive result. Prior to implementation of the new algorithm, only 22% of results were reported in less than two days, compared to 96% after implementation.¹⁷

The improved detection of acute HIV infections should not only reduce onward transmission of HIV but also can help lower healthcare costs. The HIV Prevention Trials Network has reported that early initiation of antiretroviral therapy to HIV-infected individuals substantially protected their uninfected sexual partners from acquiring HIV infection, with a 96% reduction in risk of HIV transmission.¹³ According to CDC, every case of HIV that is prevented saves an estimated $380,000 in lifetime treatment costs.¹⁸

New strains of HIV will continue to evolve throughout the world and challenge our ability to design HIV diagnostic tests capable of identifying infections caused by both common and newly emergent HIV. Therefore, ongoing surveillance is essential. To help reduce the incidence of HIV, an increase in routine testing for HIV using assays capable of detecting acute, recent, and chronic infections regardless of the HIV strain is critical.