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

Preprint: Infectivity and immune escape of the new coronavirus variant of interest C.37 Lambda

“We also observed that the spike protein of the Lambda variant presented increased infectivity when compared with the spike protein of the Alpha and Gamma variants, both of them with reported increased infectivity and transmissibility. Together, our data show for the first time that mutations present in the spike protein of the Lambda variant confer escape to neutralizing antibodies and increased infectivity.”

“The evidence presented here reinforces the idea that massive vaccination campaigns in countries with high SARS-CoV-2 circulation rates must be accompanied by strict genomic surveillance aimed to rapidly identify new viral isolates carrying spike mutations as well as studies aimed to analyze the impact of these mutations in immune escape and vaccines breakthrough.”

Medrxiv preprint : Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda

 

Preprint: The emergence of Sars-CoV-2 #coronavirus variant Lambda C.37 in South America

 

 

Photo by Paula Porto on Unsplash

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

Delta coronavirus variant now dominant in the USA

The highly transmissible Delta variant is the most common strain of the Covid-19 virus circulating in the U.S., new data shows.  An analysis of genetic sequencing data as of June 27 showed that the Delta strain, also known as B.1.617.2, now makes up about 40% of positive Covid-19 test samples.

Wall Street Journal report

** Outbreak.info is showing that the Delta variant has risen to about 47% in the last three weeks.

Chart courtesy of Outbreak.info

 

 

Image by Ronile from Pixabay

Brazil: new strain of #coronavirus identified in Rio de Janeiro, designated P5

Monitoring in Rio de Janeiro, Brazil, has identified a possible new Sars-Cov-2 lineage, originating from P.1.1.28, in the region of Barra Mansa and Porto Real, on the border with the State of São Paulo, and which has only now been called P5. This strain has, among others, two mutations in the Spike protein (E484Q and N501T) that may be associated with escape from the immune system and with virus transmissibility. The discovery was widely reported in newspaper and television news throughout the week.

The results also describe the descendant lineage of VOC gamma (P.1) which was named P.1.2. This strain was initially found in the northern region of the state and is now widespread in all regions of the state of Rio and other states. Monitoring data still show that the P.1 lineage continues to be the most frequent (78%) in the state, and the low frequency of VOC Alpha (B.1.1.7) and the decline of P.2 since November of the year past.

According to Ana Tereza Vasconcelos, from the National Laboratory for Scientific Computing (LNCC), real-time municipal monitoring carried out by Rio de Janeiro is extraordinary for Brazil, and is within the recommendations of the World Health Organization, which recommends 18 days as optimal interval between the release of new data. Of the 92 municipalities in Rio de Janeiro, 91 are already being monitored. From March to June 2021, more than 2,300 samples have already been sequenced and processed on the LNCC supercomputer Santos Dumont, an institution linked to the Ministry of Science, Technology and Innovation (MCTI). Only the municipality of Comendador Levi Gasparian has not yet collected samples.

The data are from patients with a confirmed diagnosis of SARS-CoV-2 infection monitored in reference centers and hospitals in the State of Rio de Janeiro. Reports are issued every 15 days with updated data from 380 samples sequenced in the period and which are immediately available on the website http://www.corona-omica.rj.lncc.br/#/ .

Faperj.br report (in Brazilian)

 

 

Photo by Alex Teixeira on Unsplash

 

Chile: Santiago goes back into lockdown despite 60% #coronavirus vaccination rate

As of the early hours of this Saturday, 12th June 2021, Santiago de Chile has once again entered quarantine. The entire region begins with the mobility restriction measure when 57.8% of the country’s target population has completed their covid-19 vaccination schedule, but ICUs are on the brink of collapse.

According to the latest figures provided by the Undersecretary of Health, Paula Daza, the occupation of critical beds reaches 96% nationwide. But the vast majority of seriously ill patients are not immunized and there is a worrying decrease in the age of patients admitted to critical beds. Patients under 50 years of age in ICUs have tripled compared to the worst moment of last year, according to ICOVID, an initiative led by the University of Chile, the Pontificia Universidad Católica de Chile and the University of Concepción based on official data . The deaths reach 38,685, between confirmed and suspected.

El Pais report (in Spanish)

 

 

 

Lineage chart courtesy of Outbreak.info

Daily cases chart courtesy of OurworldinData.org

 

Image by javier alamo from Pixabay

UK: What happens after June 21st 2021 – Britain’s #coronavirus “Freedom Day”?

By Step 4 which will take place no earlier than 21 June, the UK government hopes to be in a position to remove all legal limits on social contact. We hope to reopen remaining premises, including nightclubs, and ease the restrictions on large events and performances that apply in Step 3.

UK COVID-19 Response – Spring 2021

 

Prague COVID-19 Response – July 2020:

 

“Those who cannot remember the past are condemned to repeat it”

 

#Czech hospitals in #coronavirus crisis “Each vacated bed fills up immediately”

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

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

Brazil: new #coronavirus strain P.1.2 confirmed circulating in Rio de Janeiro

The State Department of Health of Rio de Janeiro (SES-RJ) announced the identification of the new variant of the Covid virus in Rio de Janeiro late this morning. The strain received the name of P.1.2, because it is a change that occurred in the P.1 line – which appeared in Manaus.

“The objective of the study is to foresee the evaluation of the epidemiological scenario in the state of Rio de Janeiro to anticipate possible genomic alterations of the already known variants and to prepare the state and the municipalities to face any alteration that may change the pattern of the disease”, he affirmed. the superintendent of Epidemiological Surveillance of the Secretary of State for Health, Mário Sérgio Ribeiro.

Also according to the superintendent, still it is not possible to know whether P.1.2 is more lethal or more transmissible . The epidemiological impact is yet to be assessed.

The technical note of the state presents the genomic study with samples carried out between March 24th and April 16th. The study was carried out in partnership between the Lacen-RJ laboratory and the State Department of Health. According to the City Hall of Rio das Ostras, variants P.1 and P.2 have already been confirmed, previously, in the city.

“The presence of these variants in the municipality and the emergence of a new strain reinforce the importance of surveillance and monitoring of virus dispersions, the need to maintain all measures to prevent contagion and to maintain sanitary barriers”, warned the municipality.

Globo.com report

 

Local TV report on Brazilian variant P.1.2 : https://globoplay.globo.com/v/9499613/ (in Brazilian)

 

Brazil: P.1 mutates into new #coronavirus variant P.1.2

 

 

 

Image by Andrea Meakin from Pixabay

Brazil: P.1 mutates into new #coronavirus variant P.1.2

A new variant of the Brazilian coronavirus has been identified this week, according to Rio de Janeiro health authorities. The P1 Manaus strain seems to have mutated. Hence, the new version has been named P.1.2., scientists in Rio said.

The new variant P.1.2 was identified in 5.85% of the 376 samples taken in 57 municipalities of the state of Rio, second only to São Paulo in the total number of cases nationwide.

“So far it cannot be said that this variant is more contagious or lethal, which is a mutation of P1,” Rio State Health Undersecretary Claudia Mello said in a statement. She also explained that “the new variant was found mainly in the northern region of the state of Rio de Janeiro, but also the metropolitan area and coastal municipalities.”

MercoPress.com report

 

The new variant of Covid-19 was discovered during an investigation to identify which strains of the virus more circulate in the state. P1 remains in almost all regions and P2 in the north and in the lowlands. 376 samples were investigated, from 57 municipalities, selected from genomes sent to the Noel Nutels Central Laboratory (Lacen / RJ), between March 24th and April 16th.

Olhardigital.com report

 

Brazil: rapid spread and high impact of the #coronavirus VOC P.1 in Sao Paulo – March 2021

 

 

Image by Heiko Behn from Pixabay

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

 

 

 

UK SAGE: Lab studies suggest that the N501Y spike protein mutation increases binding to rat and mouse ACE2 leading to viral replication

A report issued by the UK government’s Scientific Advisory Group for Emergencies (SAGE) found the likelihood that a variant of concern (VOC) that has arisen in humans could infect a rodent and then spread among the animals is high. Researchers say lab evidence indicates that while rats and mice appear unable to contract the most common forms of coronavirus COVID-19, the N501Y spike protein mutation “has an increased affinity” for rodents.

The report said: “There is a plausible pathway for infection of rodents with new variants of concern from infected humans following contamination of an environment. “Experimental evidence has shown SARS-CoV-2 with N501Y has increased affinity for lab rodents and there is nothing to suggest the same would not be true for wild rodents.

SAGE: Coronavirus (COVID-19) response, 8 April 2021

 

 

Image by sipa from Pixabay