Through routine scanning of variation in Delta, a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1. A second clade found in sequences uploaded to GISAID from the USA, now designated AY.2.
As of 16 June 2021, 161 genomes of Delta-AY.1 have been identified on GISAID. from Canada (1), India (8), Japan (15), Nepal (3), Poland (9), Portugal (22), Russia (1), Switzerland (18), Turkey (1), USA (83).
There are currently 38 cases of Delta-AY.1 in England (36 confirmed sequencing and 2 probable genotyping). Cases have been detected in 6 different regions in England. Delta-AY.2 has not been detected in England.
UK Variants of Concern Technical Briefing 15 (PDF download)
According to Bani Jolly of the Institute of Genomics and Integrative Biology, the phylogeny of Delta has two separate clades. While AY.1 is found in a few countries including the UK, India and Nepal, the other clade (AY.2), is largely from the sequences from California (USA).
“The split between the two clades seems to be based on two spike mutations — A222V and T95I. While all sequences in the California cluster share spike A222V, all sequences in the larger international cluster share spike T95I,” Jolly tweeted.
Stating that AY.1 has arisen independently a number of times and could be more prevalent than observed in countries with limited genomic surveillance, she tweeted that given that Delta is a variant of concern, it is important to take note of any sub-lineages that may emerge.
The Nepalese Ministry of Health and Population (MoHP) said that out of 47 confirmed delta variant samples, nine were found to have K417N mutations.
According to the ministry, the new mutation has also been named AY.1 (aka Delta-AY.1 or “Mountaineers” variant).
Issuing a press statement on Monday, the MoHP revealed that AY.1 mutation has been confirmed in more than 10 countries, including Nepal.
With this, Nepal has witnessed Alpha and Delta as the variant of concern and Kappa variant of concern, the Ministry said.
The Ministry had selected 48 samples from the National Public Health Laboratory from the people of all age groups from April 29 to June 3 and tested them in WHO identified Center for Excellence in Genomics, The Institute of Genomics and Integrative Biology (IGIB).
Out of them 47 samples had come with delta variant B.1.617.2 and one had come with alpha variant B.1.1.7. Among the 47 delta variant samples nine had shown K417N mutation, the Ministry said.
Of the 36 cases of Delta-AY.1 (mountaineers) variant, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS).
“Through routine scanning of variation in Delta a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1. A second clade found in sequences uploaded to GISAID from the USA. There is limited epidemiological information available at present.
As of 7 June 2021, 63 genomes of Delta with K417N have been identified on GISAID. from Canada (1) Germany (1), Russia (1), Nepal (2), Switzerland (4), India (6), Poland (9), Portugal (12), Japan (13), USA (14).
There are currently 36 cases of Delta-AY.1 in England (35 confirmed sequencing and 1 probable genotyping) plus an additional 10 sequences which include some cases in other UK nations and some genomes for which case data is being sought. The first 5 cases were sequenced on 26 April 2021 and were contacts of travellers to Nepal and Turkey. All these cases were detected in the West Midlands. Cases have been detected in 6 different regions in England (Table 21, Figure 26). The majority of cases are in younger individuals, with 2 cases of age 60 or over (Figure 27). Out of the 36 cases, there were 11 travel associated cases (6 travellers and 5 cases amongst contacts of travellers). Twelve cases have no history of travel or contact with travellers. Countries of travel included red-list countries (Nepal and Turkey), amber-list countries (Malaysia) and green-list countries (Singapore).
Of the 36 cases, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS), when linked on NHS number. Of these, 18 cases occurred in people who were not vaccinated, 2 cases in people who had received their first dose within 21 days of specimen date, 5 cases in people who had received their first dose more than 21 days after specimen date. There was a total of 2 cases where there were more than 14 days between the second dose of vaccine and a positive specimen. No deaths have been recorded amongst the 36 cases.”
PHE download – SARS-CoV-2 variants of concern and variants under investigation in England – Technical briefing 15 (PDF)
The Delta variant with the K417N mutation, also known as the “Mountaineers” variant, has cropped up 14 times in Japan, and 13 of those samples were in travellers from Nepal – mostly climbers from Everest expeditions. At least 100 cases were reported at the Everest base camp, it is believed that the variant could have been spread by climbers ascending the mountain despite widespread national lockdowns across the globe. Cases have also been identified in India, Japan, Portugal, and the UK.
According to Dr Jeff Barrett, director of the COVID-19 Genomics Initiative at the Wellcome Sanger Institute in the UK, at least one case has been found in the US.
The mountaineers variant B.1.617.2 + K417N has also been blamed for the axing of Portugal from the UK’s green travel list. See this report
The Nepalese Ministry of Health and Population (MoHP) has said that no new variant of coronavirus has been detected in the country so far. According to the Spokesperson at the MoHP, Dr. Krishna Prasad Paudel, no new variant has been detected in the country as reported by British newspapers. He said that the Ministry was not aware of any such variant called ‘Nepal variant’ as no such variant has been detected. According to him, the Ministry has also written to the concerned health agency of the United Kingdom about the news reports.
Meanwhile, the World Health Organization (WHO) said it is not aware of any new variant of SARS-CoV-2 being detected in Nepal. WHO statement comes after British tabloid Daily Mail reported a news story with the headline: “Nepal Variant Threat to Our Holidays”.
WHO said that no new variant, other than the previously confirmed ones, has been detected in Nepal.
“WHO is not aware of any new variant of SARS-CoV-2 being detected in Nepal. The three confirmed variants in circulation are Alpha (B.1.1.7), Delta (B.1.617.2), and Kappa (B.1.617.1). The predominant variant currently in circulation in Nepal is Delta (B.1.617.2),” the WHO tweeted.
So, more of a “Western mountaineers” variant then?
Grant Shapps, UK Transport Secretary “we’ve seen two things really which caused concern. One is the positivity rate has nearly doubled since the last review in Portugal and the other is there’s a sort of Nepal mutation of the so-called Indian variant which has been detected and we just don’t know the potential for that to be a vaccine-defeating mutation”
Time for a Cabinet reshuffle surely?
There’s plenty of coverage in the UK press today about a so-called “Nepal Variant” of Sars-CoV-2. But what is the “Nepal Variant”? Does it exist? The quick answer is no, it doesn’t exist.
Nepal has seen a huge rise the Delta variant B.1.617.2 recently due to its proximity to India, but then Britain has also seen a huge increase in the B16172 Delta variant too. No asian newspapers have mentioned a “Nepal Variant” recently.
In fact, the ONLY place we can find mention of a “Nepal Variant” is in the UK newspapers today:
And all this, just three days after the WHO agreed to rename Sars-CoV-2 variants to avoid stigmatisaton. The UK press is awash with stories about a new “Nepal Variant”, stigmatising a country that is presumably too small and too busy fighting Covid-19 to respond.
** UPDATE 3rd June 2021: “The World Health Organisation has said it is “not aware” of any variant of concern detected in Nepal. It comes after reports that Portugal may be dropped from the green list amid fears a new variant is spreading there.”
** Update 2: We note that all three of the above mentioned newspapers have now changed their copy and removed any mention of a “Nepal Variant” although the original URL’s are still in use.
Nepal recorded a total of 9,196 new cases of coronavirus infection in the past 24 hours. According to the Ministry of Health and Population, 9,023 persons have been tested positive for COVID-19 through the RT-PCR method while 173 have been tested positive through the Antigen method. According to the Ministry, 3,089 persons in Kathmandu, 643 in Lalitpur, and 374 in Bhaktapur have been tested positive for the pandemic virus, making the capital valley’s fresh coronavirus cases 4,106 in past 24 hours.
According to the Ministry, 50 people have succumbed to COVID-19 related death in past 24 hours taking the death tally to 3,579 as of Friday afternoon.
Authorities in Nepal are grappling to contain the rapid rise of COVID-19 cases with experts fearing that thousands of people in the Himalayan state have caught the more infectious mutant strains emerging out of India. Nepal, which shares a long porous border with India, reported 3,032 new infections on Sunday, the highest daily number recorded this year.
It took the total caseload since the pandemic first struck Nepal to 300,119 with 3,164 deaths so far, according to government data.
“We have detected the UK variant and the double mutant variant detected in India,” Krishna Prasad Paudel, the director of Nepal’s Epidemiology and Disease Control Department Paudel told Reuters news agency, adding that experts were checking for other variants too.
SEE UPDATE 01/05/2021: