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.
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:
A post on the AY.4 sub-lineage of the Delta Sars-Cov-2 variant. Also known as B.1.617.2.4, this sub-lineage hasn’t received a lot of press attention yet, but it seems to have become the biggest sub-lineage of Delta across the globe so far.
In the USA, the Delta AY.4 sub-lineage is currently appearing in about 20% of sequences (light blue area) according to Outbreak.info:
In the UK, AY.4 currently appears in about 46% of samples (light blue area), and is now outcompeting B.1.617.2 (dark blue area).
AY.6 seems to be coming up on the rails though at 3%:
In Australia, AY.4 (dark blue area) clearly predominates over B.1.617.2 (light blue area) with 67% of sequences, B.1.617.2 is at 16% and AY.12 is at 10% :
In the USA, the estimated number of AY.4 cases was over 80,000 in early August 2021:
In the UK, the estimated number of AY.4 cases was about 13,000 in late August 2021
In Australia, the estimated number of cases was over 600 in late August 2021
In the USA, the demographics for AY.4 show it spreading across almost all age ranges,
But in the UK, AY.4 seems to be spreading amongst young children:
And in Australia, AY.4 seems to be spread across all age ranges:
The global reach of the AY.4 sub-lineage is really quite astounding considering it’s relatively recent appearance:
Further reading: New AY lineages and an update to AY.4-AY.12
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 Outbtreak.info 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.1.618.104.22.168, 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.1.622.214.171.124, Denmark lineage
AY.7.2 342 0 Alias of B.1.6126.96.36.199, 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 cov-lineages.org