The Nepal coronavirus variant: does it even exist?

Doubts have been raised over the existence of the so-called Nepal Covid-19 variant after the World Health Organization (WHO) said it is “not aware” of the strain thought to be spreading across Europe.

The WHO yesterday posted on Twitter that it “is not aware of any new variant of SARS-CoV-2 being detected in Nepal”, despite reports of cases of Covid stemming from a new, mutated version of the variant first discovered in India.

Transport Secretary Grant Shapps yesterday appeared to confirm the emergence of the mutation, saying: “There’s a sort of Nepal mutation of the [Delta] Indian variant which has been detected” that could be “vaccine defeating”, ITV News reports.

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What do we know?

Public Health England (PHE) has said it is urgently investigating the new mutation, with Dr Mike Gent, the agency’s Covid incident director, telling The Telegraph that PHE is “aware of reports” linking the Nepal variant to the Delta strain, previously known as the Indian variant.

“This variant is present in multiple countries including a small number of cases in the UK, detected through rapid testing and whole genome sequencing,” he said, adding that PHE was investigating further “to better understand its significance”.

Dr Jeff Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute, told ITV News that the Nepal variant – known as K417N – has been “seen in numerous countries, including the UK, Portugal, the USA, and India”.

He added: “It has also been observed once in Nepal, which does very little sequencing, and 14 times in Japan, of which 13 are samples from airport quarantine from travellers from Nepal.” Barrett also explained that the same mutation present in the Nepal strain “has also been observed in other variants including the one first identified in South Africa”, the broadcaster reports.

Shapps said the Nepal mutation had “caused concern” for the government, which is currently considering whether to end all coronavirus restrictions on 21 June, as laid out in the timeline for ending lockdown.

Missing variant?

Nepal has reported “at least one case of Delta variant, first found in India, that carries a mutation called K417N”, The Guardian reports. But as “the same K417N mutation is found in the Beta variant first detected in South Africa” some experts are yet to regard the variant found in Nepal as “new”.

Professor Peter Openshaw of Imperial College London, who is also a member of the government’s New and Emerging Respiratory Virus Threats Advisory Group group, told The Independent that so far there is nothing in genomic sequencing databases to back up talk of a new variant.

“Inevitably the virus is going to continue to evolve and in remote parts of the world where we have little access to samples or data it will be difficult to get information in the early stages of a variant evolving,” he said. “This really just emphasises how vital it is to get vaccines rolled out as soon as possible and as widely around the world as we can.”

The WHO says the only “confirmed variants in circulation are: Alpha (B.1.1.7), Delta (B.1.617.2) and Kappa (B.1.617.1)”, adding that “the predominant variant currently in circulation in Nepal is Delta (B.1.617.2)”, namely the Indian variant.

Nepal’s Ministry of Health and Population has also sought to distance the country from the new variant, with a spokesperson saying that “so far, no new variant has been detected. We have confirmed three variants only.”