As barely a third of European countries meet targets to track concerning Covid-19 variants, diagnostics and genomics companies are scrambling to help them tackle this challenge.
New strains of the Covid-19 coronavirus are sweeping Europe as vaccine distribution efforts roll on. These variants often gain traction when mutations let them become more virulent or spread faster than the original strain. Some strains could also eventually become resistant to current vaccines.
Regularly sequencing circulating Covid-19 strains allows variants of concern to be spotted early on. The sequences can also be used to adapt vaccines to future strains.
However, just nine of the 28 countries in the European Union and European Economic Area have reached the target amount of sequencing recommended by the European Centre for Disease Prevention and Control (ECDC). By the end of February, the minimum of 10%, or 500 random samples sequenced per week was only met by Belgium, Denmark, Finland, Germany, Iceland, Ireland, Italy, Luxembourg, and Norway.
“We have quite a number of European countries that are not … at a level that would enable them to rapidly identify and monitor, and therefore control, variants of concern,” the ECDC’s Head of Surveillance, Bruno Ciancio, told the European Parliament’s Environment, Public Health and Food Safety Committee this week.
“It is encouraging to see that, over time, the capacity in various member states is increasing, but many are far from the target.”
Biotechs are working hard to track three main variants of concern, named after where they were first identified in the UK (B117), South Africa (B1351), and Brazil (P1). These companies are also identifying potentially worrying new viral mutations through collaboration, diversification, and innovation.
The German firm Centogene, whose core business is testing for rare diseases, is one such company. The firm is providing a portfolio of Covid-19 tests at 10 German walk-in centers, including the gold-standard PCR test.
Centogene’s Chief Information Officer, Volkmar Weckesser, said the behavior of new variants, for example in terms of the risk of infection, could only be known after they were detected. Therefore, whenever the company’s tests detect the Covid-19 virus in a sample, Centogene follows up with sequencing to get the full genetic data.
“We hope to deliver a picture, not only of the development of the number of infections in general, but also of the development of the virus itself as a basis for politics to react accordingly,” said Weckesser.
Yet the company believes that viral sample sequencing in Germany may be hampered due to a lack of resources. For example, the German government only funds the sequencing of samples that are no older than one week.
Meanwhile in the UK, the genomics firm Nonacus has launched a whole genome sequencing service after receiving a grant from the public agency Innovate UK. Its genomic screening tests are designed to be faster and cheaper than current services. These tests will be used to check for variants of concern in all samples from international travelers testing positive on the second day after arriving in the UK.
Further afield, in South Korea, the company Seegene has been working around the clock to design a new type of PCR test that can screen for Covid-19 and identify multiple mutations in a single step. This could make it easier and faster to track variants of concern than with whole genome sequencing.
These tests are currently under review for European approval and Seegene expects the process to be finished by the end of March, with tests shipped out in April.
Seegene maintains there are particular challenges in monitoring and tracking new variants due to a lack of information, together with being unable to predict in which direction the virus will mutate.
“Developing a Covid-19 variant test is quite difficult compared to developing a Covid-19 wildtype diagnostic test,” said a Seegene representative.
“Conventional technology can be applied for the detection of a single variant but not for multiple variants in a single test. But more recently, Seegene was able to develop a coronavirus variant test that can detect multiple Covid-19 virus variants and wildtype virus in a single tube using our unique high multiplex technology.”
The ECDC is developing specific guidelines for sequencing that are tailor made for each new variant, using data from genome sequencing shared across the EU and with international partners.
Together with the European Commission, the ECDC is also providing support to monitor and control the emergence of variants, such as offering sequencing to countries that are struggling to get it in place.
The service began in February and aims to eventually sequence 15,000 or more samples per week, while the organizations also try to increase member states’ capacity in a sustainable way.
To date, there have been more than 23 million Covid-19 cases in the EU and EEA, and more than two and a half million deaths in the region. As the technology and logistics behind testing and screening of samples improve, healthcare systems may be able to better control outbreaks while gradually reopening the economy.
Cover image from Elena Resko