Inexpensive workflow for simultaneous monitoring of HIV viral load and detection of SARS-CoV-2 infection

  1. Gaurav K Gulati
  2. Nuttada Panpradist
  3. Samuel W A Stewart
  4. Ingrid A Beck
  5. Ceejay Boyce
  6. Amy K Oreskovic
  7. Claudia García-Morales
  8. Santiago Avila-Ríos
  9. Peter D. Han
  10. Gustavo Reyes-Terán
  11. Lea M. Starita
  12. Lisa M Frenkel
  13. Barry R Lutz
  14. James J Lai
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Abstract

Background

COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are at high risk for exposure to SARS-CoV-2 infection and severe disease once infected. For this population, it is urgent to closely monitor HIV plasma viral load (VL) and screen for SARS-COV-2 infection.

Method

We have developed a non-proprietary method to isolate RNA from plasma, nasal secretions (NS), or both. HIV, SARS-CoV-2, and human RP targets in extracted RNA are then RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status (i.e., HIV as VL failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). We evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-seropositive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 pooled plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house extraction to those using a commercial extraction kit.

Results

In-house extraction had a detection limit of 200-copies/mL for HIV and 100-copies/mL for SARS-CoV-2. In-house and commercial methods yielded positively correlated HIV VL (R2: 0.98 for contrived samples; 0.81 for seropositive plasma). SARS-CoV-2 detection had 100% concordant classifications in contrived samples, and in clinical NS extracted by in-house method, excluding indeterminate results, was 95% concordant (25 positives, 6 presumptive positives, and 31 negatives) to those using the commercial method. Analysis of pooled plasma/NS showed R2of 0.91 (contrived samples) and 0.71 (clinical specimens) for HIV VL correlations obtained by both extraction methods, while SARS-CoV-2 detection showed 100% concordance in contrived and clinical specimens.

Interpretation

Our low-cost workflow for molecular testing of HIV and SARS-CoV-2 could serve as an alternative to current standard assays for laboratories in low-resource settings.

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