Germany wants to jump-start gene sequencing efforts to closely track coronavirus mutations and catch up with European nations such as Britain and Denmark which have taken the lead on decoding viral genomes.
More contagious coronavirus variants are believed by scientists to have fuelled a surge in global coronavirus cases which have now passed 90 million, and nations are racing to procure vaccines and tighten lockdown measures.
A draft government order released for discussion by the German Health Ministry this week would require 5% of all samples from positive coronavirus tests to be sent to specialised laboratories for a complete genetic read-out.
That compares with a rate of about 5%-10% of viral samples being sequenced in Britain, according to the Robert Koch Institute (RKI), Germany’s infectious disease agency.
Denmark, another pioneer in the field, has said it has the capacity to analyse up to 10,000 positive samples per week.
Around 13% of all positive samples have so far been sequenced, a process that determines the order of chemical building blocks in a DNA molecule, allowing researchers to identify changes in genes and ways to respond.
Denmark hopes to increase its sequencing capacity further.
“There is nothing to prevent us from analysing all samples in Denmark – realistically within three weeks,” Mads Albertsen, biotechnology professor at Aalborg University and the head of Denmark’s largest genome sequencing facility, told Reuters.
The RKI estimates that 200 to 250 cases were sequenced in December in Germany, which is home to COVID-19 vaccine developers BioNTech and CureVac.
Britain, which has made mass gene sequencing a national priority, is sequencing several thousand cases each day.
It started tracking virus mutations broadly across its population early during the pandemic, led by the COVID-19 Genomics UK (COG-UK) consortium with partners including the National Health Service and the Wellcome Sanger Institute.
In its attempt to catch up, Germany would reimburse laboratories 200 euros ($243) per viral genome sequenced under the draft order, while the government has earmarked 200 million euros for the effort.
Marco Binder, a virologist at the German Cancer Research Center (DKFZ) in Heidelberg, which runs the country’s largest human genome sequencing facility, said the German science community traditionally had other priorities.
Sporadic coronavirus sequencing had previously been enough to stay on top of its relatively slow genomic shifts, but the emergence of faster-spreading variants posed a new imperative.
“We probably underestimated that,” he said. “It is indeed important and worth the effort to be able to track this fast and well, also on a local level.”
“We in Germany clearly have less visibility than is the case, say, in the UK or Denmark,” he said.
The association of German diagnostic labs, ALM, said the industry had the capacity to meet the government’s call.
“The 5% strike rate is quite doable,” said ALM board member Evangelos Kotsopoulos. “The capacity is there, the equipment is there, the people are there.”
The ALM said some work was needed to ensure that German laboratories pursued a common sequencing method, praising the open collaboration of Britain’s genomic sequencing effort. Scientists also see a need for a coordinated European approach.
“This is not the last variant that we will encounter,” Andreas Bergthaler, of the Research Center for Molecular Medicine at the Austrian Academy of Sciences, said of the new strain in Britain.
“We should keep our eyes open and build these systems and technologies much more systematically.”
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