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 CovSpectrum.org

 

 

 

Image by Josch13 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 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.1.617.2.3.1, 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 cov-lineages.org

 

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

India: Delta Plus Delta-AY.1 dominant in Tripura – found in 138 out of 151 coronavirus sequences

At least 138 of the 151 Covid-19 samples sent by Tripura for genome sequencing have tested positive for the Delta Plus variant, State Health Surveillance Officer Dr Deep Kumar Debbarma said. Tripura, thus, is the first state in the northeast to have recorded a case of the Delta Plus variant.

Addressing reporters on Friday evening, Debbarma said the samples were sent to a laboratory at Kalyani, West Bengal, for the virological test. “Delta Plus variant was found in 138 of the 151 samples. 10 others tested positive for the Delta variant while three cases of alpha variant were found,” Debbarma added.

Indian Express Report

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)

 

Poland: 106 cases of Delta and 12 cases of Delta Plus aka Delta-AY.1 coronavirus variant

Poland has confirmed 106 cases of the Delta and 12 cases of the Delta Plus (Delta-AY.1 or Delta with K417N mutation) coronavirus variants that originated in India, a deputy health minister has announced.

Speaking to Polish public Radio One on Friday, Waldemar Kraska presented a report on the new variants.

“I have just received a report showing that currently we have 106 confirmed Delta cases. We also have 12 confirmed cases of Delta Plus,” Kraska said.

TheFirstNews.com report

 

USA/UK: 2 separate clades of Delta #coronavirus variant with K417N – AY.1 and AY.2

 

 

 

Image by Dimitris Vetsikas from Pixabay

USA/UK: 2 separate clades of Delta #coronavirus variant with K417N – AY.1 and AY.2

Through routine scanning of variation in Delta, a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1.  A second clade found in sequences uploaded to GISAID from the USA, now designated AY.2.

As of 16 June 2021, 161 genomes of Delta-AY.1 have been identified on GISAID. from Canada (1), India (8), Japan (15), Nepal (3), Poland (9), Portugal (22), Russia (1), Switzerland (18), Turkey (1), USA (83).

There are currently 38 cases of Delta-AY.1 in England (36 confirmed sequencing and 2 probable genotyping). Cases have been detected in 6 different regions in England. Delta-AY.2 has not been detected in England.

UK Variants of Concern Technical Briefing 15 (PDF download)

 

According to Bani Jolly of the Institute of Genomics and Integrative Biology, the phylogeny of Delta has two separate clades. While AY.1 is found in a few countries including the UK, India and Nepal, the other clade (AY.2), is largely from the sequences from California (USA).

“The split between the two clades seems to be based on two spike mutations — A222V and T95I. While all sequences in the California cluster share spike A222V, all sequences in the larger international cluster share spike T95I,” Jolly tweeted.

Stating that AY.1 has arisen independently a number of times and could be more prevalent than observed in countries with limited genomic surveillance, she tweeted that given that Delta is a variant of concern, it is important to take note of any sub-lineages that may emerge.

Time of India report

 

 

 

Image by PublicDomainPictures from Pixabay

Nepal: nearly 20% of Delta #coronavirus sequences have K417N mutation – mountaineers variant increasing

The Nepalese Ministry of Health and Population (MoHP) said that out of 47 confirmed delta variant samples, nine were found to have K417N mutations.

According to the ministry, the new mutation has also been named AY.1 (aka Delta-AY.1 or “Mountaineers” variant).

Issuing a press statement on Monday, the MoHP revealed that AY.1 mutation has been confirmed in more than 10 countries, including Nepal.

With this, Nepal has witnessed Alpha and Delta as the variant of concern and Kappa variant of concern, the Ministry said.

The Ministry had selected 48 samples from the National Public Health Laboratory from the people of all age groups from April 29  to June 3 and tested them in WHO identified Center for Excellence in Genomics, The Institute of Genomics and Integrative Biology (IGIB).

Out of them 47 samples had come with delta variant B.1.617.2 and one had come with alpha variant B.1.1.7. Among the 47 delta variant samples nine had shown K417N mutation, the Ministry said.

Kharbarhub.com report

 

UK: Delta with K417N – the “mountaineers” variant – PHE #coronavirus Delta-AY.1 update

 

UK: “Everest climbers could have spread potentially more infectious and vaccine resistant’ variant

UK: Delta with K417N – the “mountaineers” variant – PHE #coronavirus Delta-AY.1 update

Of the 36 cases of Delta-AY.1 (mountaineers) variant, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS). 

“Through routine scanning of variation in Delta a small number of sequences were detected which had acquired the spike protein mutation K417N. Information suggests that there are at least 2 separate clades of Delta with K417N. One clade is large and internationally distributed with PANGO lineage designation AY.1. A second clade found in sequences uploaded to GISAID from the USA. There is limited epidemiological information available at present.

International Epidemiology
As of 7 June 2021, 63 genomes of Delta with K417N have been identified on GISAID. from Canada (1) Germany (1), Russia (1), Nepal (2), Switzerland (4), India (6), Poland (9), Portugal (12), Japan (13), USA (14).

Epidemiology
There are currently 36 cases of Delta-AY.1 in England (35 confirmed sequencing and 1 probable genotyping) plus an additional 10 sequences which include some cases in other UK nations and some genomes for which case data is being sought. The first 5 cases were sequenced on 26 April 2021 and were contacts of travellers to Nepal and Turkey. All these cases were detected in the West Midlands. Cases have been detected in 6 different regions in England (Table 21, Figure 26). The majority of cases are in younger individuals, with 2 cases of age 60 or over (Figure 27). Out of the 36 cases, there were 11 travel associated cases (6 travellers and 5 cases amongst contacts of travellers). Twelve cases have no history of travel or contact with travellers. Countries of travel included red-list countries (Nepal and Turkey), amber-list countries (Malaysia) and green-list countries (Singapore).

Of the 36 cases, 27 cases were known to have a vaccination status within the National Immunisation Management System (NIMS), when linked on NHS number. Of these, 18 cases occurred in people who were not vaccinated, 2 cases in people who had received their first dose within 21 days of specimen date, 5 cases in people who had received their  first dose more than 21 days after specimen date. There was a total of 2 cases where there were more than 14 days between the second dose of vaccine and a positive specimen. No deaths have been recorded amongst the 36 cases.”

PHE download – SARS-CoV-2 variants of concern and variants under investigation in England  – Technical briefing 15 (PDF)

 

UK: The “mountaineers variant” – B.1.617.2 with K417N mutation

 

UK: “Everest climbers could have spread potentially more infectious and vaccine resistant’ variant

 

 

Image by Simon from Pixabay