MICA: Community Based Point-of-Need Integrated Diagnostics for SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (Covid-19), a disease which first disease emerged in China in December 2019. The virus has now spread across the world, with all but a very few countries now having cases. Although the disease is fatal in a small number of individuals, the majority of Covid-19 cases either are asymptomatic or result in only mild disease. Internationally there have been a variety of different strategies to reduce the burden of the disease including vaccine development, the search for new medicines and finally the identification (or diagnosis) and isolation of those infected (to prevent the disease spreading throughout communities).

Over the last 9 months there has been a huge effort in developing diagnostic sensors, using a range of strategies including those for laboratory-based testing and those can be used within communities. Within these sensors developed, there are sensors that can tell if you have previously been infected (based upon determining antibodies in the blood) and those that tell whether you are currently infected (by measuring the viruses' genetic material from a throat swab). This proposal is concerned with detecting those people who are currently infected in a format that can be readily used by GPs in primary care, care homes and schools.

One significant challenge is that many of the those infected with the SARS-CoV-2 virus have symptoms that are similar either to those with a cold (commonly caused by the Respiratory Syncytial Virus in children and adults) and flu (caused by the influenza virus). We have therefore chosen to make a low-cost, disposable sensor, that can not only be used in the community without the need for a centralised testing laboratory, but which also tells the GP if the individual being tested has COVID-19, flu or a cold. The proposal aims to simplify the method of sample testing that it can be caried out simply, giving a test result that is easily read by eye, in a manner similar to a pregnancy test (as a band, on a strip of paper).

Currently, validated diagnostic tests for SARS-CoV-2 infections include laboratory-based tests involving Reverse Transcriptase (RT) Polymerase Chain Reaction (PCR) or RT-isothermal Loop-Mediated Amplification (RT-LAMP), using swabs from the upper respiratory tract, as well as blood-based IgM/IgG/IgA enzyme-linked immunosorbent assays (ELISAs). Rapid diagnostic tests (RDTs) lateral flow immunodiagnostic devices (LFD) are also available for community testing. Most recently DNA testing ex-laboratories has been achieved, albeit with complex and expensive units (e.g. DNAnudge). In general, although these commercial products provide solutions for testing in many scenarios, there remains a need for low-cost, point-of-need nucleic acid sensors, able to detect SARS-CoV-2 infections in a timely manner, providing multiplexed tests (e.g. with RSV, influenza), without the need for expensive equipment.

We have developed a novel SARS-CoV-2 LAMP assay, targeting sequences in the ORF1 ab region and N gene simultaneously (as recommended by China CDC and FDA). The assay has been optimised, now giving a limit of detection <64 copies/ml and validated clinically against 7 other respiratory viruses, showing no cross reactivity. We propose to incorporate this into a multiplexed community-use, hand-held nucleic acid-based sensor as a self-contained single-use disposable device. A nasopharyngeal swab or saliva sample will be placed into an injection-molded cartridge, containing all reagents to perform sample enrichment and RT-LAMP. The multiplexed result is read visually on an integrated paper-LFD. The device enables (i) sample enrichment, reducing the elution volume from a swab and (ii) simple methods for thermal management, and will be validated in a statistically-powered study, to accelerate translation.