Coronavirus: scientists say more genomic surveillance is needed to detect new variants sooner


The world could be slow to detect new coronavirus variants given that just 2 per cent of global Covid-19 cases have been sequenced. That is according to an analysis by researchers in China and Britain, who called for more effective and coordinated global virus surveillance.

In their study, published in the journal Nature on Wednesday, the team said “limited genomic surveillance [of the coronavirus] in many low-income countries may cause delays in identifying variants”. They said identifying strains was key to pandemic control and sheds light on their transmissibility, infectivity and disease severity.

“The virus has entered a new evolutionary phase characterised by the frequent emergence and spread of variants that affect immune escape and reduce the efficacy of vaccines,” the researchers said.

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“It is likely that there are additional new variants that have not yet been detected, given the limited genomic surveillance in a number of regions,” they said, though they noted the coronavirus had prompted by far the largest project undertaken to sequence pathogen genomes.

The researchers said Britain and the United States had generated around half of the 2.8million complete genomes as of August, while countries that have seen major outbreaks, such as India and Brazil, had sequenced a much smaller number of cases.

They called for more infrastructure and training for effective genomic surveillance of the coronavirus and other emerging viruses, rapid information exchange and closer international cooperation to contain the current and future pandemics.

The paper was written by researchers with the Shandong First Medical University in China, the University of Southampton in Britain, and George Gao Fu, director of the Chinese Centre for Disease Control and Prevention.

Why it’s too early to panic about Omicron’s ability to evade vaccines

It was published as scientists around the world race to find out more about Omicron, the latest coronavirus variant of concern that has now been reported in 57 countries, according to the World Health Organization. There are still questions over how easily the highly mutated strain spreads, how well vaccines work against it, and the severity of symptoms it causes.

South African researchers on Tuesday suggested the variant was significantly better at evading virus-fighting antibodies produced by the Pfizer/BioNTech vaccine than previous strains, in findings made public ahead of peer review. However, evasion was not complete and boosters could help increase protection, the findings indicated.

WHO emergencies director Michael Ryan on Tuesday said while it was likely more transmissible than previous variants, Omicron was “highly unlikely” to completely evade vaccine protections.

“The preliminary data doesn’t indicate that this is more severe. In fact, if anything, the direction is towards less severity,” Ryan told Agence France-Presse, though he said more research was needed.

On Monday, WHO director general Tedros Adhanom Ghebreyesus warned that vaccines alone would not be enough to end the pandemic. “The emergence of Omicron highlights the need to scale up equitable access to testing and sequencing, as well as to oxygen and new antivirals,” he said.

In the Nature paper, the scientists said genomic surveillance would be more informative if coupled with a risk assessment system “that integrates pathogen surveillance, immune escape data and near real-time human mobility metrics”.

They also said variants of concern had raised the possibility that the virus could become a recurrent seasonal infection and had led vaccine manufacturers to explore redesigns of their jabs to boost protection.

The team also weighed in on the origins of the coronavirus. “Many researchers in the global scientific community have reached the consensus that Sars-CoV-2 is unlikely to have escaped a laboratory and there is no scientific evidence that Sars-CoV-2 has been genetically manipulated,” the paper said.

“However, the exact spillover event and emergence process of Sars-CoV-2 is still unclear, and more information from the earliest stage of the epidemic is clearly important to understand how Sars-CoV-2 came into contact with people.”

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