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.
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)
Japanese researchers have captured microscopic images of cells infected with coronavirus, using an ultra-high definition camera. A group of Osaka University researchers and NHK jointly carried out the experiment, using an optical microscope equipped with an 8K camera. The images show cultured animal cells starting to deform four hours after they are injected with coronavirus. The cells later break apart into pieces.
In this study, we conducted genetic surveillance and identified R.1 lineage harboring E484K mutation in RBD by whole genome sequencing. The R.1 lineage was observed in three patients and transmitted among relatives in Japan. To investigate the global distribution of R.1 lineage, we next collected registration data from the EpiCoV of GISAID database . As of March 5, 2021, a total of 305 samples of R.1 lineage had been registered from all over the world, with the majority spread in the USA (44%, 135/305) and Japan (28%, 84/305) (Figure 1A and Table 1). R.1 lineage was first reported in Texas, USA at the end of October 2020, and was found in Japan at the end of November 2020. The number of detected lineages has changed in a similar trend between the USA, Japan and other countries (Figure 1A), implying that SARS-CoV-2 R.1 lineage may have emerged in several regions at approximately the same time.
The text of the following statement was released by the Governments of the United States of America, Australia, Canada, Czechia, Denmark, Estonia, Israel, Japan, Latvia, Lithuania, Norway, the Republic of Korea, Slovenia, and the United Kingdom.
The Governments of Australia, Canada, Czechia, Denmark, Estonia, Israel, Japan, Latvia, Lithuania, Norway, the Republic of Korea, Slovenia, the United Kingdom, and the United States of America remain steadfast in our commitment to working with the World Health Organization (WHO), international experts who have a vital mission, and the global community to understand the origins of this pandemic in order to improve our collective global health security and response. Together, we support a transparent and independent analysis and evaluation, free from interference and undue influence, of the origins of the COVID-19 pandemic. In this regard, we join in expressing shared concerns regarding the recent WHO-convened study in China, while at the same time reinforcing the importance of working together toward the development and use of a swift, effective, transparent, science-based, and independent process for international evaluations of such outbreaks of unknown origin in the future.
The mission of the WHO is critical to advancing global health and health security, and we fully support its experts and staff and recognize their tireless work to bring an end to the COVID-19 pandemic, including understanding how the pandemic started and spread. With such an important mandate, it is equally essential that we voice our shared concerns that the international expert study on the source of the SARS-CoV-2 virus was significantly delayed and lacked access to complete, original data and samples. Scientific missions like these should be able to do their work under conditions that produce independent and objective recommendations and findings. We share these concerns not only for the benefit of learning all we can about the origins of this pandemic, but also to lay a pathway to a timely, transparent, evidence-based process for the next phase of this study as well as for the next health crises.
We note the findings and recommendations, including the need for further studies of animals to find the means of introduction into humans, and urge momentum for expert-driven phase 2 studies. Going forward, there must now be a renewed commitment by WHO and all Member States to access, transparency, and timeliness. In a serious outbreak of an unknown pathogen with pandemic potential, a rapid, independent, expert-led, and unimpeded evaluation of the origins is critical to better prepare our people, our public health institutions, our industries, and our governments to respond successfully to such an outbreak and prevent future pandemics. It is critical for independent experts to have full access to all pertinent human, animal, and environmental data, research, and personnel involved in the early stages of the outbreak relevant to determining how this pandemic emerged. With all data in hand, the international community may independently assess COVID-19 origins, learn valuable lessons from this pandemic, and prevent future devastating consequences from outbreaks of disease.
We underscore the need for a robust, comprehensive, and expert-led mechanism for expeditiously investigating outbreaks of unknown origin that is conducted with full and open collaboration among all stakeholders and in accordance with the principles of transparency, respect for privacy, and scientific and research integrity. We will work collaboratively and with the WHO to strengthen capacity, improve global health security, and inspire public confidence and trust in the world’s ability to detect, prepare for, and respond to future outbreaks.
As Japan prepares for its COVID-19 vaccine rollout for its older population next month, a program underway since December in Britain has impressed many older Japanese residents there with its emphasis on a speedy deployment.
Red tape has been cut to allow roughly 30% of the British population to receive their first vaccine doses in just three months.
But it is not something many Japanese who have received vaccination in the U.K. expect to see repeated in Japan, believing prevention of missteps will take precedence over a speedy rollout.
“It took only 10 minutes or so from the time I arrived at the inoculation site till I left,” said Tetsuro Hama, a 72-year-old company operator who has been living in Britain for 48 years.
Japantimes.co.jp report (paywall)
The Philippines now has all three variants of the coronavirus that have been fuelling record-breaking spikes in infections across the globe, and a Philippine variant (PHL-B.1.1.28) that has the same lineage as the infectious Brazilian variant.
There are currently 177 cases of the British variant and 90 cases of the South African variety in the Philippines.
A fourth variant (PHL-B.1.1.28) that originated in the Philippines itself is also spreading. It was first identified in a Filipino who travelled to Japan. This so-called Philippine variant has the same lineage as the Brazilian strain.
Over 90 cases of this local strain are now being monitored.
See also [HERE]: Japan identifies a B.1.1.28 #coronavirus strain with E484K and N501Y mutations from a traveller from the Philippines
See also [HERE]: New #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28
The National Institute of Infectious Diseases, Japan, identified a B.1.1.28 strain with E484K and N501Y mutations from a SARS-CoV-2-positive sample collected on February 25, 2020 at a point of entry to Japan from a traveller from the Philippines（virus name : hCoV-19/Japan/IC-0824/2021, GISAID Accession ID: EPI_ISL_1198832) (1).
These mutations are found in known VOCs (501Y.V2, 501Y.V3). This variant isolate also has the P681H mutation in the spike protein as with B.1.1.7 lineage (VOC-202012/01) which is suggested to be associated with increased transmissibility.
34 draft genome sequences of B.1.1.28 lineage with E484K/N501Y mutations have been uploaded to GISAID from the Philippines (1 sequence on February 26, 33 sequences on March 3) .
The Department of Health, Republic of Philippines, published that they found 34 cases with E484K and N501Y mutations on March 2 (1).
This variant isolate does not meet the criteria of VOC as we do not know how widely this variant strain is spreading within the Philippines and whether this variant strain is associated with the recent increase in reported cases in the Philippines. However, this variant strain may be circulating in the Philippines at a certain level as the similar strain has been reported domestically and identified from travelers.
The potential public health impact from this variant strain shall be considered to be equivalent to those from known VOCs as this variant strain shares the same mutations of concern with VOCs
See also: New #coronavirus variant with #E484K, #N501Y & #P681H mutations found in the Philippines, designated PHL-B.1.1.28
Nearly 400 people in Japan have been infected with a new variant of the novel coronavirus different from those found in Britain, South Africa and Brazil, Japan’s National Institute of Infectious Diseases said Tuesday.
While differing from those discovered earlier in the three countries, the new strain found in Japan shares some commonality with those from South Africa and Brazil, the institute said. It is suspected that the commonality may cause more reinfection and that current vaccines may be less effective against it.
See also: Domestic Influx of B.1.1.316 in Japan
Fujifilm Holdings Corp will restart a clinical trial in Japan of its antiviral drug Avigan for the treatment of COVID-19, the Nikkei newspaper reported on Sunday.
Domestic approval of the drug was delayed after a health ministry panel said in December that trial data was inconclusive. The new study will involve about 270 patients and Fujifilm will aim to seek approval again in October, Nikkei said.
Japan’s government has called on Fujifilm to triple national stockpiles of the drug, which has been approved for COVID-19 treatment in Russia, India and Indonesia.
Image: By Yikrazuul – Own work; PMID 19428599, Public Domain, https://commons.wikimedia.org/w/index.php?curid=32973361
Japan: “Domestic diffusion of strains carrying the Spike protein E484K mutation (Pangolin B.1.1.316)
E484K COVID-19 genome surveillance * 3. mutation to the same Spike protein as the mutant strains (N501Y.V2 and N501Y.V3) reported in South Africa and Brazil from the beginning of December 2020 onwards in the national survey of B.1.1.316 strain (2 cases of airport quarantine, 91 cases throughout Kanto area) was detected (as of 02/02/2021).
The B.1.1.316 strain does not have the N501Y mutation, which is a mutation that may increase infectivity and transmission, and it is presumed that the phenotype is different from that of the mutant strain having the N501Y mutation. According to genome network diagram the evaluation of the , this B.1.1.316 is not at least the genealogy of the current two mainstream strains in Japan, but a 13-base mutation (approximately 7) from the European strain (B.1.1.114) from March to April 2020. There was a time difference of months).
The sample that fills the blank link of this 13-base mutation in the domestic sample has not been specified, and it was judged that the genealogy did not acquire the mutation in Japan. In addition, a search for all GISAID registered genomic information has not identified the country of origin indicating the origin of this influx B.1.1.316 strain (that is, the region such as the United Kingdom cannot be determined). On the other hand, no strains that have acquired the E484K mutation from two mainstream strains in Japan (B.1.1.284 and B.1.1.214) have been detected so far.
Japan has confirmed that a new variant of Sars-COV-2 with the E484K mutation on the spike protein has been found in 91 patients.
An infection cluster emerged at a Tokyo immigration facility, presenting new challenges as the country tries to overcome a third wave of the pandemic.
The new mutant strain, which is partly similar to different variants reported in the U.K. and South Africa, was detected in four infected people who arrived from Brazil, the ministry said.
The National Institute of Infectious Diseases (NIID) said there was no evidence at present that the new variant was highly infectious, but it was investigating whether it could cause severe symptoms and whether or not it is resistant to vaccines.
Of the four people, a man in his 40s showed no symptoms upon arrival, but later developed breathing difficulties and was hospitalized, the ministry said. A woman in her 30 has symptoms such as headache. A male in the 10-19 age group has a fever, while a woman in the same age group is free of symptoms.
There have now been more than 60,000,000 confirmed coronavirus infections globally and the infection rate is still increasing.