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22nd April 2020  Editorial by: Paul Carton

Next-Generation Sequencing Delivers 30x Faster COVID-19 Testing than qPCR

Next-generation sequencing (NGS) platforms that were acquired by research laboratories worldwide for the Human Genome Project will now be put to work to test for COVID-19.

Since then these sequencers have been typically used in cancer screening and microbiome projects, and now several companies who provide these types of sequencing services have developed NGS COVID-19 tests, thus enabling a faster testing regime worldwide.

BillionToOne (BTO), a cancer molecular diagnostics company, has developed a qSanger-COVID-19 test, that can run COVID-19 tests 30 times faster than standard qPCR methods (1,536 samples on qSanger at a time vs 48 samples on qPCR). 

BillionToOne is applying to the US FDA to have its reagents granted Emergency Use Authorisation for the duration of the crisis. However, international companies who don't need FDA-EUA, can use in-house reagents and take advantage of BillionToOne's bioinformatics pipeline. The BTO bioinformatics pipeline consists of its proprietary software and is used to analyse sequencing data.

International companies who wish to purchase the full kit can do so too, as BillionToOne have already taken pre-orders.

Only a single amplicon of the virus genome is required for sequencing and allows rapid turnaround from sample to result. In addition to this, the RNA extraction step is skipped, as laboratories need only to add UTM (universal transport medium) directly to the BillionToOne plates.

The reagents cost is $15 per sample, with the price for running one sample estimated to be <$20 per test.

Other NGS COVID-19 kits are being deployed to monitor mutations in viral populations. The UK-based company Youseq have developed a SARS-COV-2 Coronavirus NGS Library Prep Kit, which is an all-in-one kit, requiring no extra reagents.

Its sequencing protocol is said to have exceptional sensitivity when working with low viral loads, which is a big advantage, as low viral loads are suspected as a cause for the high-rate of false-negatives been reported with standard qPCR tests. 

In China, the National Medical Products Administration (NMPA) have approved one NGS COVID-19 kit, developed by BGI Biotechnology. BGI has developed a metagenomic sequencing detection kit (2019-nCoV nucleic acid detection kit- combinatorial Probe-Anchor Synthesis sequencing method) to monitor mutations of the viral population.

The metagenomic sequencing kit can identify and diagnose other coronaviruses, including new coronaviruses and respiratory tract infections, and achieve rapid detection of viral sequences.

BGI's reagents are only approved by the NMPA for use on the ultra-high-throughput DNBSEQ-T7 sequencing system and BGI's analysis software. 

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Date Published: 22nd April 2020

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