Category: Mutation
Japan: Delta sub-lineage AY.29 found in 88% of samples
In the present study, we report a new sub-lineage of the SARS-CoV-2 Delta variant called AY.29, which has C5239T and T5514C mutations. We investigated the monthly trend of AY.29 in Japan within 11,954 Delta variants downloaded on September 3, 2021. Among the total Japanese Delta variants, the AY.29 sub-lineage accounted for 88.4%. In terms of monthly changes, the sequences became predominant in June, and accounted for 93.2% and 94.2% of the reported sequences in July and August, respectively.
Preprint: Genomic Surveillance in Japan of AY.29 – A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations
Image by abdulla binmassam from Pixabay
Delta 4+ variant: Complete vaccine escape & enhanced infectivity with Pfizer vaccine
“Here we suggest an evolutionary pathway by which the Delta variant could achieve complete escape from vaccine-induced immunity”. Although Pfizer-BioNTech BNT162b2-immune sera neutralized the Delta variant, when four common mutations were introduced into the receptor binding domain (RBD) of the Delta variant (Delta 4+), some BNT162b2-immune sera lost neutralizing activity and enhanced the infectivity.
Unique mutations in the Delta NTD were involved in the enhanced infectivity by the BNT162b2-immune sera. Sera of mice immunized by Delta spike, but not wild-type spike, consistently neutralized the Delta 4+ variant without enhancing infectivity.
The 4 key mutations inserted were K417N, N439K, E484K and N501Y.
Preprint: The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines
Public Health England releases detailed vaccine breakthrough information
New C.1.2 variant mutating 41 times a year, twice as fast other known Sars-CoV-2 variants
Scientists first detected C.1.2 in May 2021, finding that it was descended from C.1, which scientists found surprising as C.1 had last been detected in January. The new variant has “mutated substantially” compared to C.1 and is more mutations away from the original virus detected in Wuhan than any other Variant of Concern or Variant of Interest detected so far worldwide.
The study also found that the C.1.2 lineage has a mutation rate of about 41.8 mutations per year, which is nearly twice as fast as the current global mutation rate of the other variants. The scientists stated that this short period of increased evolution was also seen with the Alpha, Beta and Gamma variants, suggesting that a single event, followed by a spike in cases, drove faster mutation rates.
Medrxiv preprint: The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection
Delta attempting to brute-force its way past the human immune system
Photo by Abby Savage on Unsplash
Preprint: Just three mutations for SARS-CoV-2 to escape from highly neutralizing convalescent plasma
“Only three mutations were sufficient to generate this escape variant.” This work shows that, under strong immune pressure, SARS-CoV-2 can use mutations in both the N-terminal domain and the receptor-binding domain to escape potent polyclonal neutralizing responses. Indeed, after a long period under immune selective pressure, SARS-CoV-2 evolved to evade the immunity of a potent polyclonal serum from a COVID-19 convalescent donor. Only three mutations were sufficient to generate this escape variant. The new virus was resistant to 70% of the neutralizing antibodies tested and had a decreased susceptibility to all convalescent sera.
Preprint: SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
Delta attempting to brute-force its way past the human immune system
Delta attempting to brute-force its way past the human immune system
The Delta variant of Sars-CoV-2 seems to have taken a leaf from a computer hacker’s manual by attempting to brute-force its way past human and vaccine immunity systems by spitting out slightly mutated versions of itself almost on a daily basis.
Similar to cracking a password, brute-forcing means that the virus is trying every possible combination of variations to find the most effective one, and it’s doing it incredibly quickly. The most successful new mutations then become dominant through selection pressure.
Many of these new Delta plus variants are distinguishable only by a single mutation, but the brute-force technique the virus is now using represents the biggest threat to humanity so far, as we have no obvious means to prevent it.
For example, two weeks ago, we took a snapshot of Outbtreak.info that showed a big rise in the AY.3 Delta plus variant in the USA.
Now, just two weeks later, the AY.3 variant has already been supplanted by the AY.4 variant:
The number of Delta plus variants seems to be rising ever more quickly, each variant with its own individual key combination to try to pick the immunity lock. With no lockout mechanism for failed attempts, the virus can just keep trying until it succeeds.
Here’s a list of the Delta Plus variants so far, taking us up to AY.15, with many more to be added soon we’re sure:
AY.1 United States of America 44.0%, Portugal 10.0%, United Kingdom 10.0%, Japan 10.0%, Switzerland 7.0% 2021-04-07 243 562 Alias of B.1.617.2.1, in several European countries, from pango-designation issue #95
AY.2 United States of America 99.0%, Mexico 0.0%, Spain 0.0%, Aruba 0.0%, Albania 0.0% 2021-03-31 201 1232 Alias of B.1.617.2.2, in USA with K417N, from pango-designation issue #107
AY.3 United States of America 98.0%, Mexico 1.0%, United Kingdom 0.0%, Japan 0.0%, Germany 0.0% 2021-04-13 846 7503 Alias of B.1.617.2.3, USA lineage, from pango-designation issue #121
AY.3.1 United States of America 100.0%, India 0.0% 2021-05-18 197 983 Alias of B.1.617.2.3.1, USA lineage, from pango-designation issue #147
AY.4 United Kingdom 68.0%, United States of America 12.0%, Denmark 3.0%, Spain 2.0%, France 2.0% 2021-01-05 3684 152304 Alias of B.1.617.2.4, UK lineage, from pango-designation issue #180
AY.5 United Kingdom 68.0%, Portugal 12.0%, Spain 4.0%, France 4.0%, Ireland 3.0% 2021-04-15 436 6837 Alias of B.1.617.2.5, UK lineage, from pango-designation issue #180
AY.6 United Kingdom 79.0%, United States of America 8.0%, Ireland 2.0%, Italy 2.0%, Denmark 1.0% 2021-01-08 201 7007 Alias of B.1.617.2.6, UK lineage, from pango-designation issue #180
AY.7 Denmark 71.0%, United Kingdom 23.0%, Italy 3.0%, France 1.0%, Germany 1.0% 2021-05-01 134 6417 Alias of B.1.617.2.7, UK lineage, from pango-designation issue #180
AY.7.1 4624 0 Alias of B.1.617.2.7.1, Denmark lineage
AY.7.2 342 0 Alias of B.1.617.2.7.2, predominantly Italy lineage in multiple other European countries
AY.8 United Kingdom 100.0%, Australia 0.0%, Belgium 0.0% 2021-04-20 703 707 Alias of B.1.617.2.8, UK lineage, from pango-designation issue #180
AY.9 United Kingdom 64.0%, Denmark 11.0%, Germany 5.0%, Switzerland 4.0%, Belgium 3.0% 2021-04-01 322 6892 Alias of B.1.617.2.9, UK lineage, from pango-designation issue #180
AY.10 United Kingdom 73.0%, Canada 8.0%, United States of America 7.0%, Gambia 5.0%, France 2.0% 2021-04-12 71 771 Alias of B.1.617.2.10, UK lineage, from pango-designation issue #180
AY.11 United Kingdom 33.0%, United States of America 16.0%, South_Africa 11.0%, Turkey 10.0%, Ireland 6.0% 2021-02-06 522 2138 Alias of B.1.617.2.11, UK lineage, from pango-designation issue #142
AY.12 Denmark 11.0%, United States of America 11.0%, United Kingdom 10.0%, Germany 10.0%, Israel 7.0% 2020-09-07 579 26845 Alias of B.1.617.2.12, Israel lineage, from pango-designation issue #170
AY.15 94 0 Alias of B.1.617.2.15, Canada lineage
Lineage information courtesy of cov-lineages.org
280 cases of Delta variant with N501Y, some with E484K too
Delta + Alpha + Beta + Gamma recombinant variant found in Turkey.
I'm observing some interesting development in Turkey since some weeks. Since 28/7/2021 of about 3.200 Turkish GISAID sequences around 280 are showing Delta with additional mutations: N501Y known from Alpha and E484K from Beta/Gamma.
This could mean even higher transmissibility
— Gönndalf (@drallcome) August 15, 2021
Image by Elliot Alderson from Pixabay
USA: All captive mink in Oregon must be vaccinated by 31st August 2021
By August 31, 2021, any person holding captive mink in Oregon must vaccinate all captive mink on their premises against the SARS-CoV-2 virus using an approved vaccine according to all vaccine manufacturer instructions. Any captive mink born or imported after August 31, 2021 must be vaccinated within 120 days of the birth of any captive mink, or within 60 days of the date that any captive mink are imported into Oregon.
SURVEILLANCE TESTING FOR SARS-COV-2 IN MINK
Any person holding captive mink in Oregon must participate in surveillance testing for SARS-CoV-2 according to guidelines established by the Oregon Department of Agriculture in cooperation with the U.S. Department of Agriculture.
Oregon Department of Agriculture Statement
** We know that vaccines don’t prevent transmission of, or infection by, the Delta variant of Sars-CoV-2. It’s unlikely that vaccinating mink will prevent mutations of the virus being created either. Not destroying these animals is a huge and unnecessary risk to humanity. Ed.**
Mink: 100% infection, recovery and then 75% re-infection of farmed mink
Preprint: Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
In this study, we reported the emergence and spread of the novel B.1.621 lineage of SARS-CoV-2, a new VOI with the insertion 146N and several amino acid substitutions in the Spike protein (T95I,Y144T, Y145S, R346K, E484K, N501Y and P681H). Although B.1.621 does not meet all of the VOC classification criteria so far, the set of mutations gathered the Spike protein could confer a synergistic impact on attributes such as reduction of vaccine-induced protection from severe disease, increased transmission and disease severity
Medrxiv preprint: Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Image by gustavo9917 from Pixabay
USA: Republican Mike McCaul’s final report into the origins of the Sars-CoV-2 pandemic
Mike McCaul’s final report on the origins of the pandemic can be downloaded here.
A House Republican lawmaker’s investigation into the origins of COVID-19 is raising concerns that the pandemic outbreak stemmed from a genetically modified virus which leaked from the Wuhan Institute of Virology, the Chinese city where the disease was first detected in December 2019.
USA: AY.3 genomes increasing faster than Delta B.1.617.2
A long and detailed Twitter thread by Vinod Scaria on the rise of the AY.3 Delta plus variant in the USA which seems to be outcompeting Delta B.1.672 in some states. Outbreak.info is showing that AY.3 genomes are found in 37% of recent sequences.
Closely tracking the delta+ lineages now across the world, one of the lineages AY.3 seems to be emerging in the United States of America. This tweetorial is to summarise the observations. I will be updating this thread as new evidence emerges.
Thanks pic.twitter.com/2YtsbqmC6y— Vinod Scaria (@vinodscaria) July 24, 2021
Nextstrain makes AY.3 looks pretty widespread in the US already… pic.twitter.com/jO3hrKLRl3
— Ryan M. Ferris (@rferrisx) July 24, 2021
Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA
Kit Yates on “We have to learn to live with the virus”
What do the people who say “learn to live with the virus” actually mean?
They mean: fail to learn any of the lessons of the last 18 months, fail to mitigate against the spread of the virus and tolerate avoidable deaths and disease burden.
I’d rather we didn’t.
— Kit Yates (@Kit_Yates_Maths) July 30, 2021
Over to you Kirsty….
CDC: the next variant that might emerge, just a few mutations potentially away, could eventually evade our vaccine
CDC Director Rochelle Walensky spells out what the next Sars-CoV-2 variant after Delta may be capable of
CDC Director Dr. Rochelle Walensky says “the big concern is that the next variant that might emerge, just a few mutations potentially away, could eventually evade our vaccine.”
She adds: “Right now … these vaccines operate really well in protecting us…” pic.twitter.com/QfpRhppfqS
— The Recount (@therecount) July 27, 2021
Israel: We have to learn to live with Covid
“We all need to change our thinking and draw a road map for living with Covid,” says Dr. Manfred Green. We disagree, and we will be explaining why we disagree in a post later.
Editors note: This report comes just 48 hours after our warning that Boris Johnson’s government was proposing to his countrymen that they should also “learn to live with Covid” (see original post below).
Have you ever wondered what happens when you search for “We have to learn to live with Ebola”? Try it.
It’s an idea so insane that only one person in recorded history has actually written it down.
Netherlands: the reproduction R rate is now 2.17 – the highest since February 2020
For the first time since the start of the coronavirus pandemic, people in the Netherlands infected with the SARS-CoV-2 virus were likely infecting at least two other people. The basic reproduction (R) number has swelled to an estimated 2.17, said Aura Timen of the RIVM. That estimate suggests 100 contagious people infect 217 others, who can in turn give the infection to 471 more individuals.
The new R-number is an estimate for June 30. It has only been higher on February 24, 2020 when the RIVM model put that number at an estimated 2.18, according to the Ministry of Health’s Coronavirus Dashboard.
The most recent genome sequencing results are showing the Delta variant at about 50% and increasing. There’s undoubtedly a lesson here for Boris Johnson and hos proposed unlocking of the UK in just 6 days time.
OurWorldinData.org is showing the R rate as over 3!
The Netherlands now has one of the HIGHEST R RATES EVER RECORDED in the pandemic. Below we have charted the very few countries that have had similar or higher R rates in the past.
UK: vaccine breakthroughs now nearly HALF of all new Covid-19 cases