Rapidly expanding Belgium/France B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L mutations

geertmartens commented 2 years ago

Description

Sub-lineage of: B.1.617.2 (current lineage designation by Pangolin, no AY. designation yet) with 5 additional mutations. These additional defining mutations are:

_ ORF | Amino Acid | Nucleotide | Codon -- | -- | -- | -- ORF1a | A211V | C897T | 896 - 898 ORF1a | T1822I | C5730T | 5729 - 5731 ORF1b | Q1441H | G17790T | 17788 - 17790 ORF7b | E3* | G27762T | 27762 - 27764 ORF2 (Spike

Earliest sequence B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L mutations :

· AZ Delta COVID-19 Genomics Core (Province of West-Flanders, Belgium): 31/08/2021, hCoV-19/Belgium/AZDelta-05069-2134R/2021|EPI_ISL_3933434|2021-08-31: in this province the highest number of sequences were recorded, indicating the epicenter of the newly proposed lineage.

· UGent Genomics Core (the adjacent Province of East Flanders, Belgium): 24/08/2021, hCoV-19/Belgium/UGent-10364/2021|EPI_ISL_4805613|2021-08-24

· This same variant was also identified by other Belgian surveillance labs: Aalst-OLV, CHU Namur, IPG, MBLGPF, ULB-IBC, ULG, ZNA, using various technologies (ARTIC-Nanopore, Illumina SARS-CoV-2 Research panel and others) indicating that it is not an artefact.

Most recent sequence: variant is actively circulating with rapidly increasing prevalence. Variant was observed consistently since week 34 up to most recent GISAID upload in week 42, indicating strong and persistent forward transmission. Latest sequence: hCoV-19/Belgium/AZDelta-2142-15496/2021|EPI_ISL_5855301|2021-10-28

Trend of incidence as recorded by baseline surveillance in the province of West-Flanders

Week number | Date, from | Date, to | Number ORF7b E3* variants | Total viral isolates sequenced | % of all isolates -- | -- | -- | -- | -- | -- 30 | 26/07/2021 | 01/08/2021 | 0 | 111 | 0% 31 | 02/08/2021 | 08/08/2021 | 0 | 125 | 0% 32 | 09/08/2021 | 15/08/2021 | 0 | 120 | 0% 33 | 16/08/2021 | 22/08/2021 | 0 | 170 | 0% 34 | 23/08/2021 | 29/08/2021 | 1 | 121 | 1% 35 | 30/08/2021 | 05/09/2021 | 1 | 119 | 1% 36 | 06/09/2021 | 12/09/2021 | 7 | 133 | 5% 37 | 13/09/2021 | 19/09/2021 | 13 | 69 | 19% 38 | 20/09/2021 | 26/09/2021 | 7 | 98 | 7% 39 | 27/09/2021 | 03/10/2021 | 19 | 130 | 15% 40 | 04/10/2021 | 10/10/2021 | 5 | 130 | 4% 41 | 11/10/2021 | 17/10/2021 | 21 | 154 | 14% 42 | 18/10/2021 | 24/10/2021 | 32 | 173 | 18%

) | P1263L | C25350T | 25349-25351

Earliest sequence B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L mutations :

· AZ Delta COVID-19 Genomics Core (Province of West-Flanders, Belgium): 31/08/2021, hCoV-19/Belgium/AZDelta-05069-2134R/2021|EPI_ISL_3933434|2021-08-31: in this province the highest number of sequences were recorded, indicating the epicenter of the newly proposed lineage.

· UGent Genomics Core (the adjacent Province of East Flanders, Belgium): 24/08/2021, hCoV-19/Belgium/UGent-10364/2021|EPI_ISL_4805613|2021-08-24

· This same variant was also identified by other Belgian surveillance labs: Aalst-OLV, CHU Namur, IPG, MBLGPF, ULB-IBC, ULG, ZNA, using various technologies (ARTIC-Nanopore, Illumina SARS-CoV-2 Research panel and others) indicating that it is not an artefact.

Most recent sequence: variant is actively circulating with rapidly increasing prevalence. Variant was observed consistently since week 34 up to most recent GISAID upload in week 42, indicating strong and persistent forward transmission. Latest sequence: hCoV-19/Belgium/AZDelta-2142-15496/2021|EPI_ISL_5855301|2021-10-28

Trend of incidence as recorded by baseline surveillance in the province of West-Flanders

Week number | Date, from | Date, to | Number ORF7b E3* variants | Total viral isolates sequenced | % of all isolates -- | -- | -- | -- | -- | -- 30 | 26/07/2021 | 01/08/2021 | 0 | 111 | 0% 31 | 02/08/2021 | 08/08/2021 | 0 | 125 | 0% 32 | 09/08/2021 | 15/08/2021 | 0 | 120 | 0% 33 | 16/08/2021 | 22/08/2021 | 0 | 170 | 0% 34 | 23/08/2021 | 29/08/2021 | 1 | 121 | 1% 35 | 30/08/2021 | 05/09/2021 | 1 | 119 | 1% 36 | 06/09/2021 | 12/09/2021 | 7 | 133 | 5% 37 | 13/09/2021 | 19/09/2021 | 13 | 69 | 19% 38 | 20/09/2021 | 26/09/2021 | 7 | 98 | 7% 39 | 27/09/2021 | 03/10/2021 | 19 | 130 | 15% 40 | 04/10/2021 | 10/10/2021 | 5 | 130 | 4% 41 | 11/10/2021 | 17/10/2021 | 21 | 154 | 14% 42 | 18/10/2021 | 24/10/2021 | 32 | 173 | 18%

Genomes We provide a CSV table with GISAID accessions/data of sampling/Nextclade analysis of QC and mutations, of N=126 genomes of B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3, S:P1263L mutations: • N=106 collected by the submitting lab, AZ Delta, West-Flanders (week 34-42) • N=20 collected by the sentinel lab in the adjacent province, East-Flanders, by UGent (week 34-39, data back log) Attachment: Nextclade Delta-ORF7bE3stop_N126_East and West Flanders We conducted an additional analysis of worldwide GISAID entries (EpiCov Seach tool), selected for high coverage and presence of S:P1263L and ORF7b:E3 variants. We thus identified N=145 of this newly proposed lineage. All these also had the ORF1a:A211V, ORF1a:T1822I and ORF1b:Q1441H mutations indicating a clear sublineage defined by at least 5 key mutations. Worldwide analysis indicates that the predominant cluster is in the province of West-Flanders, but with ramifications allover Belgium and the north of France. Attachment: GISAID Delta-ORF7bE3stop_global prevalance_N145 We provide a FASTA file with N=63 high coverage sequences generated by AZ Delta of B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3, S:P1263L mutations and a CSV with additional metadata (sampling location and time): FASTA high cov_B.1.617.2 with ORF7bE3stop_N63 Metadata high cov_B.1.617.2 with ORF7bE3stop_N63 Evidence On a total of 1579 viral isolates sequenced since August 1, 2021, as part of the baseline (unbiased) surveillance in the province of West-Flanders, we detected N=106 isolates with the ORF7b E3 stopcodon and the other 4 defining mutations, highlighted for genotype in blue in the radial plot below.

Possible impact and reason why we feel this variant deserves a separate Pango designation In SARS-CoV, the ORF7b is a highly hydrophobic 44-amino acid peptide, hypothesized to be a transmembrane protein and part of the virion. It is not essential for viral replication, but triggers specific antibodies in infected humans [1]. SARS-CoV-2, the ORF7b protein appears involved in the regulation of IFN-gamma production in vitro triggered by SARS-CoV-2 and hence possibly plays a role in vivo for the virus’ immunogenicity [2,3]. In a recent preprint (bioRxiv preprint doi: https://doi.org/10.1101/2021.02.05.428650) it was hypothesized based on in vitro studies by Fogeron et al. that ORF7b might play a role in the induction of COVID-19 symptoms such as heart damage and anosmia. Theoretically the ORF7b E3 mutation abrogates translation of the ORF7b right from the start, leading to complete loss of expression of the 43 amino acid peptide. This is not expected to influence replication and infectiousness, but if ORF7b is no longer or much less expressed, it might have an impact on the virus’ ability to induce interferon responses and trigger inflammatory damage. Such a loss of expression could thus possibly be make the virus less pathogenic though not less transmissible. Perhaps it might be associated to less symptomatic disease, making the virus more ‘stealthy’ and prone to asymptomatic transmission. In the coming weeks we will intend to collect two types of confirmatory data: • Clinical data: are infections with viral sublineages with ORF7b stop codon less symptomatic: this information will be requested through the national contact tracing agencies to the extent this info is available • Viral studies: we will attempt to detect expression and level of the ORF7b peptide and investigate using high resolution proteomics if the ORF7b E3 mutation does in fact leads to loss of ORF7b expression, or not. A collaboration with the group at Ghent University with B. Van Puyvelde and M. Dhaenens has been put in place to do so in short term [4] and samples have been bio-banked to this purpose [4]. New lineage proposal_B.1.617.2 with ORF7b stop E3.pdf [Metadata high cov_B.1.617.2 with ORF7bE3stop_N63.csv](https://github.com/cov-lineages/pango-designation/files/7487919/M GISAID Delta-ORF7bE3sto [Nextclade Delta-ORF7bE3stop_N126_East and West Flanders.csv](https://github.com/cov-lineages/pango-designation/files/7487921/Nextclade.Delta-ORF7bE3stop_N126_East.and.West.Flanders.csv) p_global prevalance_N145.csv etadata.high.cov_B.1.617.2.with.ORF7bE3stop_N63.csv)

corneliusroemer commented 2 years ago

Sub-lineage of: B.1.617.2 (current lineage designation by Pangolin, no AY. designation yet) with 5 additional mutations. These additional defining mutations are:

ORF	Amino Acid	Nucleotide	Codon
ORF1a	A211V	C897T	896 - 898
ORF1a	T1822I	C5730T	5729 - 5731
ORF1b	Q1441H	G17790T	17788 - 17790
ORF7b	E3*	G27762T	27762 - 27764

We provide a CSV table with GISAID accessions/data of sampling/Nextclade analysis of QC and mutations, of N=126 genomes of B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L mutations:

N=106 collected by the submitting lab, AZ Delta, West-Flanders (week 34-42)
N=20 collected by the sentinel lab in the adjacent province, East-Flanders, by UGent (week 34-39, data back log)

We conducted an additional analysis of worldwide GISAID entries (EpiCov Seach tool), selected for high coverage and presence of S:P1263L and ORF7b:E3* variants. We thus identified N=145 of this newly proposed lineage. All these also had the ORF1a:A211V, ORF1a:T1822I and ORF1b:Q1441H mutations indicating a clear sublineage defined by at least 5 key mutations. Worldwide analysis indicates that the predominant cluster is in the province of West-Flanders, but with ramifications allover Belgium and the north of France.

We provide a FASTA file with N=63 high coverage sequences generated by AZ Delta of B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3, S:P1263L mutations and a CSV with additional metadata (sampling location and time): FASTA high cov_B.1.617.2 with ORF7bE3stop_N63 Metadata high cov_B.1.617.2 with ORF7bE3stop_N63 Evidence On a total of 1579 viral isolates sequenced since August 1, 2021, as part of the baseline (unbiased) surveillance in the province of West-Flanders, we detected N=106 isolates with the ORF7b E3 stopcodon and the other 4 defining mutations, highlighted for genotype in blue in the radial plot below.

Possible impact and reason why we feel this variant deserves a separate Pango designation

In SARS-CoV, the ORF7b is a highly hydrophobic 44-amino acid peptide, hypothesized to be a transmembrane protein and part of the virion. It is not essential for viral replication, but triggers specific antibodies in infected humans [1]. SARS-CoV-2, the ORF7b protein appears involved in the regulation of IFN-gamma production in vitro triggered by SARS-CoV-2 and hence possibly plays a role in vivo for the virus’ immunogenicity [2,3]. In a recent preprint (bioRxiv preprint https://doi.org/10.1101/2021.02.05.428650) it was hypothesized based on in vitro studies by Fogeron et al. that ORF7b might play a role in the induction of COVID-19 symptoms such as heart damage and anosmia.

Theoretically the ORF7b E3* mutation abrogates translation of the ORF7b right from the start, leading to complete loss of expression of the 43 amino acid peptide. This is not expected to influence replication and infectiousness, but if ORF7b is no longer or much less expressed, it might have an impact on the virus’ ability to induce interferon responses and trigger inflammatory damage. Such a loss of expression could thus possibly be make the virus less pathogenic though not less transmissible. Perhaps it might be associated to less symptomatic disease, making the virus more ‘stealthy’ and prone to asymptomatic transmission.

In the coming weeks we will intend to collect two types of confirmatory data:

Clinical data: are infections with viral sublineages with ORF7b stop codon less symptomatic: this information will be requested through the national contact tracing agencies to the extent this info is available
Viral studies: we will attempt to detect expression and level of the ORF7b peptide and investigate using high resolution proteomics if the ORF7b E3* mutation does in fact leads to loss of ORF7b expression, or not. A collaboration with the group at Ghent University with B. Van Puyvelde and M. Dhaenens has been put in place to do so in short term [4] and samples have been bio-banked to this purpose [4].

corneliusroemer commented 2 years ago

Here's an Usher tree with sequences from Europe with the signature, looks interesting, has popped up 20 times in France, 4 times in Czechia, a couple in Denmark/UK. Looks real.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a785_579330.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:G17790T,G27762T

And here it is on a Belgium tree:

https://nextstrain.org/groups/neherlab/ncov/belgium?branchLabel![image](https://user-images.githubusercontent.com/25161793/140561832-deb2eae8-1743-4807-8b9a-1cb83fb742a8.png)aa&c=gt-nuc_897

geertmartens commented 2 years ago

Dear Cornelius,

Thanks for your strong commitment and fast review of our newly proposed sublineage: Rapidly expanding Belgium/France B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L mutations (Issue #306)

How does the review proceed from here?

I will urgently notify our National Genomic Surveillance network, since I see a rapid expansion of this new lineage, with in my latest NGS run 20 of 80 (25%) sequences carrying this 5-mutation signature, and I am worried about its rapid spread. It would be relevant if we can designate a clear Pango (sub)lineage to this viral evolution.

Best wishes, Geert

FedeGueli commented 2 years ago

Here the covspectrum: https://cov-spectrum.ethz.ch/explore/Belgium/AllSamples/Past3M/variants?aaMutations=S%3AP1263L%2COrf1a%3A211V%2Corf1A%3AT1822I%2Corf1b%3AQ1441H&pangoLineage=B.1.617.2*

VariantTimeDistributionChart (1)

geertmartens commented 2 years ago

Our working title for this new B.1.617.2 variant with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L is the 'Poppy variant', in reference to the famous poem by John McCrae about Flanders fields, where this variant appears expanding In Flanders fields the poppies blow Between the crosses, row on row That mark our place; and in the sky The larks, still bravely singing, fly Scarce heard amid the guns below.

geertmartens commented 2 years ago

The main cluster is around the region of Kortrijk-Waregem, and there appears to have a growth advantage of 12% (8%-16%)

corneliusroemer commented 2 years ago

I support designation @chrisruis This is going up pretty smoothly consistent with a transmission advantage like AY.4.2 It's now got 370 sequences of it in Europe, should be enough for designation.

About 20% of sequences have also picked up S:222V and some of these have reached Spain and Denmark.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15bdc_6afd20.json?branchLabel=Spike%20mutations

FedeGueli commented 2 years ago

Screenshot_2021-11-20-09-30-33-310_com android chrome

growing reaally fast in the last two weeks it reached 7% in Belgium

chrisruis commented 2 years ago

Thanks @geertmartens We've added this as AY.123 in v1.2.99 to start on the branch with G17790T (Orf1ab:Q5842H) and G27762T (Orf7b:E3) to coincide with both Orf7b:E3 and the likely introduction(s) into Belgium

cov-lineages / pango-designation

Rapidly expanding Belgium/France B.1.617.2 with additional ORF1a:A211V, ORF1a:T1822I, ORF1b:Q1441H, ORF7b:E3*, S:P1263L mutations #306