Designing NGS probes and reagents to study COVID-19

30 October 2020 Roche
Lab technician inspecting sample

As the novel coronavirus SARS-CoV-2 continues to spread, Roche has remained committed to understanding the mechanism by which the virus interacts with the human genome and improving healthcare response to COVID-19. By using next-generation sequencing (NGS), scientists can become more informed about how molecular genetics play a role in disease severity and susceptibility. This could lead to improved diagnostics and treatments not only for COVID-19 but also for other viruses that will emerge in the future.

Coronaviruses (CoV), which are named after the crown-like spikes on its surface, are a large family of zoonotic viruses that can be transmitted between animals and people.1,2 The current, novel coronavirus disease (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Patients with COVID-19 exhibit a wide range of symptoms, from asymptomatic to severe illness, suggesting that host genetic factors impact susceptibility and severity of COVID-19.3 With significant advances at all stages of the NGS process, from sample collection to library quantification, researchers have the opportunity to identify specific host genetic factors and create better diagnostic tests, vaccines and therapeutic interventions.

Roche’s Expert Design of NGS probes and reagents

How will NGS identify these host genetic factors and associated disease severity? Roche Sequencing Solutions has pioneered high performing probe design and optimized reagent products for NGS sample preparation. Roche’s product portfolio and library preparation kits have already enabled researchers to unearth some of these important genetic measures in COVID-19. 

For example, a recent study using transcriptome sequencing (RNA-seq) showed higher gene expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2) -- proteins which mediate SARS-CoV-2 infection of host cells -- in asthma patients, males, African Americans, and a history of diabetes mellitus.4 These data identify subgroups of host genetic factors for patients that may be at risk for COVID-19 morbidity. Another study used RNA-seq to determine the susceptibility of SARS-CoV-2 with ACE2 and TMPRSS2 expression in the intestines of patients with inflammatory bowel disease (IBD).5 In a separate study, researchers conducted an in-depth analysis of the transcriptional response to SARS-CoV-2 compared with other respiratory viruses, showing that COVID-19 patients had signature inflammatory responses.6

As the need for studying susceptibility factors and viral genome characterization grows, the NGS toolkit can be used for better identification of host genetics.

Roche’s Commitment to NGS during COVID-19

Roche has been committed to improving consistency and reducing library preparation time through a streamlined protocol for human whole-genome sequencing, whole exome sequencing, and custom targeted enrichment. With Roche’s newly designed, integrated workflow and an on-bead hybridization setup, laboratories can automate protocols with higher cost-efficiency and confidently detect genetic variants by creating a DNA library highly enriched for specific targets, all in a single tube.

“NGS has proven to be a valuable tool in this pandemic to gain insights into important aspects covering both virus and patient, and ultimately will help to find treatments and vaccines that will enable us to end this pandemic and respond to future ones much faster than ever before,” said Toumy Guettouche PhD, Director, Reagent and Assay Development at Roche Sequencing Solutions.

Related article:
Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series.

 

References

  1. https://www.niaid.nih.gov/diseases-conditions/coronaviruses. Accessed August 2020.
  2. https://www.cdc.gov/coronavirus/types.html. Accessed August 2020.
  3. The COVID-19 Host Genetics Initiative. Eur J Hum Genet. 2020;28: 715–718.
  4. Peters M.C. et al. Am J Respir Crit Care Med. 2020 Jul 1;202(1):83-90.
  5. Burgueño J.F. et al. Inflamm Bowel Dis. 2020 May 12;26(6):797-808.
  6. Blanco-Melo D. et al. Cell. 2020 May 28;181(5):1036-1045.e9.