Real-time isothermal nucleic acid amplification detection in resource-limited settings: a description of an open-source miniature fluorimeter

Background

The detection and quantification of nucleic acids traditionally relies on PCR, which requires the use of expensive thermocyclers with integrated fluorescence detection of amplicons. While isothermal nucleic acid amplification technologies eliminate the need for thermocycling, fluorescence-based detection of products is still required for real-time, quantitative readout. Several commercially available isothermal heaters with integrated fluorescence detection exist, but the cost of these devices remains a significant barrier to the use of isothermal nucleic acid amplification in low-resource settings. A low-cost device for nucleic acid amplification detection could be used to contain the spread of the SARS-CoV-2 virus during the current pandemic as well as other disease targets in the future. Increasing COVID-19 testing capacity is particularly relevant when variations of the virus that appear to be more infectious are spreading rapidly and efforts to scale up delivery of COVID-19 vaccines are in the early stages. Here, we describe a modular, low-cost fluorimeter for use in resource-limited settings that lack access to and infrastructure for traditional testing platforms.

Methods

We present a fluorimeter that is constructed from off-the-shelf components enclosed in a compact 3D printed housing that removes the need for specialised optical alignment. The fluorimeter is designed to be placed atop a commercially available heat block holding a PCR-tube and was optimised to detect fluorescein (FITC) dye. The modular design allows it to be easily adapted for use with other dyes commonly used as reporters in nucleic acid amplification reactions.

Findings

Clinical applicability of the system was demonstrated using the system to measure amplification with two different isothermal amplification technologies with significantly different temperature, volume, and fluorescence requirements: recombinase polymerase amplification (RPA) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). RPA detection was demonstrated with a positive control DNA provided in a commercial kit while RT-LAMP detection of clinically meaningful levels of SARS-CoV-2 RNA was demonstrated in a custom RT-LAMP assay. In a preliminary analysis of nasopharyngeal swab samples from 74 individuals, the custom RT-LAMP assay showed a positive agreement of 92·3% and a negative agreement of 91·4% with the SARS-CoV-2 RT-qPCR test developed by the US Centers for Disease Control and Prevention.

Interpretation

This open-source system was designed to improve accessibility to nucleic acid testing with isothermal amplification methods. The system can be easily produced using only a low-end 3D printer. Moreover, the use of single-board computers obviates the need to produce printed circuit boards. At a time when global supply chains are at their most fragile, open-source diagnostic equipment has the potential to reduce pandemic-related health inequities.

Funding

International AIDS vaccine Initiative IAVI and USAID: award AID-OAA-A16-00032.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for point-of-care detection of SARS-CoV-2: a clinical study to evaluate agreement with RT-qPCR

Background

The global COVID-19 pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for rapid, accurate, and accessible diagnostics to enable timely treatment and outbreak control. However, current diagnostic tests based on RT-qPCR are insufficient to meet the global testing demand because of their high cost and complexity and supply chain shortages. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a promising alternative to RT-qPCR because of its sensitivity, speed, and robustness to sample inhibitors. Here, we describe the development and optimisation of a sample-to-answer workflow, including a simple lysis and inactivation protocol that provides results in <1h, using inexpensive and readily available reagents. Further, we assess the sensitivity and specificity of the developed RT-LAMP assay against a RT-qPCR.

Methods

We collected samples from asymptomatic healthcare workers at The University of Texas MD Anderson Cancer Center and inpatients at Lyndon B Johnson Hospital in Houston, TX, USA. Nasopharyngeal swabs were collected by medical providers and were placed directly into 300 μL of an optimised lysis buffer. Samples were heat inactivated at 95°C for 5 mins before direct amplification in a RT-LAMP assay using previously published primer sets. Heating and real-time monitoring was performed using a Bio-Rad CFX96 thermocycler and an Axxin T8-ISO, a benchtop fluorimeter designed for point-of-care settings. We compared results from the RT-LAMP test with standard-of-care RT-qPCR results on paired nasopharyngeal swabs collected into Universal Viral Transport Media.

Findings

The developed RT-LAMP assay demonstrated a limit of detection of 4–5 virions/μL. The test requires a swab, two tubes, prepared lysis buffer, a heat block, pipettes, RT-LAMP reagents, and the real-time fluorimeter. Samples were collected between April 14, 2020 and Aug 12, 2020, and results from 74 enrolled participants were analysed in the optimised workflow. Thirty nine participants tested positive for SARS-CoV-2 and 35 participants tested negative in the hospital-administered RT-qPCR test. All 74 nasopharyngeal swab eluates were tested with our assay on the Bio-Rad CFX96; 72 nasopharyngeal swab eluates were also tested on the Axxin T8-ISO. The developed assay showed sensitivity of 92·31% and 91·89% when tested on the CFX96 and T8, respectively, and specificity of 91·43% and 97·89%, respectively.

Interpretation

RT-LAMP could be used for SARS-CoV-2 testing and overcomes the challenges of adapting an assay to a point-of-care instrument. Further, the reduced instrumentation cost and complexity, along with the simple workflow, highlight the potential for implementation of RT-LAMP for SARS-CoV-2 testing in resource-limited settings.

Funding

USAID, IAVI, and Rice University.

Open-Source Miniature Fluorimeter to Monitor Real-Time Isothermal Nucleic Acid Amplification Reactions in Resource-Limited Settings

Traditional methods to detect and quantify nucleic acids rely on polymerase chain reaction (PCR) and require the use of expensive thermocyclers with integrated fluorescence detection of amplicons. Isothermal nucleic acid amplification technologies eliminate the need for thermal cycling; however, fluorescence-based detection of products is still required for real-time, quantitative results. Several portable isothermal heaters with integrated fluorescence detection are now commercially available; however, the cost of these devices remains a significant barrier to widespread adoption in resource-limited settings. Described here is a protocol for the design and assembly of a modular, low-cost fluorimeter constructed from off-the-shelf components. Enclosed in a compact 3D printed housing, the fluorimeter is designed to be placed atop a commercially available heat block holding a PCR tube. The fluorimeter described here was optimized to detect fluorescein isothiocyanate (FITC) dye, but the system can be modified for use with dyes commonly used as reporters in real-time nucleic acid amplification reactions. Clinical applicability of the system is demonstrated by performing real-time nucleic acid detection with two isothermal amplification technologies: recombinase polymerase amplification (RPA) for detection of positive control DNA provided in a commercial kit and reverse transcription loop-mediated isothermal amplification (RT-LAMP) for detection of clinically meaningful levels of SARS-CoV-2 RNA.

Microfluidic devices with templated regular macroporous structures for HIV viral capture

There is a need to develop inexpensive, portable and easy-to-use devices for viral sample processing for resource-limited settings. Here we offer a solution to efficient virus capture by incorporating macroporous materials with regular structures into microfluidic devices for affinity chromatography. Two-dimensional simulations were first conducted to investigate the effects of two structures, a nanopost array and a spherical pore network, on nanoparticle capture. Then, the two structures were created in polymers by templating anodic aluminum oxide films and 3D close-packed silica particles, respectively. When the microdevices containing functionalized porous materials were tested for human immunodeficiency virus (HIV) isolation, capture efficiencies of 80-99% were achieved under a continuous flow. Comparatively, functionalized flatbed microchannels captured around 10% of HIV particles. As the characteristic dimensions of the nanostructures are tunable, such devices can be adapted for the capture of different submicron bioparticles. The high capture efficiency and easy-to-operate nature suit the needs of resource-limited settings and may find applications in point-of-care diagnostics.