UK: PHE Technical Briefing and Variants of Concern update 18

PHE England have recently published new reports on the SARS-COV-2 variants circulating in Britain: Alpha, Beta, Gamma, Zeta, Eta, B.1.1.318, Theta, Kappa, B.1.617.3, AV.1, C.36.3, Lambda, C.37

SARS-CoV-2 variants of concern and variants under investigation in England

Variants under surveillance
Variant prevalence
Secondary attack rates
SARS-CoV-2 Immunity and Reinfection Evaluation (the SIREN study) cohort monitoring

Part 2: Delta (B.1.617.2) surveillance
Surveillance through genomic data
Delta with K417N (Delta-AY.1)

 

Investigation of SARS-CoV-2 variants of concern: routine variant data update

Data on individual variants
Alpha
Beta
Gamma
International Epidemiology
Zeta
Eta
VUI-21FEB-04 (B.1.1.318)
Theta
Kappa
VUI-21APR-03 (B.1.617.3)
VUI-21MAY-01 (AV.1)
VUI-21MAY-02 (C.36.3)
Lambda (C.37, VUI-21JUN-01)

 

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

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

UK: B.1.617.2 Delta #coronavirus variant cases double in four days to 2,323

The number of confirmed UK cases of the Covid variant first detected in India has almost doubled in four days, Health Secretary Matt Hancock said, as experts warned it could become the dominant type of the virus imminently. Speaking on the day indoor hospitality and other venues were allowed to reopen, Hancock told MPs that 2,323 cases of the variant known as B.1.617.2 had been confirmed, up from 1,313 on Thursday, with 483 of those in the outbreaks in Bolton and Blackburn.

Guardian report

 

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

 

UK: B.1.617.2 #coronavirus variant trajectory about 7 weeks behind India

 

Image by David Mark from Pixabay

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

From a Coronaheadsup post, 16th March 2020:   “why are our borders STILL open?

 

Canada CDC: ‘Researchers are monitoring for … B.1.617.4’

British Columbia CDC: “Researchers are monitoring for specific sublineages of this variant, including B.1.617.1, 1.617.2, B.1.617.3 and B.1.617.4”  (is this a typo?)

BCCDC.ca report

 

 

Image by Brigitte makes custom works from your photos, thanks a lot from Pixabay