Github: AY.3.1 – a new sub-lineage of AY.3 concentrated in Mississippi, USA

AY.3 is the main variant being sequenced weekly in Mississippi (>70% of all recent sequences), most falling within this sub-lineage of AY.3 that is distinguished by the mutations described below (>60% of all recent sequences). For example, of 91 Pangolin-typeable sequences generated on 13 July 2021 by Dr. Robinson’s team, from broad sampling across Mississippi, 68 are AY.3 and 13 are unclassified B.1.617.2. Of those 81 Delta sequences, 60 are this new sub-lineage (those sequences are not yet in GISAID and are thus not included in the counts above for the USA or MS). Thus, there is clear epidemiological relevance of this sub-lineage in a region of the USA.

Github: A new sub-lineage of AY.3 concentrated in Mississippi, US


USA: AY.3 genomes increasing faster than Delta B.1.617.2


Image by Mark Dawdy from Pixabay

USA: Washington State Vaccine Breakthroughs by Variant up to 7th July 2021

Updated figures from Washington State showing vaccine breakthrough cases by the Sars-CoV-2 variant causing them up to 7th July 2021. Some changes from the previous file, notably an increase for Alpha breakthroughs, and a doubling of Delta breakthroughs from 5% to 10%.

Vaccine Breakthroughs up to 7th July 2021

7th July 2021

LineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Percentage of
Sequences From
All Covid-19
Cases With
Number Increase
From Previous

PREVIOUS WEEK: Vaccine Breakthroughs up to 30th June 2021

DateVariantLineageNumber of Vaccine
Breakthrough Cases
With Variant
Percentage of Vaccine
Breakthrough Cases With
Percentage of
Sequences From
All Covid-19
Cases With
30th June 2021AlphaB.1.1.728637%38%


USA: Washington State Vaccine Breakthroughs by Variant up to 14th July 2021


USA: vaccine breakthough cases in Washington State by coronavirus variant to 30th June 2021



Image by David Mark from Pixabay

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
International Epidemiology
VUI-21FEB-04 (B.1.1.318)
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: Transmission event of Delta coronavirus variant reveals multiple vaccine breakthrough infections

Here we describe a transmission of a Delta variant containing SARS-CoV-2 strain, between family members associated with events surrounding a wedding with 92 attendees, near Houston, Texas. Attendance required guests be fully vaccinated and took place outdoors in a large, open-air tent. To date, 6 individuals have tested positive for SARS-CoV-2, all patients were symptomatic, one patient severely enough to receive monoclonal antibody infusion treatment (Regeneron Pharmaceuticals Inc.) and one patient has died.

Encounter timings and viral sequence similarities suggest the strain containing the Delta variant was transmitted to wedding guests from two patients travelling from India. With no history of vaccine failure in these patients, our observations suggest these are true cases of vaccine breakthrough, mediated by the Delta variant.

Full Medrxiv Preprint: Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections 


Israel: Hebrew University study finds Pfizer vaccine just 70% effective against Delta variant


Israel: Pfizer vaccine effectiveness against coronavirus infection has dropped to just 64%


Image by Free-Photos 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

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

Chart courtesy of



Image by Ronile from Pixabay

From Alpha to Delta – how Britain won and then lost the fight against coronavirus

After months of being ravaged by the Alpha variant (B.1.1.7) in 2020, Britain seemed to turn a corner in its fight with the coronavirus in early 2021. After a gruelling lockdown, the Alpha variant was fading fast, and, by the middle of May 2021, Britain was within touching distance of Zero Covid. Then, through lax border controls, Delta was allowed to enter the country, and the infection cycle restarted.

Will Britain make the same mistake with the *next* variant of concern? With borders opening and “Freedom Day” on the horizon, it’s a racing certainty.

Images courtesy of

Israel: 50% vaccine breakthrough for coronavirus cases in the last month

Half of those recently infected with Covid-19 in Israel were fully vaccinated. Head of Public Health Services, Dr. Sharon Alray-Price, revealed the disturbing facts at a media presentation on Wednesday. According to her data, of the 891 cases of coronavirus confirmed in the last month alone, half had received both doses of Pfizer’s mRNA vaccine.

According to a report on Channel 12, in the months since the vaccines were rolled out, 6,765 people who received both shots have contracted coronavirus, and epidemiological tracing has revealed that an additional 3,133 people contracted Covid-19 from those vaccinated individuals. The 6,765 represent a little more than one percent of the total number of those vaccinated, which now stands at over 5,100,000. report


Binyamina, a town near Haifa in the north, was officially labelled a “red” location on Wednesday, according to the Health Ministry’s COVID guidelines.

The town had 122 active COVID cases as of Thursday morning, according to the Health Ministry, with a 3 percent overall positive rate among those tested, compared to 0.3% for the country as a whole. Binyamina is currently the only red location in the country, and the first to be designated as such in several months. Modiin, which had 71 active cases as of Thursday morning, was labelled “yellow.” Every other municipality in the country is considered “green.” report


USA: vaccine breakthough cases in Washington State by #coronavirus variant


Israel: increasing number of Delta #coronavirus outbreaks in schools


So what is Plan B if the vaccines fail with a new #coronavirus super-variant?



Image by Ri Butov from Pixabay

Germany: Delta #coronavirus infections double in one week

In Germany, the proportion of Delta variant infections is growing significantly.  In a sample, it almost doubled compared to the previous week to 15.1 percent, according to a report by the Robert Koch Institute (RKI). The information refers to the week from June 7th to 13th.

According to the RKI, Delta has been detected in all federal states in the past four weeks. Information from the reporting system was available for around 1,440 cases during this period, it said. The absolute number of weekly delta cases has increased since the 21st reporting week, from around 270 to around 470 in the 23rd reporting week. report (in German)



Image by FelixMittermeier from Pixabay

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). 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. 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

Canada: 82% Delta vaccine breakthrough in Calgary Hospital #coronavirus outbreak

An outbreak of the Delta coronavirus variant at the Foothills Medical Centre in Calgary has seen 16 patients and six health-care workers tested positive for the variant.  Six of the patients and five of the health-care workers had received two doses of the vaccine, while seven patients and one health-care worker had a single dose. The total vaccine breakthrough rate is 81.82%.  All of those infected were vaccinated with an mRNA vaccine. report



Image by  Qyd, CC BY-SA 3.0, via Wikimedia Commons

UK: BMJ letter – “we need an urgent focus on mitigations in schools” for Delta #coronavirus variant

“On the 17 May 2021, the UK government removed the requirement for face coverings in secondary schools in England. Writing in The BMJ on 14 May 2021, we argued that this was ill advised given the clear evidence for the role of children and schools in transmission of SARS-CoV-2 and the rise of the new variant, subsequently designated as delta, which was already implicated in school outbreaks at the time.

There has been a lack of transparency from Public Health England (PHE) around the spread of the delta variant in schools. On 22 May, an article in The Observer reported that these data had been withheld by PHE at the request of 10 Downing Street. On 31 May 2021, The Citizens, a group promoting accountability in public life, and the data rights firm AWO sent a pre-action letter warning that they would seek judicial review unless PHE published the data on the grounds they it had acted “unlawfully” by withholding data on the spread of the variant in schools, and had “surrendered its independent judgement.”

Concerningly, even now, PHE has failed to release the full data. In a detailed technical report released on the 3 June, it only provided data on the number of “incidents” or outbreaks involving two or more students in schools.  It did not provide numbers of delta variant cases linked to schools, which had been specifically and repeatedly requested by unions and scientists, and specified in the pre-action letter. Despite including several complex analyses, the 66-page report presented no breakdown of cases by age group. However, even the limited data provided on school outbreaks raises concerns. According to the report, 140 outbreaks of the delta variant had been identified in educational settings up to 30 May, the largest number in any of the settings specified. The data on “common exposures” (defined as two or more infected children with sequenced virus) for the week ending 11 May, just prior to dropping recommendations for masks in schools, showed that there were over 1000 common exposures for children infected with the delta variant in educational settings. Additionally, data from PHE and Office for National Statistics (ONS) showed that the highest overall infection rates were among secondary school age children.

PHE has continued to put out contradictory claims. Just a day after reporting that infection rates were currently highest in 10-19 year olds, it claimed that cases among school-age children were low.  This contradicted other ONS data released the same day that showed rapid rises in prevalence in this age group, with this now being much higher than all other groups. A day later the health secretary Matt Hancock stated that a “huge proportion of latest cases are in children.” This is reminiscent of messaging by the government from autumn and winter 2020 where the mantra “schools are safe” was used repeatedly to rationalise the lack of mitigations in schools, right up to the point they were closed on 5 January (following a day when many schools reopened briefly). At that point the Boris Johnson, the UK prime minister described them as “vectors for transmission, causing the virus to spread between households.”

Back to the present, the government has finally acknowledged the high rates of infection and transmission in children. As with its many previous errors, there is no acknowledgement that it has not followed advice from its own advisors. The government has left children, staff, and communities exposed to rapid spread of a new and more transmissible variant, and at risk of long covid.  Yet, even as we see absenteeism related to covid-19 rising in schools, with 31% children absent from secondary schools in Bolton, the government’s messaging remains focussed on rapid tests. This is despite dropping uptake over time, and clear evidence that tests alone have not been able to contain spread in schools. Even after acknowledging the risks of infection and transmission in children, there is still no emphasis on urgent mitigations, including masks and ventilation, that are vital if schools are to remain open. While we welcome the health secretary’s announcement that children may be eligible to be vaccinated in August this does not help right now. According to SAGE modelling, the current wave is expected to peak in late July. By that time thousands of children and their family members will have been affected.

Data from Bolton, and several other places, where the delta variant gained dominance suggested early on that infection spread first among school age children, and then to other age groups.  It is likely that lack of mitigations in schools played an important role in this highly transmissible, more virulent, escape variant gaining dominance rapidly across England.  Spread of the delta variant is likely to have played an important role in the exponential rises we are seeing of cases in England, and hospitalisations in North West England.

During the current crisis the focus on the Stage 4 re-opening on the 21 June by government and media detracts from actions that need to be taken immediately to pre-empt the potentially devastating impact of a third wave. Our concern here has been with the actions that must be taken in schools to keep our children safe.

First, we must reintroduce masks both at primary and secondary levels and both in classrooms and communal areas. Unions have jointly called for an immediate re-introduction of masks in secondary schools and several local authorities have already reinstated these. This needs to be incorporated into Department for Education guidance as a recommendation for all schools.

Second, there needs to be central investment in ventilation and air cleaning in schools, including CO2 monitors, and air filtration devices, to supplement ventilation where needed. Risk can also be reduced by moving to learning outdoors, where possible, including physical education activities.

Third, there must be practical, financial, and remote learning support for families with children who are isolating. And lastly, the Government must provide adequate catch-up resources for children who have lost out on education over the past year, to bridge gaps and worsening inequities in education.

In sum, schools are the place where infections are rising fastest. Yet schools are a place where the basic mitigations of face coverings, space, and fresh air are not simply missing, but—in the case of masks—have actually just been removed. This makes no sense. The government must act urgently to protect and support its children at this critical juncture.”

Deepti Gurdasani, senior lecturer in machine learning, Queen Mary University of London.

Hisham Ziauddeen, consultant psychiatrist, Cambridge and Peterborough NHS Foundation Trust, UK.

Stephen Reicher, professor, School of Psychology and Neuroscience, University of St. Andrews. Member of Independent SAGE and the advisory group to the Scottish chief medical officer.

Martin McKee, professor of European public health at the London School of Hygiene and Tropical Medicine. Member of Independent SAGE.

BMJ letter


UK: Dominic Cummings – Herd Immunity was always the official #coronavirus plan



On 16th March 2020 the first UK national lockdown was announced



Image by Wokandapix from Pixabay

UK: Delta variant is more infectious than the Alpha variant despite vaccinations

Shown above, the UK 2nd coronavirus wave, from September 6th to October 2nd 2020.

The Alpha variant (B.1.1.7) took about 26 days to infect around 90 people per million



Shown below, the UK 3rd coronavirus wave, from May 24th to June 10th 2021.

The Delta variant (B.1.617.2) has taken about 16 days to infect around 90 people per million, despite the massive UK vaccination campaign


And this is what happened after October 2nd 2020 with the Alpha variant:

Just one month later, on the 5th November 2020, Britain went into its second national lockdown. “England’s four-week lockdown will make a ‘real impact’, the prime minister says at a news briefing”


UK: massive rise in Delta #coronavirus vaccine breakthrough cases


** Coming soon **  15 months of unrelenting censorship of this blog and our Twitter feed. Don’t miss it!

UK: one week until B.1.617.2 Delta #coronavirus variant takes off

If the previous waves of Sars-CoV-2 in the UK are anything to go by, Britain is less than one week away from the B16172 Delta variant exploding into another full-blown national health crisis. The country’s current coronavirus case rate is roughly the same as it was on the 26th September 2020. Just five days later, on October 1st, the third wave of infections moved into a different gear entirely, swamping hospitals and causing thousands of deaths. 

It’s time to plan for the worst and hope for the best.



10th June 2021:

Vietnam: More than 6,000 Covid patients being treated at 107 medical facilities

“The pressure to treat Covid-19 patients is too large and too heavy”. More than 6,000 Covid patients are being treated at 107 medical facilities [in Vietnam], of which 37 are critical and 11 are ECMO interventions, putting pressure on the treatment system.

According to the Subcommittee on Treatment, the Ministry of Health, by the afternoon of June 9, more than 6,000 Covid-19 cases were being treated, the largest number of patients ever, of which more than half were in Bac Giang with more than 4,000 cases. Next is Bac Ninh, Ho Chi Minh City and Hanoi.

Among the patients, 97 had severe prognosis, 125 severe cases required oxygen, 43 severe cases required non-invasive ventilation, 26 critical cases required invasive ventilation; and 11 critical cases requiring ECMO (extracorporeal circulation). report (in Vietnamese)


Vietnam: Young #coronavirus patients with no underlying health conditions have ‘white lungs after a few days of Covid-19 symptoms’



Image by InstagramFOTOGRAFIN from Pixabay