Vaccine breakthrough cases in Oregon by variant to 16th September 2021

Vaccine breakthrough data for Oregon state by Sars-CoV-2 variant up to 16th September 2021.

The Delta variant is currently responsible for the majority of vaccine breakthrough cases in Oregon. Oregon state is currently sequencing about 5% of their case samples.

 

Vaccine breakthroughs in Oregon to 16 September 2021. The cumulative total is now 19,549 breakthrough cases.

16th Sept 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.71400
GammaP.1471
EpsilonB.1.427/429380
DeltaB.1.617.2690111
IotaB.1.526290
BetaB.1.351160
SequencedSequenced960112
Weekly Total of all VB casesWeekly Total of all VB cases2632-242

 

Vaccine breakthroughs in Oregon to 09 September 2021. The cumulative total is now 16,417 breakthrough cases.

9th Sept 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
AlphaB.1.1.7140
GammaP.146
EpsilonB.1.427/42938
DeltaB.1.617.2579
IotaB.1.52629
BetaB.1.35116
SequencedSequenced848
Weekly Total of all VB casesWeekly Total of all VB cases2874

 

Source: Oregon Vaccine Breakthrough file

 

 

 

 

Image by jacobdeb from Pixabay

USA: 55% increase in Delta vaccine breakthrough cases in Washington State

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 11th August 2021. Of note this week is another big jump for Delta B.1.617.2 vaccine breakthrough cases, which have increased by 55% from 405 to 629 in one week.  There is also a sudden and rather alarming 74% increase in vaccine breakthrough cases where the Sars-CoV-2 variant is defined as “other”.

** There is an UPDATE of this post here **

Vaccine Breakthroughs up to 11th August 2021

11th August 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
DeltaB.1.617.262944%12%224
AlphaB.1.1.735225%39%9
GammaP.118213%9%7
EpsilonB.1.4291168%14%0
IotaB.1.526282%3%1
EpsilonB.1.427111%2%0
BetaB.1.351101%1%0
EtaB.1.52540%0%0
KappaB.1.617.110%0%0
OtherOther876%20%37
TotalTotal1420100%100%278

Vaccine Breakthroughs up to 4th August 2021

4th August 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
DeltaB.1.617.240535%10%151
AlphaB.1.1.734330%41%6
GammaP.117515%9%7
EpsilonB.1.42911610%15%0
IotaB.1.526272%3%1
EpsilonB.1.427111%2%0
BetaB.1.351101%1%0
EtaB.1.52540%0%0
KappaB.1.617.110%0%0
OtherOther504%19%-4
Total1142100%100%161

Vaccine Breakthroughs up to 28th July 2021

28th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.733734%43%29
GammaP.116817%10%12
EpsilonB.1.42911612%15%3
DeltaB.1.617.225426%7%141
IotaB.1.526263%3%4
BetaB.1.351101%1%0
EpsilonB.1.427111%2%0
EtaB.1.52540%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther546%18%4
Total981100%100%193

Vaccine Breakthroughs up to 21st July 2021

21st July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730839%44%-1
GammaP.115620%10%9
EpsilonB.1.42911314%16%0
DeltaB.1.617.211314%4%23
IotaB.1.526223%3%0
BetaB.1.351101%1%-1
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther506%19%0
Total788100%100%30

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

Vaccine Breakthroughs up to 7th July 2021

7th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of Breakthroughs
From Previous
Week
AlphaB.1.1.729741%44%11
GammaP.113919%9%6
EpsilonB.1.42911316%16%0
DeltaB.1.617.27010%4%30
IotaB.1.526213%3%7
BetaB.1.351112%1%1
EpsilonB.1.427112%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
Other497%20%0
Total716100%100%55

Vaccine Breakthroughs up to 30th June 2021

30th June 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
AlphaB.1.1.728637%38%
GammaP.113317%8%
EpsilonB.1.42911315%14%
DeltaB.1.617.2405%2%
IotaB.1.526142%3%
BetaB.1.351101%1%
EpsilonB.1.427111%2%
EtaB.1.52541%0%
KappaB.1.617.110%0%
ZetaP.200%0%
Other4921%32%
Totals661100%100%

 

 

Image by Frank Ravizza from Pixabay

USA: Washington State Vaccine Breakthroughs by Variant up to 28th July 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 28th July 2021. Of note this week is huge jump for Delta B.1.617.2 breakthrough cases, which have more than doubled in one week from 113 to 254. There are further increases in vaccine breakthroughs for other variants too.

Vaccine Breakthroughs up to 28th July 2021

28th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.733734%43%29
GammaP.116817%10%12
EpsilonB.1.42911612%15%3
DeltaB.1.617.225426%7%141
IotaB.1.526263%3%4
BetaB.1.351101%1%0
EpsilonB.1.427111%2%0
EtaB.1.52540%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther546%18%4
Total981100%100%193

Vaccine Breakthroughs up to 21st July 2021

21st July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730839%44%-1
GammaP.115620%10%9
EpsilonB.1.42911314%16%0
DeltaB.1.617.211314%4%23
IotaB.1.526223%3%0
BetaB.1.351101%1%-1
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther506%19%0
Total788100%100%30

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

 

USA: Washington State Vaccine Breakthroughs by Variant up to 21st July 2021

 

So what is Plan B if the vaccines fail with a new #coronavirus super-variant?

Image by David Mark from Pixabay

USA: Washington State Vaccine Breakthroughs by Variant up to 21st July 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them. Of note this week is another large jump for Delta B.1.617.2 breakthrough cases, and a further increase for Gamma P1 breakthroughs.

Vaccine Breakthroughs up to 21st July 2021

21st July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730839%44%-1
GammaP.115620%10%9
EpsilonB.1.42911314%16%0
DeltaB.1.617.211314%4%23
IotaB.1.526223%3%0
BetaB.1.351101%1%-1
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther506%19%0
Total788100%100%30

Vaccine Breakthroughs up to 14th July 2021

14th July 2021

Variant
LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Variant
Percentage of
Sequences From
All Covid-19
Cases With
Variant
Increase in
Number of
Breakthroughs
From Previous
Week
AlphaB.1.1.730941%44%12
GammaP.114719%10%6
EpsilonB.1.42911315%16%0
DeltaB.1.617.29012%4%20
IotaB.1.526223%3%1
BetaB.1.351111%1%0
EpsilonB.1.427111%2%0
EtaB.1.52541%0%0
KappaB.1.617.110%0%0
ZetaP.200%0%0
OtherOther496%20%0
Total757100%100%39

USA: vaccine breakthough cases in Washington State by coronavirus variant to 30th June 2021

Washington State has recently published an update on the number of vaccine breakthrough cases. Importantly, it shows which Sars-CoV-2 variant is responsible for 661 of those cases through genome sequencing. This hugely important information is not available for most states in the USA, so the fact that Washington State continues to publish this information for the Covid variants currently circulating in that state makes it all the more valuable.  Spoiler alert: Delta B.1.617.2 is NOT YET the most common variant for vaccine breakthrough cases in Washington State! That situation will almost certainly change over the next few weeks as Delta becomes more dominant across the U.S.

The most common variant currently causing vaccine breakthroughs in Washington State up to 30th June 2021 is Alpha, (B.1.1.7),  at 37%, followed by Gamma (P.1) at 17%. The Delta variant (B.1.617.2) currently only accounts for about 5% of vaccine breakthrough infections.

The Epsilon variant (B.1.429) is showing as being responsible for 15% of all breakthrough cases, yet represents just 3% of the total genome sequences for May to June, and never rose above 10% of genome samples from April 2021.

Washington State data on all breakthrough cases:

Source: Washington State Vaccine Breakthrough Report

 

Sars-CoV-2 variants circulating in Washington State April – June 2021:

 

Source: Washington Covid-19 Dashboard

As you can see, Washington State has recorded 2,228 vaccine breakthrough cases in total which represents a tiny fraction of the 6 million people now vaccinated in that state.

Our thanks to The Washington State Department of Health for providing this vital information.

 

USA: Washington State Vaccine Breakthroughs by Variant up to 14th July 2021

 

USA: Washington State Vaccine Breakthroughs by Variant up to 7th July 2021

 

Israel: 50% vaccine breakthrough for coronavirus cases in the last month

WHO announce new names for Sars-CoV-2 #coronavirus variants

The WHO have announced new names for the confusingly named sars-cov-2 variants. The new names are based on the Greek alphabet.

Variants of Concern = Alpha, Beta, Gamma, Delta

 

Variants of Interest = Epsilon, Zeta, Eta, Theta, Iota, Kappa

 

WHO introduces new naming system for Sars-CoV-2 variants based on Greek alphabet –  Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa etc

B1427/B1429 are listed as Variants of Concern by the CDC, as Variants of Interest (VOI) by WHO

The World Health Organization lists as B.1.427 and B.1.429 as Variants of Interest. The CDC website, however, lists B.1.427 and B.1.429 as Variants of Concern along with B.1.1.7 (UK variant), P.1 (Brazilian Variant) and B.1.351 (South African Variant).

 

CDC:  SARS-CoV-2 Variant Classifications and Definitions

WHO: COVID-19 Weekly Epidemiological Update

 

 

 

L452R mutation is present in more than 400 SARS-CoV-2 #coronavirus genomes isolated from over 20 countries (and a gorilla in San Diego Zoo too!)

Scientists have examined the Nextstrain and GISAID databases and found that the L452R mutation is present in more than 400 SARS-CoV-2 genomes isolated from over 20 countries. This indicates a strong positive selection for L452R mutation.

The scientists identified L452R amino acid substitution in the spike region as the dominant mutation in specimens collected since November 2020. Specifically, they observed that two independent SARS-CoV-2 variants (CAL.20C and CAL.20A) containing spike L452R mutation emerged recently in the state of California. Of these variants, CAL.20C (clade 20C; lineage B.1.429) is considered to be the predominant variant in California since November 2020. However, the CAL.20A variant (clade 20A; lineage B.1.232) identified in this study has emerged much more recently than CAL.20C and is primarily circulating in California. Based on the phylogenetic analysis, the scientists indicated that L452R mutation is the primary driving force behind the emergence of both variants. Such an increase in L452R mutation frequency in recent SARS-CoV-2 variants directly indicates its crucial involvement in viral adaptive evolution due to positive selection.

Interestingly, they found CAL.20A variant from a gorilla at the San Diego Zoo, which contains two additional mutations in the non-structural protein 2 (NSP2).

In contrast to CAL.20C, no massive clonal expansion was observed for CAL.20A. According to the study findings, CAL.20C contains two additional spike mutations along with L452R, which are missing in CAL.20A. The scientists believe that these additional mutations may be responsible for increasing the adaptive benefits of L452R, and because of this reason, CAL.20A could not achieve the same expansion rate as CAL.20C.

News-Medical,net report

Biorxiv preprint

 

Image by Free-Photos from Pixabay

Emergence of a #coronavirus SARS-CoV-2 E484K variant of interest in Arizona – VOI B.1.243.1

We sequenced the SARS-CoV-2 genome from 688 positive samples collected from December 28 2020 to March 13 2021 in Arizona, USA.  638 high-quality complete genomes were successfully sequenced that included variants such as B.1.1.7, B.1.427/429 and P.2. We detected 7 genomes associated with a common B.1.243 variant that had acquired an E484K mutation in the spike protein. 

The novel variant had 11 lineage-defining mutations including V213G and E484K in the spike gene, a 9-nt deletion in ORF1ab (ΔSGF3675-77), a 3-nt insertion in the non-coding intergenic region upstream of the N gene and other synonymous substitutions (Figure 1A, Supplementary Table 1). These 11 conserved mutations are distinct from the mutations associated with the parental lineage, B.1.243. The parental B.1.243 lineage is a common circulating variant in the US that was first observed at the start of the pandemic as early as March 2020 (Figure 1B, 96.9%). The B.1.243 parent lineage encodes the spike gene D614G substitution, but none of the other concerning mutations (Figure 1A, Supplementary Table 2). Therefore, we designate the new E484K harboring variant the provisional name of B.1.243.1.

Medrxiv preprint

 

Image by dianakuehn30010 from Pixabay

California #coronavirus variant CAL.20C accounts for nearly half of COVID-19 cases in Southern California and about a 1/3 of cases in the state

The CAL.20C variant accounts for nearly half of COVID-19 cases in Southern California and about a third of cases in the state based on an analysis of viral genomes posted to a global database called GISAID.

What’s more, the researchers found that by the end of January, the variant had spread to 19 other states, up from five states in November 2020. It has also spread beyond the U.S. to six other countries — Australia, Denmark, Israel, New Zealand, Singapore and the United Kingdom.

Livescience article

Jama Network Paper

 

Image by David Mark from Pixabay

Emergence of a novel #SARSCoV2 strain in Southern California, USA – CAL.20C

“We detected a novel strain descended from cluster 20C and defined by five mutations (ORF1a: I4205V, ORF1b:D1183Y, S: S13I;W152C;L452R)(Figure 1). This strain, CAL.20C, was first observed in July 2020 in 1/1230 samples from LA county and not detected in Southern California again until October. Since then, this strain’s prevalence has increased absolutely and relatively in Southern California, where by December it accounted for 24% of all samples (Figure 2A) and 36.4% (66/181) of our local Los Angeles cohort.”

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

 

Photo by National Cancer Institute on Unsplash