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DNA sequencing used to combat coronavirus

3 February 2020
Appeared in BioNews 1033

DNA sequencing is helping to rapidly identify and characterise the coronavirus at the centre of the recent outbreak.

The sequence has helped researchers understand the virus's origin, how it first infected humans in 2019 and better predict future transmission, as well as to speed up the development of a vaccine.

'The genetics can tell us the true timing of the first cases,' Dr Kristian Andersen, an expert on viral genetics from Scripps Research, California told STAT. 'It can also tell us how the outbreak started from a single event of a virus jumping from an infected animal to a person or from a lot of animals being infected.'

Viruses store instructions for making protein in their genome (coronaviruses' genomes are made of RNA rather than DNA), which are read by infected host cells. These proteins control all parts of a virus life cycle, including host cell infection, virus replication, and host-to-host transmission. Researchers sequenced the genome by isolating its RNA and converting it to DNA.

Coronaviruses such as SARS-CoV, which caused an epidemic in 2002 are typically found in animal populations, where they do not cause symptoms. Periodically a mutation allows a strain to 'jump' to infecting humans, as has happened with the current strain, which is known as 2019-nCoV. 

Comparing the genome of 2019-nCoV with other known coronaviruses has shown the likely animal reservoir that it evolved from to be bats, although there was probably an intermediate animal host. Comparing viral genomes from nine different human patients by researchers at the National Institute for Viral Disease Control and Prevention in Beijing, China, revealed in The Lancet, that the current outbreak is the result of a single coronavirus which made the jump into humans and has since spread by human-to-human transmission only. This confirms that animal contact is not causing more cases.

Sequencing is continuing globally on more samples, at a pace which Dr Andersen described as 'unprecedented and completely unbelievable'. Multiple teams are racing to develop a vaccine less than two months after the first confirmed infection, using the decoded virus genome as a roadmap. 

The Coalition for Epidemic Preparedness Innovations (CEPI) in Oslo, Norway, hopes to begin clinical testing of a vaccine in as little as 16 weeks. For comparison, a vaccine against SARS only entered trials 20 months after the genome was published.

'This is an extremely ambitious timeline and even if we are successful – and there can be no guarantee – there will be further challenges to navigate before we can make vaccines widely available,' said CEPI's CEO, Dr Richard Hatchett. 

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