Next Generation Sequencing, Diagnostics, and COVID Variants

Testing has been at the forefront of public health efforts and challenges since the beginning of the pandemic caused by SARS-CoV-2, the virus responsible for COVID-19 disease. By April last year, it became increasingly clear that testing would be crucial to public health and safety. However, global testing capacities substantially lagged behind demand as shortages loomed. In addition to nucleic acid testing, sequencing has been vital in efforts against SARS-CoV-2 to monitor changes to the virus  over time, and to undertake the massive broad spectrum and targeted R&D efforts that have brought therapeutics and vaccines to market with unparalleled speed.

In response to a bottleneck in clinical diagnostic testing early in the pandemic, companies like Illumina, Oxford Nanopore, nference, and BGI Genomics worked independently and with their respective partners to decode SARS-CoV-2, supply reagents for COVID-19 testing, and synthesize unique single cell RNA data sets to combat it. By June 2020, the US FDA authorized emergency use of the first sequencing-based test for rapid SARS-CoV-2 detection, the Illumina COVIDSeq Test. The RUO test sequences the 30,000 nucleotides in the single stranded SARS-CoV-2 RNA genome directly from patient samples, yielding real-time non-biased information about COVID-19 infection status, genetic variations, and viral lineage.

Next generation sequencing (NGS) enhanced detection of the SARS-CoV-2 genome for the purpose of supporting diagnostics, research, and tracking small mutations that impact the ability of the virus to remain infectious and persist. These mutations, or variants, include deletions, additions, or RNA base modifications that change the structure of key portions of the virus, like the spike protein. This allows the virus to evade the immune system and can reduce the effectiveness of antibodies the immune system developed to the prior versions of the viral RNA. Mutations in viral sequences are a normal part of viral adaptive mechanisms. With advances in third generation sequencing, detection of modifications to the 30,000-base single-stranded SARS-CoV-2 RNA are relatively rapid and cheaper than prior iterations of sequencing techniques, even though most samples are not processed through sequencing due to the emergence of other more rapid cost-effective options.

Fast-forward to the present, when emerging variants have become an important area of interest for researchers and public health officials alike. Currently, there are 3 major mutations of concern detected for SARS-CoV-2: the B.1.1.7 strain (UK variant), the B1.351 strain (South Africa variant), and the P1 strain (Brazil variant). Since March 2021, the B.1.351 variant from South Africa has been the focus of vaccine trials which have relied on access to sequencing data from across the world. This data is available due to efforts over the past year to bring sequencing to the bedside or, rather, at least as far as diagnostics labs to capture valuable viral genomic data. Researchers continue to integrate key mutations from the B.1.351 spike protein into the mRNA code delivered through immunization measures. Although variation in the target sequence is like a set of moving goalposts, NGS continues to rise to meet the challenge.

NGS will remain a critical tool to support current and future public health needs. For an in-depth look at NGS and other categories of life science and analytical instrumentation, consult the SDi 2021 Global Assessment Report, which covers the market for 83 different analytical technologies, and provides vendor participation, competitive dynamics, and segmentation by product type, region, end market, lab function, and application.