Japan Identifies Another Alarming Variant With E484K Mutation That Likely Originated From South-East Asia, Turkey, France, India Also Sees New Variants

Japanese Authorities have identified another alarming SARS-CoV-2 variant that bears the immune evasive mutation E484K. Japanese health authorities have confirmed the identification of the  new variant of  SARS-CoV-2 coronavirus also said that an infection cluster involving this new variant has emerged at a Tokyo immigration facility, presenting new challenges as the country tries to overcome a third wave of the pandemic.


 
The reported new variant (The variant has yet to be named and the total number of mutations and deletions on it are still being studied) has been found in 91 cases in the Kanto area of eastern Japan and in 2 cases at airports, Chief Cabinet Secretary Katsunobu Kato told Thailand Medical News late on Friday via an email message.
 
The Japanese government is raising surveillance against mutant varieties as they may be more resistant to vaccines, which Japan started to distribute this week.
 
Kato added, “It may be more contagious than conventional strains, and if it continues to spread domestically, it could lead to a rapid rise in cases.”
 
There are speculations that the new variant likely originated from a South-East Asian country with a reputation of falsely boasting about its so called efficiency in controlling the COVID-19 crisis in its own country despite lack of mass testing, strict laws of divulgence on any data about the status of SARS-CoV-2 infections in its country along with lack of frequent genomic sequencings of all new cases. The country is also famous for its citizens coming to work illegally in East Asian countries as masseuses or as prostitutes.
 
Japanese experts confirmed that the new variant is different from other types that have been found sporadically in Japan and also different from those found in UK, South Africa or Brazil according to the National Institute of Infectious Diseases. It has the E484K mutation on the spike protein of the virus that has been found in other variants, which may undermine the effectiveness of vaccines.
 
It was reported that about 130 detainees at the facility have been tested positive for the SARS-CoV-2 for the virus while a number are carrying the new variant, according to a spokesperson for the Tokyo Regional Immigration Bureau.
 
The Immigration representative declined to comment on the nationality of the infected detainees, citing privacy concerns.
 
The country’s detention system for immigration law violators and asylum seekers has been widely criticized for its medical standards, monitoring of detainees and response to emergencies.
 
Motoko Yamagishi, the head of a migrants-rights group commented, “Many detainees are locked in small, closed spaces. It is regrettable that such a outbreak happened in the centre.”
 
A.27 And A.28-New Variants Of SARS-CoV-2 19B Clade Emerging In Turkey And France
 
Meanwhile virologists and genomic specialists are reporting on the emergence of new variants of the SARS-CoV-2 19B clade in countries like Turkey and also France.
 
The variant in France has been named as the A.28 variant and carries the 69-70 deletion, the mutations N501T (not Y) and H655Y. (This variant is picked up by the qPCR S drop).Mores studies are underway on this variant. https://github.com/cov-lineages/pango-designation/issues/12
 
The variant in Turkey was identified in the region of Mayotte and is named as the A.27 variants and carries 18 changes in the long branch leading to this cluster, including 7 NS changes in the spike (L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V), on a 614D background. https://github.com/cov-lineages/pango-designation/issues/11
 
India Has More Than 5,000 Unique SARS-CoV-2 Variants With Those Possessing The N440K Mutation Spreading Fast In The Southern States!
 
A disturbing study finding has emerged that India has more than 5,000 unique variants and those with the N440K mutation are fast spreading in the Southern States. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab136/6137553
 
The researchers from the Hyderabad-based Centre for Cellular and Molecular Biology (CSIR-CCMB) said there is emerging evidence that coronavirus variant N440K is spreading "a lot more" in southern states in the country.
 
Experts from CSIR-CCMB, in the study, have presented an exhaustive analysis of over 5,000 coronavirus variants in India and how they have evolved over the course of the pandemic.
 
Corresponding author Dr Rakesh Mishra, Director, CCMB told Thailand Medical News, "The novel variants that are worrying many countries globally have been identified with only a low prevalence in India so far. These include the variants with immune-escape E484K mutation and the N501Y mutation with higher transmission rate. However, their apparent low prevalence might be simply because not enough sequencing has been done. More coronavirus genomes need to be sequenced across the country to accurately identify the emergence of these and other new variants.”
 
The study team from CSIR-CCMB also finds that a few novel variants are spreading more in some states of India.
 
Dr Mishra added, "We now have emerging evidence that N440K is spreading a lot more in southern states. Closer surveillance is needed to understand its spread properly. Accurate and timely detection of new variants that may show greater infectivity or worse clinical symptoms, including immune escape, will be extremely important to preempt disastrous consequences.”
 
The study team explain how different SARS-CoV-2 coronavirus variants gained prevalence in India during the last year.
 
Dr Mishra further added, "One of the variants called the A3i had mutations that were predicted to make its spread slower. The study confirms that it was overtaken by the globally prevalent A2a variant, carrying the D614G mutation, by June 2020. The A2a variant has remained in global dominance for the major part of the year 2020. The recently discovered variants in many countries have raised concerns because of their mutations in the Spike protein that makes the coat of the virus and come in contact with the human cells.”
 
He elaborated, "The Spike protein is required for binding to the receptors on human cells. Mutations in this protein can help the virus in some cases. It can increase viral transmission rates by enhancing its affinity to human receptors. Some of these coronavirus variants can also be immune-escape and cause reinfection. Our immune systems cannot identify them from previous infections because of the changes in their protein structures.”
 
Dr Divya Tej Sowpati, the co-corresponding author added, "Spike protein mutations have implications in COVID-19 surveillance and management, vaccines, therapeutics, and the emergence of re-infections. We need to have a focused approach towards monitoring the virus mutations. India has not been sequencing SARS-CoV-2 isolates to full capacity, having deposited only about 6,400 genomes so far. The Indian government's initiative of INSACOG, which aims to sequence 5 per cent of all positive cases, should soon address this."
 
The lead author of the study, Dr Surabhi Srivastava, said the success in the development and administration of vaccines is promising but other non-therapeutic prevention measures, such as masks and physical distancing, will still prove to be the most effective in curbing further spread of the disease.
Lesser spread of the virus also decreases the scope for emergence and accumulation of harmful mutants.
 
She added, "The take-home of this comprehensive work is that due to the natural process of mutation, variants will keep emerging. The best way to control the potential damage is to exercise extensive genome surveillance and take measures to prevent the spread of new variants as and when detected.”
 
Thailand Medical News will be covering more on newly emerging variants across the world in the next few days. We do however apologize if our coverage is not in detail as the author is currently driving through bad weather from New York to California and will only provide updates during stops.
 
For more on SARS-CoV-2 variants, keep on logging to Thailand Medical News