Preprint: Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2

In this study, we reported the emergence and spread of the novel B.1.621 lineage of SARS-CoV-2, a new VOI with the insertion 146N and several amino acid substitutions in the Spike protein (T95I,Y144T, Y145S, R346K, E484K, N501Y and P681H). Although B.1.621 does not meet all of the VOC classification criteria so far, the set of mutations gathered the Spike protein could confer a synergistic impact on attributes such as reduction of vaccine-induced protection from severe disease, increased transmission and disease severity

Medrxiv preprint: Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
 

Belgium: 7 fully vaccinated care home residents die after contracting B.1.621 variant first found in Colombia

 

 

Image by gustavo9917 from Pixabay

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

Russia: #coronavirus revaccination planned for Moscow

Moscow Mayor Sergei Sobyanin has said that revaccination against coronavirus in the capital will take place with the Sputnik Light vaccine, which is also planned to be used to vaccinate labor migrants.

“It is vitally important to start revaccination now. Therefore, we will work with the government so that they quickly make a decision on the timing and technology. Revaccination will be the first component of the vaccine. If there was Sputnik, then the first component of Sputnik. There are no other options yet.” –

He said that the first component of Sputnik Light is planned to begin vaccination of labor migrants working in Moscow.

“Now the production of Sputnik Light has begun. In fact, this is the first component of the classic Sputnik . Most likely, we will receive permission to use it to vaccinate migrants,” Sobyanin wrote. He added that “according to our calculations, this will happen in early July, maybe even earlier.”

The Russian Ministry of Health clarified that Sputnik V and Sputnik Light are suitable for revaccination.

Moscow Mayor’s blog

 

Russia: New “Moscow” #coronavirus strain is Delta – Московский штамм коронавируса – Дельта

 

 

Photo by Nikita Ermilov on Unsplash

Russia: New “Moscow” #coronavirus strain is Delta – Московский штамм коронавируса – Дельта

Russian newspapers are still referring to a new “Moscow” strain of Sars-CoV-2, however it seems that the strain may simply be Delta (B.1.617.2).

Lenta.ru reports:

A modified Indian [Delta] strain of coronavirus was found in Moscow. This was announced by the head of the Gamaleya Center, Alexander Gintsburg”. 

“В Москве нашли измененный индийский штамм коронавируса. Об этом сообщил глава центра имени Гамалеи Александр Гинцбург.” Lenta .ru

 

But an Interfax report states that “Almost 90% of residents of the capital [Moscow] with coronavirus have an Indian [Delta] strain of the disease, said Moscow Mayor Sergei Sobyanin.

“The latest data that we received is that 89.3% have contracted a mutated coronavirus, the so-called ‘Delta’ is an Indian strain,” the mayor said in an interview with Channel One.

Почти у 90% заболевших коронавирусом жителей столицы выявлен индийский штамм заболевания, сообщил мэр Москвы Сергей Собянин.

“Последние данные, которые мы получили, – 89,3% заболели коронавирусом мутированным, так называемая “дельта” – это индийский штамм”, – сказал мэр в интервью Первому каналу.

Interfax.ru report

 

Moscow Mayor Sergei Sobyanin said that this strain spreads faster and is also more aggressive than others. According to the mayor, in order to resist this disease, the level of antibodies in humans must be twice as high as necessary for the “Wuhan” variant of the coronavirus. “In fact, we are starting to go through this story anew and with more serious consequences.”

 

 

Russia: “Moscow” #coronavirus variant – 1,705 new patients, 468 on ventilators, 71 deaths in one city in one day

 

Russia: “Moscow” #coronavirus variant strain announced

UK: Grant Shapps – “there’s a sort of Nepal mutation of the so-called Indian variant which has been detected and we just don’t know the potential for that to be a vaccine-defeating mutation”

Grant Shapps, UK Transport Secretary “we’ve seen two things really which caused concern. One is the positivity rate has nearly doubled since the last review in Portugal and the other is there’s a sort of Nepal mutation of the so-called Indian variant which has been detected and we just don’t know the potential for that to be a vaccine-defeating mutation”

Time for a Cabinet reshuffle surely?

Daily Mail report

The “Nepal Variant” – does it exist or is it just racist fearmongering?

 

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

 

Image by David Mark from Pixabay

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

  • UPDATED IMAGE ABOVE
  • * UK risk assessment for Delta variant as per 10th June 2021

 

Previous UK risk assessment as per 3rd June 2021

The UK government risk assessment for B.1.617.2 Delta variant has been published today and it’s NOT good news.

  • Transmissibilty between humans = Transmissibility appears greater than the wild type virus
  • Infection severity = More severe clinical picture or higher infection fatality than from wild type SARS-CoV-2 infections 
  • Immunity after natural infection = Experimental evidence of functional evasion of naturally acquired immunity 
  • Vaccines = Evidence of frequent vaccine failure or decreased effectiveness in humans 

Epidemiological and laboratory evidence of reduced vaccine effectiveness There are now analyses from England and Scotland supporting a reduction in vaccine effectiveness for Delta compared to Alpha [B.1.1.7]. This is more pronounced after one dose (absolute reduction in vaccine effectiveness against symptomatic infection of approximately 15-20% after 1 dose). Iterated analysis continues to show vaccine effectiveness against Delta is higher after 2 doses but that there is a reduction for Delta compared to Alpha. There is a high level of uncertainty around the magnitude of the change in vaccine effectiveness after 2 doses of Oxford-AstraZeneca vaccine.

Although this is observational data subject to some biases, it holds true across several analytic approaches and the same effect is seen in both English and Scottish data. It is strongly supported by pseudovirus and live virus neutralisation data from multiple laboratories. There are no data on whether prevention of transmission is affected and insufficient data to assess vaccine effectiveness against severe disease. The acquisition of an additional mutation which may be antigenically significant in a small number of cases is noted.

Overall assessment: Delta [B.1.617.2] is predominant and all analyses find that it has a very substantial growth advantage. The observed high growth rate is most likely to  be due to a combination of place based context, transmissibility and immune escape. Both English and Scottish analyses continue to support the finding of reduced vaccine effectiveness which has increased to high confidence. New early data from England and Scotland suggest a possible increased risk of hospitalisation compared to Alpha. The priority investigations are vaccine effectiveness against hospitalisation and transmission, household secondary attack rate corrected for vaccination, characterisation of the generation time, viral load and period of infectivity, and epidemiological studies of reinfections.

Download the report here: Investigation of SARS-CoV-2 variants of concern: variant risk assessments

 

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

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

 

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

More amazing work by Prof. Christina Pagel in deciphering the latest Public Health England data dumps for B16172. It’s well worth reading the whole thread!  The UK’s laissez faire attitude to border control and quarantine enforcement means that, after B.1.1.7, Britain is, once again, about to export a highly dangerous Sars-Cov-2 VOC worldwide. 

 

 

 

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

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: Detection of Spike Mutations; D80G, T95I, G142D, △144, N439K, E484K, P681H, I1130V, and D1139H, in B.1.1.482 Lineage (AV.1) Samples from South Yorkshire, UK

“Here we report the discovery of 24 recent B.1.1.482 pango lineage SARS-CoV-2 viruses in South Yorkshire that have acquired approximately 23 additional mutations when compared to the majority of other samples of this lineage. Nine of these additional mutations are found in the spike gene and six represent changes which are found in variants of interest and concern across the world and/or associated with reduced antibody binding (T95I, G142D, △144, N439K, E484K, P681H). Similar mutation profiles were also seen in B.1.1.482 samples from other regions in the UK. We recommended the monitoring of samples of this lineage which is now designated AV.1.”

Virological.org – Detection of Spike Mutations; D80G, T95I, G142D, △144, N439K, E484K, P681H, I1130V, and D1139H, in B.1.1.482 Lineage (AV.1) Samples from South Yorkshire, UK (UK Variant under investigation VUI-21MAY-01)

Virilogical.org report

 

UK: 49 cases of new #coronavirus variant under investigation VUI-21MAY-01 named AV.1

 

Image by Stanislav Hedvik from Pixabay

Vietnam: first case of #coronavirus variant B.1.617.2 found in Ho Chi Minh City

The Covid-19 research team of the Ho Chi Minh City Hospital for Tropical Diseases has just conducted rapid decoding of the genome of SARS-CoV-2 from patient 4514. This is a resident Covid-19 case, living in Thu Duc city, Ho Chi Minh City was recorded on May 18 and officially announced this morning by the Ministry of Health on May 19.

Dr. Nguyen Van Vinh Chau, Director of Ho Chi Minh City Hospital for Tropical Diseases – representative of the research team, said that the team used an RNA sample extracted from the oropharyngeal swab of patient 4514 on May 18, performed gene sequencing using Illumina MiSeq and MinION techniques, with Genious genome assembly software.

The results of identification by Pangolin software show that the obtained genome belongs to the B.1.617.2 variant. The results of mutation identification by COV-GLUE showed that the genome carried 6 typical aminoacid mutations (T19R, L452R, T478K, D614G, P681R, D950N) and a deletion mutation (156-158) on the protein region. spikes of the mutant B.1.617.2.

This leads to the conclusion: Patient 4514 is infected with a variant B.1.617.2 similar to the one causing epidemics in some places in the North.

Variant B.1.617.2 is one of three sub-branches of strain B.1.617 from India. According to TS-BS Nguyen Van Vinh Chau, this strain B.1.617.2 carries a double mutation of L452R and T478K.  The T478K mutation is also expected to specifically affect the affinity of the spike protein for the ACE2 receptor and make it easier for the virus to rapidly enter cells.

nld.com.vn report

 

Vietnam has been left relatively unscathed by the Covid-19 pandemic so far as can be seen below

 

Image by HAI DAO from Pixabay

Europe: B.1.620 #coronavirus variant – definitely one to watch

“Last month, Gytis Dudas was tracking a concerning new coronavirus variant that had triggered an outbreak of COVID-19 in his native Lithuania and appeared sporadically elsewhere in Europe and in the United States. Exploring an international database of coronavirus genomes, Dudas found a crucial clue: One sample of the new variant came from a person who had recently flown to France from Cameroon. A collaborator, Guy Baele of KU Leuven, soon identified six more sequences from people in Europe who had traveled in Cameroon. But then their quest to pinpoint the variant’s origins hit a wall: Cameroon had uploaded a total of only 48 genomes to the global sequence repository, called GISAID. None included the variant”

Sciencemag.org report

 

B.1.620 is also listed as a Variant of Interest by the ECDC:

 

More on the B.1.620 variant traced back Cameroon by Gytis Dudas in the Pango Designation

 

 

Cameroon: travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

 

Cameroon: travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

“In this study we have presented evidence that a SARS-CoV-2 lineage designated B.1.620, first detected in Europe in late February, is associated with Central Africa, where it appears to circulate at very high prevalence, and has been introduced into Europe and the US on multiple occasions. A fair number of known B.1.620 genomes that were sequenced in Europe stem from travel-related cases returning from Cameroon, suggesting that it is likely to be the immediate source of this lineage.”

VOC amino acid changes lineage B.1.620 shares most in common with:

B.1.1.7 (ORF1a: SGF3675/3677Δ, S:Y144Δ, S: HV69/70Δ, S: P681H, and S: D1118H)

P.1 (ORF1a: SGF3675/3677Δ, S:P26S, S:E484K, S: T1027I) and

B.1.351 (ORF1a: SGF3675/3677Δ, S: E484K, S: LLA241/243Δ)

MedrXiv preprint Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe

 

 

Image by rem734 from Pixabay

UK: 1600 cases of Delta variant B.1.617.2 in Britain, now at >8% of total

According to the Covid-19 genomics UK consortium database, in sequences up to 11th May, there have been 1,604 instances of B.1.617.2, making it the second most common variant in the UK.  Public Health England have designated B.1.617.2 a “variant of concern”, acknowledging it appears to be at least as transmissible as the dominant so-called Kent variant in the UK.

Covid-19 genomics UK consortium database

 

WHO: B.1.617 Indian #coronavirus strain is now a Variant of Concern or VOC

 

WHO: B.1.617 Indian #coronavirus strain is now a Variant of Concern or VOC