Large-scale Population Screening of Pooled Viral Nucleic Acid Samples Using Concurrent Isothermal Amplification and Electrochemical Detection for Novel Infectious Diseases on a Disposable Chip

Rapid host-to-host transmissions coupled with the ease of international travel has led to epidemics such as H5N1, H5N5, SARS, and, most recently, the COVID-19 pandemic. Traditional epidemic control measures, such as contact tracing and physical isolation, are paramount to mitigate the extent of disease spread at the early stage of the pandemic and these strategies depend on the accuracy and speed of diagnosing suspected patients.

Now the gold standard for pathogen detection is nucleic acid detection via polymerase chain reaction (PCR). However, this strategy is limited by the turnaround time, expensive PCR machine, and potential number of infections. Thus, other isothermal amplification methods are often used to circumvent the need for extra instrumentation and speed up the whole detection procedure.

One approach to improve infectious disease screening efficiency is the popular Dorfman testing, where samples are pooled together and tested at the same time to reduce the total number of tests performed. However, the Dorfman testing is limited to low prevalence population and has reduced sensitivity; Barcoding strategy has also been introduced to solve pooling sample test. In 2020, Schmid-Burk and his colleagues combined LAMP and barcoding which successfully developed COVID-19 from 100,000 pooled samples. However, the need of a expensive next-generation sequencer limits its widespread use.

Methods

The proposed platform aims at development of a multistep process in one device, and the capability of identifying the source of positive signals from pooled samples. The proposed design will take advantage of a barcoding strategy to tag multiple sources of analytes prior to pooling, a combination of isothermal amplification and sequence-specific electrochemical detection, and the integration of several steps in one simple device. The research project methodology will be divided into three parts.