False-negative HIV-1 polymerase chain reaction in a 15-month-old boy with HIV-1 subtype C infection

Abstract

Polymerase chain reaction (PCR) testing is the gold standard for determining the HIV status in children <18 months of age. However, when clinical
manifestations are not consistent with laboratory results, additional investigation is required. We report a 15-month-old HIV-exposed boy referred
to our hospital after he had been admitted several times for infectious diseases. A rapid antibody test on the child was positive, while routine
diagnostic HIV PCRs using the Roche COBAS Ampliprep/COBAS TaqMan HIV Qual Test were negative at 6 weeks, 6 months, 7 months and
15 months. In addition, the same PCR test performed on the HIV-infected mother was also negative. Alternative PCR and viral load assays using
different primer sets detected HIV RNA or proviral DNA in both child and mother. Gag sequences from the child and his mother classified both
infections as HIV-1 subtype C, with very rare mutations that may have resulted in PCR assay primer/probe mismatch. Consequently, the child was
commenced on antiretroviral therapy and made a remarkable recovery. These findings indicate that more reliable PCR assays capable of detecting
a wide range of HIV subtypes are desirable to circumvent the clinical problems created by false-negative PCR results.