Delta (AY.4) and BA.1 recombinant in France/Denmark [~30 seqs, isolated/passaged in Vero] #444
Comments
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I believe EPI_ISL_9857381 was collected on 2022/02/04 from Denmark? |
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Ah you're correct, my mistake. I'll go ahead and edit it. Found an additional two isolates.
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Dear Scott, very nice catch. The French NRC at Institut Pasteur confirms that the sequences EPI_ISL_9879436 and EPI_ISL_9879437 have overall high coverage, and no minor variant populations suggestive of a co-infection or contamination (both are Illumina data, not Nanopore). Those 2 genomes at least are indeed very likely recombinants. |
Hi Simon-Loriere Lab, Thank you, that's good to hear from the sequencing side. Also good eye, I've updated the post to indicate which strains were sequenced by which technologies, I definitely needed coffee that day... I think that we're seeing shared mutations with different platforms in different labs in different countries along with information from the French NRC suggest they are likely recombinants! |
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Ran the sequences through Nextclade, here's the summary: Breakpoints appear to be There are some rare mutations in ORF3a which allow tracking possible donors on the AY.4 side: It's a rather short stretch that's been inserted, two breakpoints. Not impossible but we'll have to see raw reads and maybe more examples popping up to confirm. @SVN-PhD it'd be great if you could share links to the Usher trees so that we can just look at them without having to rebuild. You can just copy the link from the browser address bar, it's something like nextstrain.org/... Here it is: |
corneliusroemer
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This might be another one: EPI_ISL_10096770 collected on Feb 13th, from Denmark.
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Dear colleagues, I have shared the raw data for EPI_ISL_9879436 on GISAID, and EPI_ISL_9879437 is on its way. Both are amplicons (Artic V4.1) / Nextera XT / 2x150 cycles. |
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I've been taking a look at the Danish sequences and I think there might be a hint, if they are truly recombinat, they may have arisen seperatley. This is based on two observations:
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I have eventually identified the likely AY.4 donor sequences: They share with the recombinant proposed lineage: Covspectrum Analysis: EDIT:
So it has A8723G, G21641T, C25667T, G25855T, G29540A , G29645T , Please @corneliusroemer @c19850727 could you check them? |
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Dear FedeGueli, thanks for also looking into this. We are focusing on a very similar pattern of mutations, just without ORF3a:S26L, absent from our recombinant sequences (and from additional suspected genomes under investigation). Dear thomasppeacock, the C20032T change in the sequences from Denmark is indeed very interesting. This variation is absent from the additional suspected sequences from France. The sequence from The Netherlands appears also quite distinct from our recombinant. Fascinating if they are independent. Our sample size is very low (yet?) but it is tempting to wonder if this reflects things on the template switch mechanism (potential “hot spots” like in other viruses) or on the fitness/compatibility of the resulting chimeric genomes... |
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I think i spotted another sequence belonging to the recombinant lineage from Denmark: |
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Has anyone figured out a good covSpectrum query to monitor this cluster? I tried the following, but it captures only 6 sequences: |
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Hi corneliusroemer, we are working with these 3 mutations for now but also working on [at least/or] variations with additional markers (1 sequence from France is quite partial and limiting us, and we are also concerned with drops in the spike). I'm counting 12 sequences from now. The 6 from France come from different regions. |
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Hi all, apologies, have been away for the last few days. Found a 13th genome, this is Denmark/DCGC-379814/2022 with accession EPI_ISL_10207240 with a recent collection date (2022-02-16). Here is a tree of these 13 sequences in context with some GISAID's Europe nextregions in context. Edit: Another new genome (the 14th), this is Denmark/DCGC-381072/2022 with accession EPI_ISL_10210832 with a collection date of 2022-02-06. Tree has been updated accordingly. |
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Great build @SVN-PhD, thanks for sharing! Some sequences have reversions to root, but only terminal tips. |
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Found another strain in this cluster on GISAID. hCoV-19/France/HDF-IPP54794/2022 | EPI_ISL_10352397 Will rebuild the tree on Monday after the weekend, stay safe everyone.
Edit on 2022-03-01
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Dear Scott, there should be 2 more from France (already on GISAID or on their way)! |
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Hi all, |
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Thank you, I have incorporated your 3 genomes with another one released today.
Interestingly, France/ARA-14290323596/2022 was sequenced by a Nanopore GridION. Here is a table of all the strains that we have found in GISAID that are members of this cluster. Strains
Updated Phylogenetic Tree
Cheers, Update on 2022-03-02 The new strains are:
Update on 2022-03-03 |
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I've updated the accessions list of the 25 genomes of this potential cluster. Please find it attached. Should this cluster be assigned or is there a further need for investigations @chrisruis @corneliusroemer @thomasppeacock @Simon-LoriereLab? Cheers, Accession |
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Thanks a lot Scott! I have been kindly given access to most of the raw data of these genomes from France (will have access soon at the data from Marseille) and all of them are clean, no issues of sequencing or contamination. |
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Of course they are clean otherwise I would not have submitted the consensus genomes to GISAID...
Best
Philippe
…---------
Prof. Philippe Colson PU-PH des disciplines pharmaceutiques, Pharm.D / Ph.D
IHU Méditerranée Infection
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Microbes Evolution Phylogeny and Infections (MEPHI), IRD
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Objet : Re: [cov-lineages/pango-designation] Potential Delta (AY.4) and BA.1 recombinant in European countries (Issue #444)
Thanks a lot Scott! I have been kindly given access to most of the raw data of these genomes from France (will have access soon at the data from Marseille) and all of them are clean, no issues of sequencing or contamination.
A Pango designation would be extremely helpful indeed as this variant now circulates (at low noise) in many regions of France.
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Hi all, Thanks again @Simon-LoriereLab for the raw reads on GISAID, it was very helpful! From what I see in IGV, the reads look pretty clean. Now I haven't used IGV much before so let's go through what I did. I used the Cecret pipeline to process raw reads and to also check the consensus genome (corresponds with the submitted sequences on GISAID). I used the sorted .bam and .bai index files to visualize the sorted and mapped reads, relative to the NC_045512.2 genome. Reads are visualized by pairs and linked. Reads that are linked have a light gray line connecting them. I can see that the 6 bp deletion (resulting in Δ157/158) in the spike gene are linked to to its respective pair with a 3 bp deletion (Δ212) with the 9 bp insertion resulting in EPE at 214. The Δ157/158 is a marker of AY.4 and Δ212 with ins214EPE are markers of Omicron. Am I interpreting this correctly as a sanity check? I've highlighted some of the reads that are linked.
This is using France/HDF-IPP08027/2022 | EPI_ISL_9879437. Thank you!! |
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@Simon-LoriereLab can you confirm that you managed to isolate the recombinant and passage as these metadata seem to indicate? Well done! |
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Dear Cornelius, I was just the messenger as I checked the NGS data, my colleagues Flora and Angela from the National Reference Center did the isolation! |
corneliusroemer
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I have locked this conversation as it has moved in a direction that would be best pursued in the MedRxiv comment section. |
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Thanks all, this has been added as lineage XD in v1.2.133 |
Potential Delta (AY.4) and Omicron recombinant
Description
Sub-lineage of: AY.4
Earliest sequence: 2022-01-17 (France | EPI_ISL_9959921 | EPI_ISL_9879436)
Most recent sequence: 2022-02-05 (Netherlands | EPI_ISL_9863764)
Countries circulating: Denmark / France / Netherlands
Proposed Lineage: If this is real, XD or whatever is next on the PANGO recombinant designations.
I don't have access to the raw sequencing reads to these strains so unsure if this is a real recombinant. However, these strains are highly related and are present in 3 countries in Europe. Additionally, these strains were sequenced in different laboratories with different sequencing platforms (Illumina: EPI_ISL_9879436, EPI_ISL_9879437, EPI_ISL_9857381, EPI_ISL_9449070, EPI_ISL_9166910) and (Nanopore MinION: EPI_ISL_9863764, EPI_ISL_9791275).
NextClade identifies these strains as 21J (Delta) and Pangolin v3.1.20 in UShER mode classifies these as AY.4.
NextClade Alignment of these sequences with some complete/high coverage genomes of Delta and a BA.1 (PHEC-5P0B7ZEF) and BA.2 (ALDP-35D5DD2):
The breakpoint appears to be right before the S gene.
Zooming in on the S gene:
Genomes
accessions_list.txt
Additional Mutations
This small cluster shares this mutation in addition to characteristics of Omicron spike mutations.
Phylogenetic Tree
Potential recombinant lineage in the context of other strains (embedded within AY.4)
Zoomed in:
Greater tree (strains highlighted by red box):
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