SARS-CoV-2 Mutations: B.1.1.7, B.1.351 & D614G Research

[Evo]

And now we can add MU.

The World Health Organization said a strain of the Coronavirus that causes COVID-19 and that was first detected in Colombia in January has become a “variant of interest” and will be closely monitored for signs it is resistant to the vaccines that have been authorized for use so far.

In its weekly epidemiological update, the agency said the variant, B.1.621, to which it has assigned the Greek letter mu, has “a constellation of mutations that indicate potential properties of immune escape.”

https://www.abcactionnews.com/news/...-organization-monitoring-new-covid-19-variant

 

[Ygggdrasil]

Another new variant C.1.2 has been detected in South Africa:

South African scientists have detected a new Coronavirus variant with multiple mutations but are yet to establish whether it is more contagious or able to overcome the immunity provided by vaccines or prior infection.

The new variant, known as C.1.2, was first detected in May and has now spread to most South African provinces and to seven other countries in Africa, Europe, Asia and Oceania, according to research which is yet to be peer-reviewed.

It contains many mutations associated in other variants with increased transmissibility and reduced sensitivity to neutralising antibodies, but they occur in a different mix and scientists are not yet sure how they affect the behaviour of the virus. Laboratory tests are underway to establish how well the variant is neutralised by antibodies.

https://www.reuters.com/world/afric...iant-still-studying-its-mutations-2021-08-30/

Here's the non-peer-reviewed pre-print describing the variant:

The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection
https://www.medrxiv.org/content/10.1101/2021.08.20.21262342v2

SARS-CoV-2 variants of interest have been associated with increased transmissibility, neutralization resistance and disease severity. Ongoing SARS-CoV-2 genomic surveillance world-wide has improved our ability to rapidly identify such variants. Here we report the identification of a potential variant of interest assigned to the PANGO lineage C.1.2. This lineage was first identified in May 2021 and evolved from C.1, one of the lineages that dominated the first wave of SARS-CoV-2 infections in South Africa and was last detected in January 2021. C.1.2 has since been detected across the majority of the provinces in South Africa and in seven other countries spanning Africa, Europe, Asia and Oceania. The emergence of C.1.2 was associated with an increased substitution rate, as was previously observed with the emergence of the Alpha, Beta and Gamma variants of concern (VOCs). C.1.2 contains multiple substitutions (R190S, D215G, E484K, N501Y, H655Y and T859N) and deletions (Y144del, L242-A243del) within the spike protein, which have been observed in other VOCs and are associated with increased transmissibility and reduced neutralization sensitivity. Of greater concern is the accumulation of additional mutations (C136F, Y449H and N679K) which are also likely to impact neutralization sensitivity or furin cleavage and therefore replicative fitness. While the phenotypic characteristics and epidemiology of C.1.2 are being defined, it is important to highlight this lineage given its concerning constellations of mutations.

Yesterday (9/1), the WHO designated the C.1.2 variant as an alert for further monitoring: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

 

[Astronuc]

Another new variant C.1.2 has been detected in South Africa:

Jan 28 - https://www.cdc.gov/coronavirus/201...riefs/scientific-brief-emerging-variants.html
From the CDC, "In South Africa, another variant of SARS-CoV-2 (known as 20H/501Y.V2 or B.1.351) emerged independently of B.1.1.7. This variant shares some mutations with B.1.1.7. Cases attributed to this variant have been detected in multiple countries outside of South Africa. This variant was reported in the US at the end of January 2021."

Is C.1.2 related to the other earlier variants?

 

[Ygggdrasil]

Jan 28 - https://www.cdc.gov/coronavirus/201...riefs/scientific-brief-emerging-variants.html
From the CDC, "In South Africa, another variant of SARS-CoV-2 (known as 20H/501Y.V2 or B.1.351) emerged independently of B.1.1.7. This variant shares some mutations with B.1.1.7. Cases attributed to this variant have been detected in multiple countries outside of South Africa. This variant was reported in the US at the end of January 2021."

Is C.1.2 related to the other earlier variants?

In the paper linked above, genetic analysis shows that C.1.2 does not appear to be closely related to or directly descended from the Beta variant (B.1.351) (in fact, the aforementioned Mu variant, colored red and labeled 21H in the figure, is closer to Beta) :

https://www.medrxiv.org/content/10.1101/2021.08.20.21262342v2

The C.1.2 variant arose from the C.1 variant, a variant that was present in the first wave of COVID-19 in South Africa, but had seemed to disappear by Jan 2021. C.1.2 began rising in prevalence in May 2021. Of the major VOCs/VOIs, C.1.2 seems most closely related to Lambda (C.37).

Shows how global viral evolution is where a new variant from Colombia (Mu) is closely related to an older variant from South Africa (Beta), whereas the newer variant from South Africa (C.1.2) is more closely related from a different variant from South America (Lambda, which was first detected in Peru).

 

[Sagittarius A-Star]

And now we can add MU.
https://www.abcactionnews.com/news/...-organization-monitoring-new-covid-19-variant

A new COVID-19 variant called Mu that might be able to evade immunity from vaccines has been detected in almost every US state

Source:
https://www.businessinsider.com/covid-19-mu-variant-detected-in-47-us-states-and-dc-2021-9

Here, we demonstrate that the Mu variant is highly resistant to sera from COVID-19 convalescent and BNT162b2-vaccinated individuals. Direct comparison of different SARS-CoV-2 spike proteins revealed that Mu spike is more resistant to serum-mediated neutralization than all other currently recognized variants of interest (VOI) and concern (VOC).

Source:
https://www.biorxiv.org/content/10.1101/2021.09.06.459005v1

 

[Astronuc]

So, as far as I can tell, C.1.2 is still a VOI and doesn't yet have a Greek letter assigned. Back in July, the B.1.621 variant, which was "being commonly referred to as the Colombian Variant, was responsible for 10 percent of COVID patients at one Miami hospital," according to a health official's report at the time (last week in July). Now it's detected in nearly every US state.

https://www.cbc.ca/news/health/latest-coronavirus-variants-mu-c12-1.6161194
According to the article by CBC.ca dated September 02, . . .

The [Mu] variant was first detected in Colombia back in January, and since then, the country has experienced hundreds of cases and the variant has also been reported in 39 other countries around the world.

Here in Canada, it's barely making a splash: Mu cases have been reported for weeks, but so far, the variant hasn't made up more than three per cent of cases in any given week and recently totalled just 0.3 per cent — though federal data since mid-July is still accumulating and could change.

with respect to C.1.2

A team of scientists from South Africa detected the new variant, which was first observed in May and has since spread to seven other countries in Africa, Europe, Asia and Oceania, according to a preprint study that hasn't yet been peer-reviewed.

"It's still not clear where this came from," noted Dr. Zain Chagla, an infectious diseases specialist with McMaster University in Hamilton. "It was first identified in South Africa but people need to know that South Africa has actually quite good sequencing networks and so it may not be the origin."

 

[Ygggdrasil]

So, as far as I can tell, C.1.2 is still a VOI and doesn't yet have a Greek letter assigned.Back in July, the B.1.621 variant, which was "being commonly referred to as the Colombian Variant, was responsible for 10 percent of COVID patients at one Miami hospital," according to a health official's report at the time (last week in July). Now it's detected in nearly every US state.

https://www.cbc.ca/news/health/latest-coronavirus-variants-mu-c12-1.6161194
According to the article by CBC.ca dated September 02, . . .

with respect to C.1.2

The WHO maintains three levels of concern regarding novel variants: variants of concern (VOC), variants of interest (VOI) and alerts for further monitoring. See the WHO page on variants for more information on the definitions: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

Currently, C.1.2 is classified as an alert for further monitoring (date of designation 1-Sep-2021). Only VOC and VOI are assigned Greek letters. We await further research/epidemiology on C.1.2 to see if it warrants classification as a VOI.

Currently, >99% of infections in the US are due to Delta:

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

Mu currently accounts for only 0.1% of infections in the US. It will be important to track this number over the next few months to see if Mu infections continue to rise even as Delta infections (hopefully) begin to fall.

Here's data from Nextstrain showing the prevalence of mutations at position 145 of the spike protein (the Y145S mutation appears to be fairly specific for Mu):

https://nextstrain.org/ncov/gisaid/global?c=gt-S_145

The global prevalence of this mutation has remained fairly low low since it first appeared ~ March 2021, which suggests that it probably is not more transmissible than Delta.

 

[Astronuc]

One point I was trying to make, but perhaps not clearly, is that back in July, the B.1.621 variant, which was then commonly referred to as the Colombian Variant, did not have a Greek letter. Then in less than 5 weeks based on Evo's post, it received a letter, and went from Florida to ~47 other states.

And now we can add MU.

I'm curious about the statement in the CBC.ca article, "It was first identified in South Africa but people need to know that South Africa has actually quite good sequencing networks and so it may not be the origin." I'm wondering if the travel of people between South America and Africa, or South Africa, is being monitored, partly based on Ygggdrasil comment: "the newer variant from South Africa (C.1.2) is more closely related from a different variant from South America (Lambda, which was first detected in Peru)." Could asymptomatic, infected people be carrying variants across borders?

Clearly, the variant from Colombia made it to Miami, Florida.

 

[Astronuc]

And now we can add MU.

https://www.abcactionnews.com/news/...-organization-monitoring-new-covid-19-variant

Mu variant outbreak in Florida with hundreds of cases!
https://www.newsweek.com/mu-covid-variant-outbreak-florida-hundreds-detected-cases-1627068

https://www.baynews9.com/fl/tampa/news/2021/09/09/mu-variant-in-florida

Mu appears to be very rare right now. According to the online database outbreak.info, mu makes up less than half a percent of global COVID cases. CDC data shows it made up just .1% of US cases last week. Florida does have more cases of the mu variant than any state except California. Outbreak.info shows 305 cases have been reported here. Teng said direct flights from Colombia to Florida are one possible reason that number is higher than other states. Iovine said it's important to keep that total in perspective. "If you look at the overall number of cases that we're having in Florida...305 is very little, relatively speaking," she said.

 

[Ygggdrasil]

From the CDC's Sep 10 COVID Data Tracker Weekly Review:

On August 30, 2021, the Mu (B.1.621) variant of the virus that causes COVID-19 was classified as a Variant of Interest (VOI) by the World Health Organization (WHO). CDC has not escalated this variant to a VOI in the United States, where the Mu variant reached its peak in late June (<5% of circulating variants) and has steadily decreased since.

https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html

The fact that it's prevalence has been decreasing in the past few months (as Delta has risen) suggests that it is less transmissible than Delta (consistent with some of the other data I've posted above). Mu is still definitely capable of causing outbreaks, but those outbreaks are likely less of a concern than the hundreds of thousands of cases of Delta currently out there.

 

[Astronuc]

A review of Coronavirus specimens collected in Los Angeles County shows the mu and lambda variants were circulating earlier this summer, but the delta variant remains dominant, officials said Friday.

The highly contagious delta has “crowded out all of the other previously circulating strains,” now accounting for 100% of all strains sequenced in L.A. County, said Barbara Ferrer, the county’s public health director.

But when the lab that sequences the cases re-analyzed samples with an updated version of the genetic library used to identify variants, it reclassified many older specimens as mu or lambda variants.

The county is now reporting a total of 232 cases linked to the mu variant so far, while last week it had said 167 cases were identified to date. Another 28 cases were linked to the lambda variant.

https://ktla.com/news/local-news/mu...lier-than-thought-but-delta-crowded-them-out/

So how did Mu get there? Direct flights from Colombia, or flights from Miami.

On September 6, LA Times reported only 167 cases attributed to Mu variant.
https://www.latimes.com/california/...-variant-recorded-in-167-people-in-l-a-county

https://www.forbes.com/sites/brucel...les-county-reports-167-cases/?sh=41693bd13032

While it sounds a bit like how a cat would say “new variant,” the Mu variant of the Covid-19 Coronavirus is far from a catastrophe. There's nothing yet to suggest that the current Covid-19 vaccines won’t work against the newly-named Mu variant. However, not enough is really known about this latest addition to the World Health Organization (WHO) “Variants of Interest” list to draw any strong conclusions. Nonetheless, it has already made its way to nearly every state in the U.S. And that includes California.

Yes, according to an announcement from the Los Angeles County Department of Public Health on Friday, the Mu variant of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has been in Los Angeles County since at least mid-June. From June 19 through Augusts 21, the Department has found the Mu variant in 167 samples. Although the variant only accounts for less than one percent of all Covid-19 Coronavirus samples that have been sequenced in California and the U.S., it’s clear that the Mu variant had entered the U.S. by the start of Summer.

Mu variant found in every US state bar Nebraska​

https://www.independent.co.uk/news/...ant-nebraska-florida-california-b1915826.html

Is Nebraska even looking? I have seen maps where Nebraska isn't reporting Covid infections.

 

[Astronuc]

The fact that it's prevalence has been decreasing in the past few months (as Delta has risen) suggests that it is less transmissible than Delta (consistent with some of the other data I've posted above). Mu is still definitely capable of causing outbreaks, but those outbreaks are likely less of a concern than the hundreds of thousands of cases of Delta currently out there.

The Delta variant was first identified in India in December 2020. Did it first infect people within 50 to 100 miles of an international airport?

WHO profile of Delta
First sample documented - India, Oct-2020, VOI: 4-Apr-2021, VOC: 11-May-2021
https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

https://cov-lineages.org/lineage.html?lineage=B.1.617.2 First date 2020-08-21, which is earlier than Oct-2020

https://cov-lineages.org/lineage_list.html

I think Mu is just getting started in the US.

From WHO page, VOI Table: Mu (B.1.621); Earliest documented sample, Colombia, Jan-2021; VOI: 30-Aug-2021

B.1.621
United States of America 45.0%, Colombia 14.0%, Mexico 10.0%, Spain 9.0%, Chile 4.0%
First date identified: 2021-01-11

B.1.621.1
United States of America 63.0%, Spain 12.0%, Austria 5.0%, Dominican_Republic 5.0%, Switzerland 3.0% First date identified: 2021-04-14

https://cov-lineages.org/index.html#global_reports

 

[atyy]

Chise on Twitter: "Mu (B.1.621) is NOT vaccine resistant. Stop the misinformation. Fold-reduction in LIVE VIRUS studies is less that than of Beta, Gamma and Delta."

 

[Astronuc]

Welcome R.1 variant.

A new variant has been detected in a Kentucky nursing home, infecting 45 residents and health care personnel. Many of these infections arose in fully vaccinated individuals. The variant, which originated in Japan, has over 10,000 entries in the GISAID SARS-CoV-2 database. The variant contains five mutations previously noted in variants of concern or interest, two of which are in the Spike protein (Figure 1). It also contains many unique mutations. Here we describe the potential effects of each mutation on replication, immune evasion, and pathogenesis.

https://www.forbes.com/sites/willia...new-usjapan-variant-to-watch/?sh=626ab6b35097

The R.1 variant shares a common origin with all variants of interest or concern. They are marked by what I call the Triad, three mutations, one the 5’ untranslated region: C241U, a second in the viral polymerase NSP12: P323L, and the third D614G in the exterior S1 domain of the spike protein. The D614G mutation increases the infectivity. The contribution of the other two members of the Triad remains a mystery. Together these three mutations characterize the first major variant first observed in early 2020. That virus soon displaced almost all of the original Wuhan isolates. The Triad virus is the parent of all variants of concern or, interest including Alpha, Beta, Gamma, Delta, Lambda, and Mu. Only two currently circulating variants, A.30 and A.23.1, both of East Africa origin, lack the Triad and are most likely independent descendants of the original Wuhan virus.

I'm guessing each country with an infected population is going to develop a unique variant. Interesting comment: "The contribution of the other two members of the Triad remains a mystery."COVID-19 Outbreak Associated with a SARS-CoV-2 R.1 Lineage Variant in a Skilled Nursing Facility After Vaccination Program — Kentucky, March 2021
https://www.cdc.gov/mmwr/volumes/70/wr/mm7017e2.htm

Detection of R.1 lineage severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan​

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009619

We aimed to investigate novel emerging severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) lineages in Japan that harbor variants in the spike protein receptor-binding domain (RBD). The total nucleic acid contents of samples from 159 patients with Coronavirus disease 2019 (COVID-19) were subjected to whole genome sequencing. The SARS-CoV-2 genome sequences from these patients were examined for variants in spike protein RBD. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. These three patients were living in Japan and had no history of traveling abroad.

. . .
As of April 22, 2021, R.1 lineage SARS-CoV-2 has been identified in 2,388 SARS-CoV-2 entries in the GISAID database, many of which were from Japan (38.2%; 913/2,388) and the United States (47.1%; 1,125/2,388). Compared with that in the United States, the percentage of SARS-CoV-2 isolates belonging to the R.1 lineage in Japan increased more rapidly over the period from October 24, 2020 to April 18, 2021. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world.

 

[pinball1970]

The Delta variant was first identified in India in December 2020. Did it first infect people within 50 to 100 miles of an international airport?

WHO profile of Delta
First sample documented - India, Oct-2020, VOI: 4-Apr-2021, VOC: 11-May-2021
https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

https://cov-lineages.org/lineage.html?lineage=B.1.617.2 First date 2020-08-21, which is earlier than Oct-2020

https://cov-lineages.org/lineage_list.html

I think Mu is just getting started in the US.

From WHO page, VOI Table: Mu (B.1.621); Earliest documented sample, Colombia, Jan-2021; VOI: 30-Aug-2021

I checked previous PHE and there was no Mu mentioned
Checking today there are 47 cases, no deaths as yet but some of those did end up in hospital. P19

https://assets.publishing.service.g...le/1014926/Technical_Briefing_22_21_09_02.pdfDELTA deaths since Feb 1st to Aug 30th page 22

Every month the unvaccinated group gets smaller but the uptake has stagnated at less that 15,000 per day on some days.
Following the roll out to kids this should accelerate again soon.

https://www.theguardian.com/world/2...for-children-aged-12-15-what-you-need-to-know

Lastly it was reported in the METRO UK today 21.9.21 that we have a surplus of 100M vaccines that could go beyond their use by date and get wasted.
Checking just now it looks like we will try and get these out to other countries.

https://www.bbc.co.uk/news/uk-57436535

 

[Astronuc]

According to the Manchester Evening News, COVID-19 was the third leading cause of death August in England, up from 9th leading cause in July.

 

[pinball1970]

Good catch @Astronuc My local news-paper, it does a quite good break downs of the boroughs in terms of numbers and initiatives, mobile vaccine centres targeting low uptake areas and such.

July was a good month, months of lock down followed by a staggered lifting of measures.

Outside venues opened middle of May, then inside venues but with masks and other restrictions middle of June.

So it took a while for cases to start go up again before restrictions lifted middle of July. 30-50 deaths per day.

Fast forward a couple of months and we are at 200 deaths per day which is over twice that of rate for lung cancer deaths in 2018.

However that is still only 1/10th of the death rate when ALPHA was at its peak in Jan, with few double vaccinated proportionally.

I would like to think the rate will not go up too much more now.

On the plus side we high vaccine levels with 3 million kids lined up for jabs, the numbers seem to have plateaued.

On the down side (in terms of spread) kids back at school and the summer festivals went ahead including Park life held in Manchester, 76,000 attendance.

The events are out side granted but there is an awful lot of mingling at these events, especially getting in and out, communal toilets bars etc.

Also the kids have got to get to from A B

So buses, trams & trains packed full of teenagers (I had to walk through them) the most mobile mixers with low vaccination rates…. mixing.

We may get a blip from that and others like it.

Statistically though, those youngsters will not need hospital treatment.

 

[Astronuc]

Looking back to the beginning, late 2019, and how SARS-Cov-2 mutated and spread, I was curious about the earliest strains/variants.

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic​

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7523107/

Abstract: We report the likely most recent common ancestor of SARS-CoV-2 – the Coronavirus that causes COVID-19. This progenitor SARS-CoV-2 genome was recovered through a novel application and advancement of computational methods initially developed to reconstruct the mutational history of tumor cells in a patient. The progenitor differs from the earliest coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple Coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide as soon as weeks after the first reported cases of COVID-19. Mutations of the progenitor and its offshoots have produced many dominant Coronavirus strains, which have spread episodically over time. Fingerprinting based on common mutations reveals that the same Coronavirus lineage has dominated North America for most of the pandemic. There have been multiple replacements of predominant Coronavirus strains in Europe and Asia and the continued presence of multiple high-frequency strains in Asia and North America. We provide a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread.

In Molecular Biology and Evolution
https://academic.oup.com/mbe/article/38/8/3046/6257226

 

[Astronuc]

Newsweek - Delta Sub-Variant AY.4.2, Possibly More Contagious Than Delta, Spreads to More States
https://www.msn.com/en-us/health/me...-than-delta-spreads-to-more-states/ar-AAPQ5GI

According to Outbreak.Info, which uses virus sequencing data from the GISAID database, AY.4.2 has now been identified in four states—North Carolina, Massachusetts, Washington and California—in addition to the District of Columbia, as of October 21.

Just two days ago, AY.4.2 had only been detected in California, North Carolina and DC.

. . .

The new AY.4.2 sub-lineage is one of more than three dozen evolutions of the original Delta variant that have been identified globally.

According to the Centers for Disease Control and Prevention, the Delta variant (first identified in the U.K. and has since become the dominant form of the SARS-CoV-2 virus) is highly contagious—scientists think it is more than twice as infectious as previous variants.

The AY.4.2 sub-lineage of Delta contains two characteristic mutations—called Y145H and A222V—on the spike protein of the SARS-CoV-2 virus, which it uses to bind and enter human cells.

 

[pinball1970]

Newsweek - Delta Sub-Variant AY.4.2, Possibly More Contagious Than Delta, Spreads to More States
https://www.msn.com/en-us/health/me...-than-delta-spreads-to-more-states/ar-AAPQ5GI

This from UKHSA

https://assets.publishing.service.g...t_data/file/1029715/technical-briefing-27.pdf

Delta AY.4.2* VUI-21OCT-01 VUI very steep curve page 14 and actual number pg 13

 

[Astronuc]

A potentially faster-spreading "sub-lineage" of the coronavirus Delta variant named AY.4.2 has been spotted by labs in at least 8 states, and health authorities in the United Kingdom say they are investigating a growing share of cases from this strain of the virus.

Labs in California, Florida, Maryland, Massachusetts, Nevada, North Carolina, Rhode Island and Washington state, plus the District of Columbia, have so far spotted at least one case of AY.4.2.

https://www.cbsnews.com/news/covid-delta-plus-variant-ay-4-2-states/

There are variants of the Covid-19 Coronavirus like the Delta variant. Then there are subvariants, which are variants of the variants. And AY.4.2 is a Delta subvariant that has now spread to at least 42 different countries, including the U.S., according to the latest World Health Organization (WHO) Weekly epidemiological update on Covid-19. This AY.4.2 takes the Delta variant and raises it three additional mutations, including two that affect the oh-so-important spike proteins that studs the surface of the virus. These mutations are called A222V and Y145H, . . .

https://www.forbes.com/sites/brucel...avirus-subvariant-has-spread-to-42-countries/

https://gvn.org/covid-19/delta-b-1-617-2/

https://www.bbc.com/news/health-58965650

https://www.cnbc.com/2021/10/21/the-delta-variant-has-a-mutation-what-we-know-so-far.html

I can't find any statement from WHO.int yet.

Repeating myself: What doesn't kill you, mutates and tries again, and again, . . .

 

[Ygggdrasil]

Regarding AY.4.2, data from England do suggest that AY.4.2 infections (purple on the graph below) continued to rise as delta infections (B.1.617.2, green on graph below) leveled off in Sep-Oct, which does suggest potential increased transmissibility of AY.4.2 over B.1.617.2:

https://covid19.sanger.ac.uk/lineages/raw

Unfortunately, it does not look like the US CDC variant tracking site tracks AY.4.2, as all of the delta lineages (except AY.1 and AY.2) are aggregated with B.1.617.2.

 

[Astronuc]

Some recent numbers on variants in California.

https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-19/COVID-Variants.aspx
low proportion of AY.1 and AY.2 in the State

 

[Ygggdrasil]

While most studies of COVID-19 variants have focused on mutations in the spike protein (which are important for determining the strength with which the virus binds to the ACE2 receptor in the cells it infects as well as binding to antibodies), here's a paper studying mutations to other proteins encoded by the SARS-CoV-2 virus. In particular, they find some mutations help to enhance the activity of Orf9b in helping the virus to evade the innate immune system.

Evolution of enhanced innate immune evasion by SARS-CoV-2
https://www.nature.com/articles/s41586-021-04352-y

Abstract:

Emergence of SARS-CoV-2 variants of concern (VOCs) suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on characterisation of spike changes in VOCs, mutations outside spike likely contribute to adaptation. Here we used unbiased abundance proteomics, phosphoproteomics, RNAseq and viral replication assays to show that isolates of the Alpha (B.1.1.7) variant3 more effectively suppress innate immune responses in airway epithelial cells, compared to first wave isolates. We found that Alpha has dramatically increased subgenomic RNA and protein levels of N, Orf9b and Orf6, all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein required for RNA sensing adaptor MAVS activation. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful Alpha transmission, and may increase in vivo replication and duration of infection4. The importance of mutations outside Spike in adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the Delta and Omicron N/Orf9b regulatory regions.