Diagnosis of Pediatric HIV Infection in HIV-Exposed Infants 

Posted November 2010


The NYSDOH strongly recommends that all New York State birth facilities use the pediatric HIV testing services at the Wadsworth Center; the service is free of charge for NYS providers caring for HIV-exposed infants.

HIV nucleic acid testing (NAT) to detect HIV RNA or DNA should be performed for early diagnosis of pediatric HIV infection at the following ages (AII):

  • Within 48 hours of birth
  • At 2 weeks of life
  • At 4 to 6 weeks of life
  • At 4 to 6 months of life

Positive HIV NAT results at any age should be confirmed by repeat testing as soon as possible on a new sample. Two independent positive test results definitively diagnose pediatric HIV infection in HIV-exposed infants and subsequent testing is not necessary. (AI)

Once a positive HIV test result is confirmed, the clinician should:

  • Consult a provider with expertise in pediatric HIV care (AII)
  • Discontinue perinatal prophylactic antiretroviral monotherapy, if still being administered (AI)
  • Evaluate for initiation of combination antiretroviral therapy (ART) as soon as possible (AI)

Two negative HIV NAT results, one obtained ≥4 weeks of age and one obtained ≥4 months of age, definitively exclude pediatric HIV infection in HIV-exposed infants. (AII)

Although rare, HIV-2 exposure should be considered when HIV-1/HIV-2 antibody screening test results are reactive and HIV-1 infection of the mother has not been confirmed and/or HIV-2 infection has not been excluded using an HIV-2 discriminatory test. If HIV-2 exposure is detected, a NAT that detects HIV-2 should be used to diagnose or exclude HIV-2 infection. (AIII)


Diagnostic HIV laboratory tests must be performed in full compliance with the New York State Public Health Law.

Clinicians must report confirmed cases of HIV according to New York State Public Health Law (for more information about required reporting, see

Diagnosing and treating pediatric HIV infection early in life improves infant morbidity and mortality. HIV infection in infants should be diagnosed using HIV virologic assays (i.e., NAT, a general term which includes DNA PCR and RNA virologic assays) because maternal HIV antibody crosses the placenta and will be detectable in all HIV-exposed infants up to 18 months of age. Therefore, standard antibody tests should not be used for HIV diagnosis in newborns. Some experts use antibody tests to confirm the absence of HIV infection at 12 to 18 months of age in children who had previous negative virologic tests results during infant screening.1

NAT assays can yield qualitative (i.e., positive or negative) or quantitative (copy number per mL of plasma) results for HIV infection. Methods used for qualitative detection of HIV DNA are laboratory-specific, because no commercially available assays have been approved for clinical use. Methods used to quantitate plasma HIV RNA levels, commonly referred to as viral load tests, utilize a variety of technologies such as conventional and real-time reverse transcriptase (RT)-PCR, as well as amplification methods known as branched chain DNA amplification (bDNA), and nucleic acid sequence-based amplification (NASBA). The intended use of viral load tests is to assess prognosis of disease progression and monitor the effectiveness of ART, rather than diagnosis of HIV infection in HIV-exposed infants.

Recent studies show that the APTIMA HIV-1 RNA Qualitative Assay (Gen-Probe) is sensitive and specific for diagnosis of acute and chronic HIV infection.2-6 This test yields a qualitative positive or negative result rather than a quantitative readout of the HIV RNA levels. The Wadsworth Center has demonstrated that HIV infection can be detected an average of 4 weeks earlier in non-breastfed infants when the APTIMA qualitative RNA NAT is used compared to the qualitative DNA-PCR test previously used.7

The recommended diagnostic HIV testing schedule for HIV-exposed infants in New York State reflects the improved sensitivity of testing young infants when the qualitative RNA NAT is used by the pediatric HIV testing services at the Wadsworth Center.7 Sequential testing early in the infant’s life allows the definitive diagnosis of HIV infection so that combination ART may be initiated, after appropriate measurement of plasma RNA levels and genotypic resistance, in consultation with an expert in pediatric HIV infection. For a comparison between the NYSDOH AIDS Institute and Department of Health and Human Services (DHHS) pediatric HIV testing schedules, see Appendix A.

The NYSDOH strongly recommends that all New York State birth facilities use the pediatric HIV testing services at the Wadsworth Center. The laboratory performs rapid turnaround NAT in addition to assays capable of detecting HIV-2 infection. The service is free of charge, including shipping, for New York State providers caring for HIV-exposed infants. For information about this service, contact the Wadsworth Center at 518-474-4177.

Key Point:

Diagnostic HIV laboratory tests and interpretation algorithms evolve; individual laboratories have internal protocols for reporting tests with preliminary results. Indeterminate, inconclusive, non-diagnostic, and pending validation are among the terms used when preliminary results cannot be classified definitively. The clinician should contact the appropriate laboratory authority to determine the significance of the non-definitive results and the supplemental testing that would be indicated. This is of particular importance with tests from pregnant women and newborn children. Clinicians should become familiar with the internal test-reporting policies of their institutions.

See Diagnostic, Monitoring, and Resistance Laboratory Test for HIV for more information about testing for HIV infection.

* Facilities that choose to use laboratories other than the Wadsworth Center should verify that the testing being used is an HIV NAT that has been validated and approved for diagnosing HIV infection, including non-B subtypes of HIV-1.

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1. Panel on Antiretroviral Therapy and Medical Management of HIV-Infected Children. Guidelines for the Use of Antiretroviral Agents in Pediatric HIV Infection. September 14, 2011; pp 1-216. Available at

2. Ren A, Louie B, Rauch L, et al. Screening and confirmation of human immunodeficiency virus type 1 infection solely by detection of RNA. J Med Microbiol 2008;57(Pt 10):1228-1233. [PubMed]

3. Kerr RJ, Player G, Fiscus SA, et al. Qualitative human immunodeficiency virus RNA analysis of dried blood spots for diagnosis of infections in infants. J Clin Microbiol 2009;47:220-222. [PubMed]

4. Nugent CT, Dockter J, Bernardin F, et al. Detection of HIV-1 in alternative specimen types using the APTIMA HIV-1 RNA Qualitative Assay. J Virol Methods 2009;159:10-14. [PubMed]

5. Stevens WS, Noble L, Berrie L, et al. Ultra-high-throughput, automated nucleic acid detection of human immunodeficiency virus (HIV) for infant infection diagnosis using the Gen-Probe Aptima HIV-1 screening assay. J Clin Microbiol 2009;47:2465-2469. [PubMed]

6. Ethridge SF, Hart C, Hanson DL, et al. Performance of the Aptima HIV-1 RNA Qualitative RNA Assay on 16- and 32-Member Specimen Pools. J Clin Microbiol 2010 Jun 30. [Epub ahead of print] [PubMed]

7. Sullivan TJ, Miller TT, Warren B, et al. Evaluation of an FDA-approved qualitative RNA detection assay for diagnosis of HIV-1 infection in perinatally exposed infants. 2010 HIV Diagnostics Conference, March 24-26, 2010, Orlando, FL. Abstract 28. [Conference Abstract]

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NYSDOH AI Recommendations (2011)a DHHS Recommendations (2011)b
HIV NAT testing should be performed at the following ages:

  • Within 48 hours of birth
  • At 2 weeks of life
  • At 4 to 6 weeks of life
  • At 4 to 6 months of life
Virologic tests should be performed at a minimum at the following ages:

  • 14 to 21 days
  • 1 to 2 months
  • 4 to 6 months
a NYSDOH Wadsworth Center uses a highly sensitive qualitative RNA NAT (APTIMA HIV-1 RNA Qualitative Assay).
b Panel on Treatment of HIV-Infected Pregnant Women and Prevention of Perinatal Transmission. Recommendations for Use of Antiretroviral Drugs in Pregnant HIV-1-Infected Women for Maternal Health and Interventions to Reduce Perinatal HIV Transmission in the United States. September 14, 2011. Available at:

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