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COVID-19 diagnostic tech tableau

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In the ramp-up of testing for COVID-19, two well-established technologies have divided the forefront: RT-PCR and immunoassays. The former tests for active infection by detecting viral RNA, while the latter can be used to detect the virus itself or antibodies that develop in response to infection.

Meanwhile, a slate of newer platforms in development offers opportunities to speed up readouts without compromising accuracy. The uses range from point-of-care virus detection to monitoring disease progression and tracking the emergence of mutations.

The latest to gain FDA emergency use authorization (EUA), announced Friday, is a five-minute point-of-care test from Abbott Laboratories (NYSE:ABT). The test is based on similar principles as PCR, but eliminates the technology's major bottleneck.


Figure: Mapping the COVID-19 diagnostic landscape

PCR in good time

The rapid publication of the SARS-CoV-2 RNA genome by a Fudan University-led consortium made it straightforward to develop RT-PCR-based tests. (RT-PCR involves reverse transcription of the RNA sequence to DNA, then amplification of virus-specific DNA sequences).

Over one hundred RT-PCR tests designed to detect SARS-CoV-2 in nasalpharyngeal swabs are now being commercialized by nearly as many companies, with several authorized for clinical use in Asia, Europe and the U.S.

Because RT-PCR depends on thermal cycling, tests typically take hours to complete. They also require specialized machinery at hospitals, or in centralized labs that process hundreds of samples at once. That can stretch the turnaround time to days due to shipping and other logistics.

Newer technologies are cutting down on thermocycling time and can be performed at the bedside.

In the last week, the Cepheid Inc. subsidiary of Danaher Corp. (NYSE:DHR) and Mesa Biotech Inc. each received EUA for quicker thermocycling tests using smaller devices that turn results around in less than an hour for individual patients at the point-of-care, and don't require trained technicians.

Good antibody spotting

Immunoassays, which use mAbs to recognize proteins of interest, can detect the virus itself in nasalpharyngeal swabs, or antibodies in blood samples that the patient has generated against the virus. The detected antibodies can be used to identify patients who had the infection and recovered, which can inform epidemiology studies and public health decisions. These serological assays can also find donor sources for convalescent serum or mAb therapies (see "Antibody Test for COVID-19").

Results from enzyme-linked immunosorbent assays (ELISAs) run in labs can take from hours to more than a day, depending on whether the test is run locally, and the frequency with which it is run.

However dipsticks akin to pregnancy test allow immunoassays to be run in minutes. In these lateral flow assays, samples run across a cellulose pad via capillary action, passing over labeled mAbs that produce a visual readout if a protein of interest is present.

Several dozen of these rapid COVID-19 immunoassays are being commercialized outside the U.S., though none has yet received an EUA from FDA.

The hurdle is to find mAbs, as well as reporter systems, that together produce sufficiently high sensitivity and specificity. This is far less predictable for immunoassays than RT-PCR, which relies on highly specific and unique PCR primer sequences.

Best of both worlds

Next-wave technologies that detect SARS-CoV-2 via genetic complementarity, but with little or no reliance on thermocycling, could enable speedy development of rapid tests that could be used in a point-of-care setting, or potentially even at home.

Abbott's five-minute test amplifies viral sequences similarly to PCR, but dispenses with thermocycling all together. The company's ID NOW device performs targeted sequence amplification at a constant temperature, and reads out via sequence-specific fluorescent probe.

Heat Biologics Inc. (NASDAQ:HTBX) is also developing an isothermal probe-based approach, but with a paper-based readout that could eventually be performed at home.

“Whole virome sequencing and tests measuring host cellular response could expand the scope of information gathered.”

CRISPR-based tests could offer paper-based readouts in 30 minutes or less.

Sherlock Biosciences Inc. and Mammoth Biosciences are developing Cas13- and Cas12-based COVID-19 tests, respectively, that trigger enzymatic cleavage of a reporter molecule upon detection of a specific RNA sequence (see "CRISPR-based Diagnostics Make Early Debut Amid COVID-19 Outbreak").

Newco Caspr Biotech published a biorxiv preprint on March 2nd describing a system based on a novel Cas12 enzyme for detecting SARS-CoV-2.

Shining more light

Whole virome sequencing and tests measuring host cellular response could expand the scope of information gathered while testing for COVID-19 infection.

Tests that capture infection-associated changes in the host can inform on disease progression and identify biomarkers associated with symptom onset and treatment response.

Adaptive Biotechnologies Corp. (NASDAQ:ADPT) is surveying COVID-19 patient blood for TCR repertoire signatures that could serve as signposts for different states of the disease. Fluidigm Corp. (NASDAQ:FLDM) is developing technology for early detection of COVID-19 that relies on epigenetic signatures in host cells.

RADLogics Inc. published a preprint this month describing an AI-based analysis of chest CT images that quantifies disease burden.

Next-generation sequencing (NGS) tests that read out the entire viral genome could provide insights into how the virus is mutating and how it has spread. The COVID-19 Genomics U.K. Consortium, launched Monday, is deploying this approach (see “U.K. Consortium to Map COVID-19 Spread”).

Further analysis of the coronavirus crisis can be found at https://www.biocentury.com/coronavirus.

Targets

TCR - T cell receptor

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