Epsilon COVID-19 mutant strain

[Mary Wilson]

COVID-19: New variant blamed for surge in coronavirus cases in Los Angeles - CAL.20C

Sunday 31 January 2021 22:45
Stuart Ramsay

Scientists in Los Angeles searching for signs that the UK COVID variant had crossed into the US have stumbled on a different one that appears to have been home grown in California - fuelling a surge in cases in the world's entertainment capital.

Nearly 50% of all new coronavirus cases in southern California in January alone are traced to the new variant, CAL.20C, one of the pathologists to identify the strain told Sky News.

... Doctors and researchers at the world-famous Cedars-Sinai medical institution are still testing to see if the California variant is more deadly, more infectious, and more resistant to vaccines, like it is feared others might be.

They found the new strain only because they realised that British scientists were far ahead in seeing the importance of testing for variants.

... The virus is constantly evolving to avoid the immune system, and what is interesting about CAL.20C is that it is developing in a completely different way to the UK, South African and Brazilian variants.

https://news.sky.com/story/covid-19...s-in-los-angeles-12204020?dcmp=snt-sf-twitter

 

[blacknail]

I have been loosely following this and I believe that CAL.20C is a variant of B.1.426 if anyone is looking to dig into it deeper...

the CAL.20C strain may be partially responsible for the magnitude of the surge in COVID-19 on the West Coast of the US. The S protein L452R mutation is within a known receptor binding domain that has been found to be markedly resistant to certain monoclonal antibodies to the spike protein(4). Mutations in this domain may be resistant to polyclonal sera as seen in convalescent patients or those post vaccination(5). The functional effect of this mutation in concert with other detected mutations in CAL.20C, both in terms of infectivity and antibody resistance is unknown at this time

source: https://www.medrxiv.org/content/10.1101/2021.01.18.21249786v1.full-text

 

[sharon sanders]

I copied a couple of posts here to make a new thread.

 

[sharon sanders]

California coronavirus strain may be more infectious—and lethal


By Meredith Wadman

Feb. 23, 2021 , 1:20 PM

Science’s COVID-19 reporting is supported by the Heising-Simons Foundation.

A new strain of the pandemic coronavirus, first identified and now spreading in California, appears to be somewhat more transmissible and heighten patients’ risk of admission to the intensive care unit (ICU) and death, according to a preprint reporting lab studies and epidemiological data.

The variant is also present in other states, but its prevalence among more than 2000 samples collected in California swelled from 0% to greater than 50% between September 2020 and late January, according to researchers at the University of California, San Francisco (UCSF). “This variant is concerning because our data shows that it is more contagious, more likely to be associated with severe illness, and at least partially resistant to neutralizing antibodies,” says senior author Charles Chiu, an infectious diseases physician and sequencing expert at UCSF. The data suggest the new strain “should likely be designated a variant of concern warranting urgent follow-up investigation,” the authors write in their preprint, which has not been peer reviewed and which they say is expected to be posted online soon.

The findings “warrant taking a much closer look at this variant,” says Angela Rasmussen, a virologist at Georgetown University’s Center for Global Health Science and Security who was not involved with the research. They “underscore the importance of pulling out all the stops in terms of both exposure reduction and increased vaccine distribution and access.”

more....

https://www.sciencemag.org/news/2021...and-cause-more

 

[sharon sanders]

US - California: What is going on there? Is the 20C/L452R California mutant strain more lethal than "regular" COVID-19? - February 27, 2021

Tracking COVID-19

State and County Data

Total Cases

3,470,877
5,151Today
+0.1% Increase from prior day total

Total Deaths

51,821
439 Today
+0.9% Increase from prior day total

Total Tests

48,219,490
223,914 Today
+0.5% Increase from prior day total
Updated February 27, 2021 at 11:00 AM with data from February 26, 2021

https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/Immunization/ncov2019.aspx


------------------------------------------------------------------


2,137 COVID-19 deaths reported for the total US deaths for February 26, 2021 per @COVID19Tracking

------------------------------------------------------------------

Roughly...California represents 21% of the US deaths for yesterday.

California has about 12% of the US population.

California appears to be over represented in the number of COVID-19 deaths for a random day selected of February 26, 2021

-------------------------------------------------------------------

Please see:

20C/L452R California COVID-19 mutant strain

 

[sharon sanders]

CDC COVID Tracker weekly review is not giving any information on this variant but is reporting others....what's the deal?


US COVID-19 Cases Caused by Variants


Updated Feb. 25, 2021


Variant

Reported Cases in US

Number of Jurisdictions Reporting


B.1.1.7

2102

45

B.1.351

49

15

P.1

6

5

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

--------------------------------------

Or on the variant report:



Download Accessible Data excel icon[CSV – 665 KB]

The emerging variants CDC is closely monitoring have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines). It’s important to understand that genetic mutations are expected, and some variants can spread and become predominant while others subside.

02/11/21 – To maintain a limited number of colors and allow for an easier comparison between states, the data ranges have changed from 1-50 to 1-100.

*The cases identified above are based on a sampling of SARS-CoV-2-positive specimens and do not represent the total number of B.1.1.7, B.1.351, and P.1 lineage cases that may be circulating in the United States and may not match numbers reported by states, territories, tribes, and local officials.

†Numbers will be updated on Sunday, Tuesday, and Thursday by 7:00 pm.

Learn more about Genomic Surveillance for SARS-CoV-2 Variants.

Last Updated Feb. 25, 2021

https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant-cases.html

 

[Mary Wilson]

Coronavirus Variants and Mutations

By Jonathan Corum and Carl Zimmer
Updated Feb. 25, 2021

Each coronavirus contains nearly 30,000 letters of RNA. This genetic information allows the virus to infect cells and hijack them to make new viruses.

... Over the course of the pandemic, a number of variants of SARS-CoV-2 have arisen. Some of them are raising worries that they may draw out the pandemic or make vaccines less effective.

Feb. 23
Feb. 23
Feb. 17
Feb. 16
Feb. 15
Feb. 15
Feb. 13
Feb. 11
Feb. 7
Feb. 7
B.1.1.7	Variant of Concern 202012/01, or 501Y.V1	Emerged in Britain in December and is roughly 50 percent more infectious. Now detected in over 70 countries and 33 states.
B.1.351	501Y.V2	Emerged in South Africa in December. Reduces the effectiveness of some vaccines.
P.1	501Y.V3	Emerged in Brazil in late 2020. Has mutations similar to B.1.351.
B.1	D614G	Appeared in early 2020 and spread around the world.
Several	N501Y	A defining mutation in several lineages, including B.1.1.7, B.1.351 and P.1. Helps the virus bind more tightly to human cells.
Several	E484K	Appears in several lineages. May help the virus avoid some kinds of antibodies.
Several	K417	Appears in several lineages, including B.1.351 and P.1. May help the virus bind more tightly to cells.
Several	L452R	Increasingly common in California, but not yet shown to be more infectious.
Several	Q677	Found in seven U.S. lineages, but not yet shown to be more infectious.
B.1.427, B.1.429	CAL.20C	Common in California, but not yet shown to be more infectious. Carries the L452Rmutation.
B.1.526	—	Spreading in New York. One version carries the E484K mutation, another carries S477N.

[TD="colspan: 2"]Added the B.1.526 variant, which is spreading in New York City.[/TD]

[TD="colspan: 2"]Studies suggest that a variant discovered in California is more contagious.[/TD]

[TD="colspan: 2"]Maryland confirms its first case of the P.1 variant.[/TD]

[TD="colspan: 2"]Massachusetts confirms its first case of the B.1.351 variant.[/TD]

[TD="colspan: 2"]Added the Q677 spike mutation, which was found in several lineages in the U.S.[/TD]

[TD="colspan: 2"] B.1.351 is confirmed in a Connecticut resident hospitalized in New York City.[/TD]

[TD="colspan: 2"]Studies suggest B.1.1.7 is likely more deadly than other circulating variants.[/TD]

[TD="colspan: 2"]Illinois and North Carolina confirm their first cases of the B.1.351 variant.[/TD]

[TD="colspan: 2"]South Africa stops using AstraZeneca’s vaccine against the B.1.351 variant.[/TD]

[TD="colspan: 2"]The B.1.1.7 variant is doubling every 10 days in the United States.[/TD]

... The CAL.20C Variant

A variant discovered in California, called CAL.20C, surged in late 2020. The variant spans the B.1.427 and B.1.429 lineages, and carries the L452R mutation listed above.

WHERE CAL.20C HAS BEEN FOUND

By early February, the variant was found in more than half of samples tested in Los Angeles.

RECENT COVERAGE OF CAL.20C

New California Variant May Be Driving Virus Surge There, Study Suggests ? Jan. 19, 2020

What to Know About the California Variant ? Jan. 27

Covid-19: California’s Surge Recedes But Alarm Grows Over Variants ? Feb. 4

Studies Examine Variant Surging in California, and the News Isn’t Good ? Feb. 23

https://www.nytimes.com/interactive/2021/health/coronavirus-variant-tracker.html#L452R

 

[Mary Wilson]

Emergence of a Novel SARS-CoV-2 Variant in Southern California

February 11, 202
Wenjuan Zhang, PhD[SUP]1[/SUP]; Brian D. Davis, BSc[SUP]2[/SUP]; Stephanie S. Chen, BSc[SUP]2[/SUP]; et al

JAMA. DOI: 10.1001/jama.2021.1612

A spike in coronavirus disease 2019 (COVID-19) has occurred in Southern California since October 2020. Analysis of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in Southern California prior to October indicated most isolates originated from clade 20C that likely emerged from New York via Europe early in the pandemic.[SUP]1[/SUP] ...

... Of 2311 samples at CSMC, 192 were selected and 185 (67 inpatient; 118 outpatient) underwent phylogenetic analysis, along with 1480 representative genomes using Nextstrain. A diverse set of lineages with 2 main clusters was identified (Figure 1). The smaller of the 2 clusters was from the 20G lineage and accounted for 22% (40 of 185) of the samples. The larger cluster (36%, 67 of 185) consisted of a novel variant descended from cluster 20C, defined by 5 mutations (ORF1a: I4205V, ORF1b: D1183Y, S: S13I; W152C; L452R) and designated CAL.20C (20C/S:452R; /B.1.429).

https://jamanetwork.com/journals/jama/fullarticle/2776543