Early infant diagnosis HIV-1 PCR cycle-threshold predicts infant viral load at birth

Background: HIV-1 viral load (VL) has been found to be an independent predictor for disease progression among untreated HIV-infected children. However, qualitative polymerase chain reaction (PCR) assays are routinely used for early infant diagnosis (EID). Objectives: To predict HIV-1 VL at birth using qualitative EID real-time PCR cycle-threshold (Ct) values. Study design: This study was a secondary analysis of results from a cohort of intrauterine HIV-1 infected neonates. Neonates were enrolled at Rahima Moosa Mother & Child Hospital in Johannesburg, South Africa between June 2014 and November 2017. Laboratory EID HIV-1 PCR testing was performed at birth using COBAS AmpliPrep/COBAS TaqMan HIV-1 Qualitative Test v2.0 (EID CAP/CTM). Some infants had simultaneous EID point-of-care (POC) testing using Xpert HIV-1 Qualitative assay (EID Xpert). Neonates with a confirmed HIV-1 detected EID result and plasma HIV-1 RNA VL test were included in this analysis. Bland-Altman analysis was used to determine extent of agreement between Ct values of both EID assays. Multivariable linear regression models adjusting for time between EID and VL testing were used to describe the association between EID Ct values and VL and to predict VL at given EID Ct values. Results: Among 107 HIV-1 infected neonates included in the study, 59 had POC EID testing. Median VL was 28 400 copies per millilitre (cps/ml) (IQR: 1 918-218 358) - two neonates had VL < 100 cps/ml prior to antiretroviral therapy initiation. There was good correlation between Ct values of both EID assays (Spearman correlation coefficient 0.9, 95% CI: 0.8-1.0). The limits of agreement between EID CAP/CTM and Xpert Ct values were 4-11 cycles. For every one cycle increase in Ct value there was 0.3 log(10) RNA decrease (95% CI: -0.3 to -0.2) for both EID assays. An EID CAP/CTM Ct value <= 23 and an EID Xpert Ct value <= 31 predicted a VL of > 5.0 log(10) cps/ml in 82.2% (95% CI: 73.9-88.3) and 84.7% (95% CI: 73.7-91.8) of cases, respectively. Conclusion: EID Ct values at birth predict VL and accurately identify infants with VL > 5.0 log(10) cps/ml.