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

Preprint: Prevalent evidence of #coronavirus variant B.1.617.2 Delta in post-vaccinated individuals in India

“We sequenced all samples of vaccination-breakthrough cases at NCDC, Delhi, over the period of the study. Two VOC lineages were seen amongst 27 cases: B.1.617.1 (n=2; 8%), B.1.617.2  (n=19; 76%). Other samples had the background B.1 lineages (16%).

It is noted that when compared to population prevalence, B.1.617.2 was over-represented and B.1.1.7 was not even detected in vaccination breakthroughs, suggesting higher breakthrough risk of B.1.617.2 compared to B.1.1.7.”

Preprint: Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India

 

UK: government risk assessment of #coronavirus Delta variant B.1.617.2 – evidence of frequent vaccine failure or decreased effectiveness in humans 

 

Image by confused_me from Pixabay

 

Australia: Kappa variant B.1.617.1 responsible for latest Melbourne outbreak

The latest  Melbourne outbreak is believed to have begun when a traveller infected with the Kappa variant (B16171) returned to Australia.

“We’ve got to run this thing to ground otherwise people will die,” Victoria’s acting state Premier James Merlino said, adding they were dealing with a virus variant “quicker and more contagious than we have ever seen before”.

Thousands of close contacts have been identified and the list of venues visited by the 60 confirmed cases has grown to about 350.

TodayOnline.com report

 

 

 

Photo by Weyne Yew on Unsplash

Preprint: B.1.617 #coronavirus variants show enhanced spike cleavage by furin

“The spike (S) glycoprotein of the SARS-CoV-2 virus that emerged in 2019 contained a suboptimal furin cleavage site at the S1/S2 junction with the sequence 681 PRRAR/S 686.  This cleavage site is required for efficient airway replication, transmission, and pathogenicity of the virus. …P681R significantly enhanced the ability of furin to cleave the peptide confirming that the arginine substitution is responsible for the enhanced cleavage of the B.1.617 S protein.

We speculate that enhanced S1/S2 cleavage seen in B.1.617 and B.1.1.7 [Alpha variant] (which contains P681H) may be contributing to the enhanced transmissibility of these SARS-CoV-2 variants.”

Biorxiv Preprint “The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin

 

WHO: Newly designated VOC within lineage B.1.617 – update on Delta #coronavirus variant

 

 

Photo by Abby Savage on Unsplash

 

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

Malaysia: Total lockdown from June 1st as #coronavirus cases hits new record

Malaysia will close all economic and social sectors by implementing a “total lockdown” throughout the country. The first phase of the lockdown will last from Jun 1 to Jun 14. This move was announced in a media statement posted on Prime Minister Muhyiddin Yassin’s Facebook page on Friday (May 28) night.

Only essential economic and service sectors listed by the National Security Council will be allowed to operate during Phase 1 of the lockdown, said the statement issued by Prime Minister’s Office (PMO). 

“This decision was made after taking into account the current situation of COVID-19 transmission in Malaysia with daily case numbers exceeding 8,000 and active cases exceeding 70,000,” the statement read.

Channel News Asia report

 

Malaysia has detected two Covid-19 Variant of Concern (VOC) and two Variant of Interest (VOI) to date.

Health director-general Tan Sri Dr Noor Hisham Abdullah said the VOC identified were the United Kingdom variant or the B.1.1.7, and the South African variant, also known as the B.1.351.

The VOI found, he said, were the Nigeria (B.1525) variant and the B.1.617.1 variant from India.

“We have detected eight cases of the UK variant, three of which were local cases from Sandakan identified through close contact screening (two) and one from the Lorong Megah Jaya cluster.

NST.com.my report

 

 

Image by Peter Nguyen from Pixabay

The highest ever #coronavirus daily case rates recorded on Planet Earth – and it’s not India or Brazil

The highest ever daily country case figure for coronavirus on Planet Earth was recorded in The Seychelles in May 2021. The Seychelles daily case figure, adjusted for population, reached an astonishing 4,083 cases per million. 

What is also surprising is that many of the countries on the list with the highest daily case rates also have excellent vaccination rates (see below). The Seychelles, for example, has vaccinated more than 60% of its population.

The reasons behind some of the high daily case numbers are given in articles we have previously published and have linked to below.

 

Seychelles: a population of 100,000 that has 900 #coronavirus vaccine breakthrough cases

Maldives: 60% positivity rate in Greater Male – “High chance of new #coronavirus variant”

Uruguay: over 1,000 daily new confirmed COVID-19 cases per million people

Sweden’s daily #coronavirus case rate far higher than Brazil or India

 

Charts courtesy of OurWorldinData.org

Singapore: 78 #coronavirus cases in current outbreak were vaccinated compared to about 300 unvaccinated cases

A total of 78 Covid-19 cases in the current outbreak in Singapore have been vaccinated – many of whom are frontline workers – compared to about 300 unvaccinated cases, said Health Minister Ong Ye Kung.  The numbers represent a ratio of about 79 per cent unvaccinated cases versus 21 per cent vaccinated ones. It’s “not quite” true that the situation in Singapore is “getting very bad”, he said.

ChannelNewsAsia.com report

Singapore is currently battling a fresh wave of B.1.617.2 infections introduced through Changi airport despite strict anti-covid protocols including regular antigen and RT-PCR testing for the workforce. About one quarter of the population of Singapore have been fully vaccinated and over one third have been partially vaccinated. Singapore has only approved the use of the Pfizer and Moderna Covid-19 vaccines for use in the country. It’s a stark warning about the difficulty of controlling the spread of the new variant first discovered in India.

 

Singapore: Changi Airport #coronavirus cluster – 18 patients with 61% vaccine breakthrough rate

 

 

Image by Pexels from Pixabay

UK: #coronavirus variant B.1.617.2 within hours of outcompeting B.1.1.7 in Britain

Well that escalated quickly. It took just a little over one month to do it, but B.1.617.2 is now just hours away from outcompeting B.1.1.7 (aka the UK or Kent variant) on a national scale in Great Britain.

Let’s not forget that B.1.1.7 virtually conquered the globe after being discovered in Britain in September 2020.  B117 Infections started to climb rapidly in Britain in December 2020, and it became the dominant sars-cov-2 variant in many countries across the globe shortly thereafter. Now, barely 5 months later, it is being dethroned by a variant that carries neither of the signature sars-cov-2 mutations that were of such concern in the existing VOC’s – E484K and N501Y.

 

This is the same B.1.617.2 / B.1.1.7 chart for India:

 

Charts courtesy of outbreak.info

 

UPDATE 24th May 2021:

UK: PHE data shows B.1.617.2 now outcompetes B.1.1.7

 

OLDER POSTS:

India: The stunning rise of the B.1.617.2 [Delta] #coronavirus variant

 

UK: eleven vaccine breakthrough cases reported for B.1.617.2

UK: Gisaid shows nearly 4,000 cases of B.1.617 #coronavirus variant across the UK

The latest data from Gisaid.org shows nearly 4,000 cases of B.1.617+ have been found in the UK and submitted to the database. This figure includes all sub-lineages including B.1.617.2, B.1.617.1 and B.1.617.3, although the latter two are still found at a relatively low level in the UK compared to B.1.617.2.

B.1.617.2 is still looking like it will outcompete B.1.1.7 across the entire UK within a short period of time.

 

Table courtesy of Gisaid

Graph courtesy of Outbreak.info

Singapore: B.1.617.2 Delta has a higher viral load in the respiratory tract of patients and stays for longer

On May 19, the director of Singapore’s National Center for Infectious Diseases, Professor Liang Yuxin, said in an exclusive interview with Singapore’s mainstream media, Lianhe Zaobao, that Singapore’s research shows that the recent local transmission of the mutant new coronavirus B.1.617.2 remains in the respiratory tract of patients in a higher amount. It also stays for longer, causing the virus to spread more easily.  A study found that patients infected with the B.1.617.2 virus had a higher amount and discharge of the virus in the respiratory tract than the original, longer time in the body, and a slower rate of decline.

Professor Liang Yuxin said that the lower the circulation threshold, the more viruses in the body. The circulation threshold of a common virus is about 20, while that of a variant virus is 15, so it may be easier to spread. She also said that the recent outbreaks of multiple infection groups in Singapore are all related to the B.1.617.2 variant virus that was first discovered in India.

Huanqiu.com report

 

Singapore: Changi Airport #coronavirus cluster – 18 patients with 61% vaccine breakthrough rate

 

 

Image by Jason Goh from Pixabay

UK: Dominic Cummings – UK’s #coronavirus border policy is a “joke”

 

UK: Matt Hancock says closing UK borders against #coronavirus are ‘Captain Hindsight’ decisions

UK: more cases of Delta #coronavirus variant found in Britain than in India

B.1.617 cases as of 16th May 2021 as per Wikipedia

 

And yes, we KNOW it’s because there is far more sequencing done in the UK than in India. The Brits should be proud of their world-class genome sequencing effort. They have been at the bleeding edge of the fight against this pandemic since day one.

 

UPDATE 17th May 2021: Wikipedia updated to show new figures:

 

 

Photo by National Cancer Institute on Unsplash