With more than 1.8 million Covid-19-related deaths worldwide and more than 350,000 deaths in the United States alone, the battle against SARS-CoV-2 is raging on into 2021.
In 2020, we’ve certainly learned that better infrastructure for detection is critical in fighting diseases like Covid-19 – and metagenomics are key to better understanding and ultimately better treatment. As a consulting infectious disease physician and frontline worker, I’ve seen the battle first-hand and there is still a lot of work to do. I was lucky to get the recently after seeing patients but we are still a long way off from controlling this pandemic. However, I’ve also seen that we’re getting closer to more effectively fighting this battle and new tools are giving us the chance to better care for our patients quicker than we have ever been able to do.
When Investment Rhymes with Canada
Canada has a proud history of achievement in the areas of science and technology, and the field of biomanufacturing and life sciences is no exception.
We are at the forefront of medical diagnostics allowing us to rapidly help our patients. Speed and comprehensiveness have never been more important than they are during the current pandemic. Using these techniques we have been able to get patients to targeted treatments for their infections quicker allowing for more rapid hospital discharges. Metagenomics applied in a rapid clinical setting was unthinkable just a few years ago but now can be deployed by any hospital with local deployment. This will support our healthcare systems and allow our patients to thrive.
In the year ahead, as the fight against Covid-19 continues, the world must focus on five key areas:
- Broader Testing for Broader Pathogens: As the vaccine is deployed, it will be important that broader testing for respiratory illnesses is also leveraged, so that health professionals, clinicians and the global health community can identify pathogens that are returning, and can track how the vaccine is fighting all pathogens, and how that is impacting the evolution of Covid-19.
- Insights into Secondary Infections: It will be critical to understanding secondary infections as a key driver of morbidity and mortality, and specifically how they intersect with Covid-19. Next-generation sequencing provides a way to rapidly identify and characterize the viral and bacterial community and pathogens in patients suffering from respiratory infections. As we gain a deeper understanding of co-infections, the world will be able to better manage the treatment of the virus and in turn, can support the available bed space in hospitals.
- Stepped-Up Surveillance: As we’ve seen this year, pathogen surveillance is as important as testing and 2021 will bring an increased awareness about the need for this approach to discover and mitigate future pandemics. In order to accomplish this large task, surveillance strategies and tactics will need to be built into our healthcare system and will be required to standardize pathogen testing. The key takeaway from 2020 should be the importance of investing in preparedness – including building a comprehensive database and techniques that integrate reservoir data from agriculture and allow the community to better respond to new threats.
- Rapid Resistance Detection: Beyond identifying pathogens, it should also be a priority to deliver more comprehensive identification of antimicrobial resistance markers. With the help of sequencing-based AMR profiles, this approach will allow providers to help ensure patients are getting on the proper antibiotics quicker, thereby getting patients out of the hospital to better manage the healthcare system’s finite bed capacity.
- Large-Volume Testing with Smaller Teams: In 2021, it will be more important than ever that labs can manage large-volume testing with a smaller workforce. In an effort to safeguard critical workforces, testing that can be completed with a reduced number of personnel will be vital and can be accomplished as more labs adopt digitization and robotics to support new testing methods.
The fight isn’t over, but as we gain deeper insights into this pathogen, we’ll all be better armed to manage this pandemic and prepared to better tackle the next one.
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Dr. Lauge Farnaes is Head of Medical Affairs at IDbyDNA, the company revolutionizing the use of metagenomics to improve health by decoding the unknown. IDbyDNA and Illumina, Inc. (Nasdaq: ILMN) recently co-launched a Respiratory Pathogen ID/AMR Target Enrichment Panel for Research Use Only that aims to accelerate and improve testing for infectious diseases. The panel targets more than 280 pathogens and can also detect genes associated with antimicrobial resistance markers, providing insight into how the misuse of antimicrobials can lead to antibiotic resistance.
Dr. Farnaes is board certified in pediatrics, pediatric infectious disease and Pediatric hematology and oncology. He works as an attending physician in the division of pediatric infectious disease at UCSD/Rady children’s hospital. Dr Farnaes did pioneering work in the cost effectiveness of rapid whole genome sequencing for critically ill children and is now working on creating similar evidence for the broad deployment of rapid infectious disease testing using next generation sequencing technology.
