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

BackgroundCOVID-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. MethodWe 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. ResultsIn-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 R2 of 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. InterpretationOur 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.

Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection (preprint)

RNA amplification tests sensitively detect SARS-CoV-2 infection, but their complexity and cost are prohibitive for expanding COVID-19 testing. We developed "Harmony COVID-19", a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device accommodating up to 4 samples simultaneously. Our ready-to-use, multiplexed reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/{micro}L and can report in 17 min for high viral load samples (5,000 copies/{micro}L). Harmony detected 97% or 83% of contrived samples with [≥]0.5 viral particles/{micro}L in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens in viral transport media (VTM, n=101) showed 100% detection of RNA extracted from specimens with [≥]0.5 SARS-CoV-2 RNA copies/{micro}L, with 100% specificity in specimens positive for other respiratory pathogens. VTM is non-ideal for Harmony system, yet extraction-free analysis (n=29) had 95% success in specimens with [≥]1 RNA copies/{micro}L. Usability testing performed first-time by healthcare workers showed 95% accuracy. TeaserA novel four-plexed RT-LAMP test kit operated by health workers can provide faster and more sensitive results than lab tests.