Preprint: Genome recombination between Delta and Alpha variants of SARS-CoV-2

Prominent genomic recombination has been observed between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from clinical specimens in Japan.

During the surveillance, we monitored several variants of concern (VOCs) of the PANGO lineage. We found six unique specimens among the 21A (Delta) clade isolates that exhibited a low quality assignment (“not determined” or “none”) in the PANGO lineage, even though their genome sequences had been completely determined with high read coverage throughout the whole genome region.

A detailed genome alignment by Nextclade suggested that despite being clonal isolates of the 21A (Delta) clade, these six isolates show identical mutation profiles with 20I (Alpha, V1), particularly between the ORF6 and N genes, located towards the latter part of the SARS-CoV-2 genome.

Additionally, the alignment clearly revealed a possible recombination spot between the ORF6 and ORF7a genes. However, the next generation sequencing (NGS)-based read mapping analysis did not indicate the presence of any heterogeneous mix of alleles in the clinical specimens, suggesting that these patients had not acquired multiple variant infections with 21A (Delta) and 20I (Alpha, V1) clades at the acute stage of the infection.

 

MedRxiv preprint: Genome Recombination between Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) 

 

 

 

Image by Iván Tamás from Pixabay

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

Vaccine breakthrough cases in Washington State to 15th September 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 15th September 2021.  The Delta variant continues to be the leading cause of breakthrough infections in the state, however a big drop in the number of cases being sequenced means that this data doesn’t have much statistical relevance to the actual number of breakthrough infections occurring.

The data might, however, be a useful indicator of the rising importance of new variants in the future, and on that basis we will continue to publish the information

 

 

 

 

Vaccine Breakthroughs up to 15th September 2021

15th Sept 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.1.1.740712%31%5
GammaP.12026%7%3
EpsilonB.1.4291264%11%2
DeltaB.1.617.2245073%30%190
IotaB.1.526351%3%1
BetaB.1.351110%1%0
EpsilonB.1.427130%1%0
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
B.1.617.3B.1.617.300%0%0
OtherOther1083%15%3
TotalTotal3359100%100%204

 

Vaccine Breakthroughs up to 8th September 2021

8th Sept 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.1.1.740213%32%3
GammaP.11996%7%3
EpsilonB.1.4291244%11%0
DeltaB.1.617.2226072%29%423
IotaB.1.526341%2%0
BetaB.1.351110%1%0
EpsilonB.1.427130%1%0
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
B.1.617.3B.1.617.300%0%0
OtherOther1053%16%-7
TotalTotal3155100%100%422

 

Vaccine Breakthroughs up to 1st September 2021

1st Sept 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.1.1.739915%33%1
GammaP.11967%8%-2
EpsilonB.1.4291245%12%0
DeltaB.1.617.2183767%25%443
IotaB.1.526341%2%0
BetaB.1.351110%1%0
EpsilonB.1.427130%1%1
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
B.1.617.3B.1.617.300%0%0
OtherOther1124%18%-111
TotalTotal2733100%100%332

 

Vaccine Breakthroughs up to 25th August 2021

25th 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.1.617.2139458%18%546
AlphaB.1.1.739817%31%40
GammaP.11988%7%12
EpsilonB.1.4291245%11%7
IotaB.1.526341%2%6
EpsilonB.1.427120%1%1
BetaB.1.351110%1%1
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
OtherOther2239%27%-540
TotalTotal2401100%100%73

 

Vaccine Breakthroughs up to 18th August 2021

18th 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.1.617.284836%12%219
AlphaB.1.1.735815%30%6
GammaP.11868%7%4
EpsilonB.1.4291175%11%1
IotaB.1.526281%2%0
EpsilonB.1.427110%1%0
BetaB.1.351100%1%0
EtaB.1.52540%0%0
KappaB.1.617.130%0%2
OtherOther76333%35%676
TotalTotal2328100%100%908

 

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 kola05 from Pixabay

UK: The Alpha variant rears its ugly head again

A big surprise in the latest UK sequencing figures show that the Alpha variant has made something of a comeback this week. Even though the percentage of Alpha cases is still tiny compared to that of Delta, the figure of more than 400 Alpha cases is the highest since mid-June 2021.

It’s unclear whether this is a localised outbreak (it may be part of the unfolding superspreader event of the Boardmasters festival in Cornwall for example), or whether these are cases scattered across the UK, but to see such a resurgence after so many weeks of Delta dominance is something of a shock as the Alpha variant was far less effective at breaking through vaccine protection than the Delta variant is.

After weeks of just a handful of Alpha cases in the UK, there is suddenly a spike of over 400 new cases:

 

Confirmation that the Delta variant has dipped recently:

Charts and data courtesy of CovSpectrum.org

 

 

 

Image by Josch13 from Pixabay

Vaccine breakthrough cases in Washington State to 1st September 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 1st September 2021. This week, the Delta variant has posted another large increase for vaccine breakthroughs, and, as it is now the predominant variant in the region, will presumably continue to do so for some time to come.

Much of the backlog of virus genome sequencing that built up two weeks ago appears to have been cleared, so there is a big reduction in sequences listed under the “other” category this week. Those sequences have now been largely identified and have moved mostly to the Delta row.

 

There is a newer version of this post here

 

Vaccine Breakthroughs up to 1st September 2021

1st Sept 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.1.1.739915%33%1
GammaP.11967%8%-2
EpsilonB.1.4291245%12%0
DeltaB.1.617.2183767%25%443
IotaB.1.526341%2%0
BetaB.1.351110%1%0
EpsilonB.1.427130%1%1
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
B.1.617.3B.1.617.300%0%0
OtherOther1124%18%-111
TotalTotal2733100%100%332

 

Vaccine Breakthroughs up to 25th August 2021

25th 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.1.617.2139458%18%546
AlphaB.1.1.739817%31%40
GammaP.11988%7%12
EpsilonB.1.4291245%11%7
IotaB.1.526341%2%6
EpsilonB.1.427120%1%1
BetaB.1.351110%1%1
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
OtherOther2239%27%-540
TotalTotal2401100%100%73

 

Vaccine Breakthroughs up to 18th August 2021

18th 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.1.617.284836%12%219
AlphaB.1.1.735815%30%6
GammaP.11868%7%4
EpsilonB.1.4291175%11%1
IotaB.1.526281%2%0
EpsilonB.1.427110%1%0
BetaB.1.351100%1%0
EtaB.1.52540%0%0
KappaB.1.617.130%0%2
OtherOther76333%35%676
TotalTotal2328100%100%908

 

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%

 

 

Photo by Alex Mertz on Unsplash

Vaccine breakthrough cases in Washington State to 25th August 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 25th August 2021.  It looks like Washington State have spent the last week cataloguing Delta samples from the previous week, as very few new breakthrough cases have been recorded this week.

Although Delta breakthroughs have seemingly increased over the week, they have mostly been moved from the “other” row where they were posted last week into the Delta column this week, as we predicted they would be last week.

We will continue to reprint these figures as long as Washington State continues to publish them, but, sadly, their value is increasingly doubtful due to an obvious lag in sequencing the samples.

 

Vaccine Breakthroughs up to 25th August 2021

25th 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.1.617.2139458%18%546
AlphaB.1.1.739817%31%40
GammaP.11988%7%12
EpsilonB.1.4291245%11%7
IotaB.1.526341%2%6
EpsilonB.1.427120%1%1
BetaB.1.351110%1%1
EtaB.1.52540%0%0
KappaB.1.617.130%0%0
OtherOther2239%27%-540
TotalTotal2401100%100%73

 

Vaccine Breakthroughs up to 18th August 2021

18th 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.1.617.284836%12%219
AlphaB.1.1.735815%30%6
GammaP.11868%7%4
EpsilonB.1.4291175%11%1
IotaB.1.526281%2%0
EpsilonB.1.427110%1%0
BetaB.1.351100%1%0
EtaB.1.52540%0%0
KappaB.1.617.130%0%2
OtherOther76333%35%676
TotalTotal2328100%100%908

 

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 USA-Reiseblogger from Pixabay

UK Covid app confirms vaccines are waning

Joinzoe: “We found that initial protection against infection a month after the second dose of the Pfizer vaccine was 88%, while after five to six months this fell to 74%.  For the AstraZeneca vaccine, there was around 77% protection a month after the second dose, falling to 67% after four to five months.

This analysis included:

  • 411,642 test results from users who were doubly vaccinated with the Pfizer mRNA vaccine at the time of the infection 
  • 709,486 test results from users who were doubly vaccinated with the AstraZeneca vaccine
  • 76,051 test results from users who were not yet vaccinated at the time of the infection

We found that initial protection against infection a month after the second dose of the Pfizer vaccine was 88%, while after five to six months this fell to 74%.”

Professor Tim Spector, lead scientist at the ZOE COVID Study, says:

“A reasonable worst-case scenario could see protection below 50 percent for the elderly and healthcare workers by winter. With high levels of infection in the UK, driven by loosened social restrictions and a highly transmissible variant, this scenario could mean increased hospitalisations and deaths. 

Joinzoe Covid App: Is COVID vaccine protection fading?

 

UK: Vaccine breakthrough rate for Delta infections still increasing

 

 

Image by mdgrafik0 from Pixabay

The future of Sars-CoV-2: Multiple vaccine breakthrough infections in one patient

The patient had three RT-PCR confirmed SARS-CoV-2 infections. Two breakthrough infections occurred in quick succession with the first over 3 weeks after complete vaccination with COVISHIELD and despite post-vaccination seroconversion. The first breakthrough infection was due to the Alpha variant and the second due to the Delta variant. The Delta variant infection resulted in hypoxia, hospitalization, and illness lasting seven weeks. Serial serology, acute phase reactants, and chest imaging supported WGS in establishing distinct episodes of infection. WGS established a fully vaccinated family member as the index case.

Research article: Severe SARS-CoV-2 Breakthrough Reinfection With Delta Variant After Recovery From Breakthrough Infection by Alpha Variant in a Fully Vaccinated Health Worker

 

Preprint: Just three mutations for SARS-CoV-2 to escape from highly neutralizing convalescent plasma

UK: Vaccine breakthrough rate for Delta infections still increasing

The latest UK PHE Technical Briefing has just been published, and it shows that the vaccine breakthrough rate for Delta infections in the UK continues to increase by about 6% per month. The curious conundrum of the fully vaccinated being more likely to die of a Delta infection than the unvaccinated also continues. Links to the relevant PHE Technical Briefing papers are given.

 

There is a newer version of this post here

 

Technical Briefing 21, 1st February 2021 to 15th August 2021. 

19% vaccine breakthrough rate for Delta variant

1st February 2021 - 15th August 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases386,735127,091183,13373,37219%vaccine breakthrough
Delta deaths1,189390679
Percentage0.21%0.93%335%greater chance of dying if fully vaccinated

 

Technical Briefing 20, 1st February 2021 to 2nd August 2021

16% vaccine breakthrough rate for Delta variant

1st February 2021 - 2nd August 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases300,01098,722151,05447,00816%vaccine breakthrough
Delta deaths253402
Percentage0.17%0.86%411%greater chance of dying if fully vaccinated

 

Technical Briefing 19, 1st February 2021 to 19th July 2021

13% vaccine breakthrough rate for Delta variant

1st February 2021 - 19th July 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases229,218105,298121,40228,77313%vaccine breakthrough
Delta deaths165224
Percentage0.14%0.78%473%greater chance of dying if fully vaccinated

 

Technical Briefing 18, 1st February 2021 to 21st June [sic] 2021

9% vaccine breakthrough rate for Delta variant

1st February 2021 - *21st June 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases123,62063,70771,93210,8349%vaccine breakthrough
Delta deaths92118
Percentage0.13%1.09%752%greater chance of dying if fully vaccinated

 

Technical Briefing 17, 1st February 2021 to 21st June 2021

8% vaccine breakthrough rate for Delta variant

1st February 2021 - 21st June 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases92,02979,33653,8227,2358%vaccine breakthrough
Delta deaths4450
Percentage0.08%0.69%745%greater chance of dying if fully vaccinated

 

Technical Briefing 16, 1st February 2021 to 14th June

7% vaccine breakthrough rate for Delta variant

1st February 2021 - 14th June 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases60,62453,17735,5214,0877%vaccine breakthrough
Delta deaths3426
Percentage0.10%0.64%565%greater chance of dying if fully vaccinated

 

Technical Briefing 15, 1st February 2021 to 7th June 2021

5% vaccine breakthrough rate for Delta variant

1st February 2021 - 7th June 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases33,20628,73819,5731,7855%vaccine breakthrough
Delta deaths2312
Percentage0.12%0.67%472%greater chance of dying if fully vaccinated

 

Technical Briefing 14, 1st February 2021 to 31st May 2021

3% vaccine breakthrough rate for Delta variant

1st February 2021 - 31st May 2021Total casesCases in last 28 daysUnvaccinatedVaccinated with 2 doses  
Delta cases9,4277,7445,1722673%vaccine breakthrough
Delta deaths112
Percentage0.21%0.75%252%greater chance of dying if fully vaccinated

 

Delta vaccine breakthrough cases in Washington State quadruple in two weeks

 

 

 

Photo by Myriam Zilles on Unsplash

Preprint: generation and transmission of recombinant SARS-CoV-2 viruses

We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern, but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants.

ScienceDirect.com article

 

 

 

280 cases of Delta variant with N501Y, some with E484K too

Delta + Alpha + Beta + Gamma recombinant variant found in Turkey.

 

 

 

 

Image by Elliot Alderson 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, Maryland: “I went to a party with 14 other vaccinated people; 11 of us got COVID”

I’m an epidemiologist at a major medical research university.  I had gone to a house party in Montgomery County. There were 15 adults there, all of us fully vaccinated. The next day, our host started to feel sick. The day after that, she tested positive for COVID-19. At this point, 11 of the 15 have tested positive for COVID.

Baltimore Sun report

 

 

Image by Bruce Emmerling from Pixabay

USA: Washington State Vaccine Breakthroughs by Variant up to 4th August 2021

This week’s update from Washington State showing vaccine breakthrough cases and which Sars-CoV-2 variant is causing them up to 4th August 2021. Of note this week is another big jump for Delta B.1.617.2 vaccine breakthrough cases, which have increased from 254 to 405 in one week. Delta is now responsible for more breakthrough cases in Washington State than any other variant.  There are also further small increases in vaccine breakthrough cases for the Alpha and Gamma variants.

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

 

 

Image by Deborah Jackson from Pixabay