USA: 40% vaccine breakthrough in Massachusetts last week

Breakthrough infections accounted for about 40% of all cases reported in Massachusetts last week. The Massachusetts Department of Public Health has tracked a cumulative 19,443 confirmed COVID-19 infections among those fully vaccinated in the state to date and a total of 144 deaths. report




Image by Oliver Fuß from Pixabay

UK: The Alpha variant rears its ugly head again

A big surprise in the latest UK sequencing figures show that the Alpha variant has made something of a comeback this week. Even though the percentage of Alpha cases is still tiny compared to that of Delta, the figure of more than 400 Alpha cases is the highest since mid-June 2021.

It’s unclear whether this is a localised outbreak (it may be part of the unfolding superspreader event of the Boardmasters festival in Cornwall for example), or whether these are cases scattered across the UK, but to see such a resurgence after so many weeks of Delta dominance is something of a shock as the Alpha variant was far less effective at breaking through vaccine protection than the Delta variant is.

After weeks of just a handful of Alpha cases in the UK, there is suddenly a spike of over 400 new cases:


Confirmation that the Delta variant has dipped recently:

Charts and data courtesy of




Image by Josch13 from Pixabay

CDC: mRNA vaccines just 53.1% effective against Delta infection among nursing home residents

“Two doses of mRNA vaccines were 74.7% effective against infection among nursing home residents early in the vaccination program. During June–July 2021, when B.1.617.2 (Delta) variant circulation predominated, effectiveness declined significantly to 53.1%”

This study could not differentiate the independent impact of the Delta variant from other factors, such as potential waning of vaccine-induced immunity. Further research on the possible impact of both factors on VE among nursing home residents is warranted. Because nursing home residents might remain at some risk for SARS-CoV-2 infection despite vaccination, multipronged COVID-19 prevention strategies, including infection control, testing, and vaccination of nursing home staff members, residents, and visitors are critical.

CDC report:   Effectiveness of Pfizer-BioNTech and Moderna Vaccines in Preventing SARS-CoV-2 Infection Among Nursing Home Residents Before and During Widespread Circulation of the SARS-CoV-2 B.1.617.2 (Delta) Variant — National Healthcare Safety Network, March 1–August 1, 2021


France: hundreds infected by Covid-19 in nursing homes in one week


Preprint: Cryptic transmission of Delta AY.3 among fully vaccinated patients

Here we report cryptic transmission associated with high Delta variant viral load among vaccinated patients on an inpatient medical-surgical ward. These findings demonstrate transmission of Delta variant with high viral load between vaccinated inpatients, the continued efficacy of masking and vaccination for protecting healthcare personnel, and the potential need for post-admission surveillance to prevent cryptic Delta variant transmission.

Medrxiv preprint: Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward





Image by Silas Camargo Silão from Pixabay

Delta attempting to brute-force its way past the human immune system

The Delta variant of Sars-CoV-2 seems to have taken a leaf from a computer hacker’s manual by attempting to brute-force its way past human and vaccine immunity systems by spitting out slightly mutated versions of itself almost on a daily basis.

Similar to cracking a password, brute-forcing means that the virus is trying every possible combination of variations to find the most effective one, and it’s doing it incredibly quickly. The most successful new mutations then become dominant through selection pressure.

Many of these new Delta plus variants are distinguishable only by a single mutation, but the brute-force technique the virus is now using represents the biggest threat to humanity so far, as we have no obvious means to prevent it.

For example, two weeks ago, we took a snapshot of that showed a big rise in the AY.3 Delta plus variant in the USA.


Now, just two weeks later, the AY.3 variant has already been supplanted by the AY.4 variant:




The number of Delta plus variants seems to be rising ever more quickly, each variant with its own individual key combination to try to pick the immunity lock. With no lockout mechanism for failed attempts, the virus can just keep trying until it succeeds.

Here’s a list of the Delta Plus variants so far, taking us up to AY.15, with many more to be added soon we’re sure:

AY.1 United States of America 44.0%, Portugal 10.0%, United Kingdom 10.0%, Japan 10.0%, Switzerland 7.0% 2021-04-07 243 562 Alias of B.1.617.2.1, in several European countries, from pango-designation issue #95

AY.2 United States of America 99.0%, Mexico 0.0%, Spain 0.0%, Aruba 0.0%, Albania 0.0% 2021-03-31 201 1232 Alias of B.1.617.2.2, in USA with K417N, from pango-designation issue #107

AY.3 United States of America 98.0%, Mexico 1.0%, United Kingdom 0.0%, Japan 0.0%, Germany 0.0% 2021-04-13 846 7503 Alias of B.1.617.2.3, USA lineage, from pango-designation issue #121

AY.3.1 United States of America 100.0%, India 0.0% 2021-05-18 197 983 Alias of B.1.617.2.3.1, USA lineage, from pango-designation issue #147

AY.4 United Kingdom 68.0%, United States of America 12.0%, Denmark 3.0%, Spain 2.0%, France 2.0% 2021-01-05 3684 152304 Alias of B.1.617.2.4, UK lineage, from pango-designation issue #180

AY.5 United Kingdom 68.0%, Portugal 12.0%, Spain 4.0%, France 4.0%, Ireland 3.0% 2021-04-15 436 6837 Alias of B.1.617.2.5, UK lineage, from pango-designation issue #180

AY.6 United Kingdom 79.0%, United States of America 8.0%, Ireland 2.0%, Italy 2.0%, Denmark 1.0% 2021-01-08 201 7007 Alias of B.1.617.2.6, UK lineage, from pango-designation issue #180

AY.7 Denmark 71.0%, United Kingdom 23.0%, Italy 3.0%, France 1.0%, Germany 1.0% 2021-05-01 134 6417 Alias of B.1.617.2.7, UK lineage, from pango-designation issue #180

AY.7.1 4624 0 Alias of B.1.617.2.7.1, Denmark lineage

AY.7.2 342 0 Alias of B.1.617.2.7.2, predominantly Italy lineage in multiple other European countries

AY.8 United Kingdom 100.0%, Australia 0.0%, Belgium 0.0% 2021-04-20 703 707 Alias of B.1.617.2.8, UK lineage, from pango-designation issue #180

AY.9 United Kingdom 64.0%, Denmark 11.0%, Germany 5.0%, Switzerland 4.0%, Belgium 3.0% 2021-04-01 322 6892 Alias of B.1.617.2.9, UK lineage, from pango-designation issue #180

AY.10 United Kingdom 73.0%, Canada 8.0%, United States of America 7.0%, Gambia 5.0%, France 2.0% 2021-04-12 71 771 Alias of B.1.617.2.10, UK lineage, from pango-designation issue #180

AY.11 United Kingdom 33.0%, United States of America 16.0%, South_Africa 11.0%, Turkey 10.0%, Ireland 6.0% 2021-02-06 522 2138 Alias of B.1.617.2.11, UK lineage, from pango-designation issue #142

AY.12 Denmark 11.0%, United States of America 11.0%, United Kingdom 10.0%, Germany 10.0%, Israel 7.0% 2020-09-07 579 26845 Alias of B.1.617.2.12, Israel lineage, from pango-designation issue #170

AY.15 94 0 Alias of B.1.617.2.15, Canada lineage

Lineage information courtesy of


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

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

UK: Is Delta already making way for a fitter variant?

One thing that we have been keeping on eye on recently is the possible successor variant to Delta B.1.617.2 in the UK.  The Alpha B.1.1.7 variant had a shelf life of about 5 months before it was displaced by Delta. Will Delta have a similar shelf life?

Delta seems to have been on the wane in the UK over the couple of weeks, so is it already making way for a stronger, fitter variant? If it is, it won’t be long before that successor variant becomes apparent, and the removal of all Covid mitigations on UK “Freedom Day” has given it plenty of opportunity to spread quickly.


Below, Alpha had a shelf life of about 5 months in the UK. Delta already seems to be waning. What will take its place?


Below, Delta may have peaked worldwide, but there is no clear successor variant yet.


Below, It doesn’t look like the successor variant will be Delta AY.3 in the UK from this chart, but it’s too early to tell….


Below, Delta peaked in early May 2021 in India, but hasn’t immediately been followed by another stronger variant. The next variant could be waiting for a fall in the population’s antibody levels from the Delta wave which could take 3-6 months, creating an opportunity from August 2021 onwards. The shelf life for Delta in India, in a largely unvaccinated population, was just three months.

The problem for the UK government, though, is that by dropping all mitigations on 19th July 2021, they may have encouraged Delta to peak early and, as a consequence, left enough time for a second larger, and perhaps far worse, autumn or winter wave to form.

As we said in this post in on 16th July:

“According to the UK’s Chief Medical Officer, the idea is that a Covid-19 wave in the summer will prevent an even worse wave in the winter.  Our prediction is that Johnson will simply get two waves for the price of one – the wave he is promoting now, by removing all mitigations, and an even worse winter wave caused by yet another new variant.”



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

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

A long and detailed Twitter thread by Vinod Scaria on the rise of the AY.3 Delta plus variant in the USA which seems to be outcompeting Delta B.1.672 in some states. is showing that AY.3 genomes are found in 37% of recent sequences.




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