Possible English recombinant descended from Omicron and Delta (UKHSA "signal under monitoring")

[yexiao-cheng]

Sequences:
hCoV-19/England/ALDP-2F86D33/2021|EPI_ISL_8166781|2021-12-19
hCoV-19/England/QEUH-312A66E/2022|EPI_ISL_8610834|2022-01-02
hCoV-19/England/ALDP-31AE19E/2022|EPI_ISL_8865709|2022-01-06
hCoV-19/England/ALDP-325CFB2/2022|EPI_ISL_8898412|2022-01-11

The ORF1ab region of these 4 genomes is more similar to Delta, while the remaining regions are more similar to Omicron. It seems that these genomes are recombinants of Delta and Omicron. Or just contamination?

[vviala]

Dear @yexiao-cheng , you must map the sequencing reads of this sample to the assembled genome and look at the regions of interests. No or very low polymorphism indicate there is no contamination. Check for regions with unique Omicron or Delta deletions, they are usually better to find contamination polymorphism in your data. One way to verify your hypothesis is to design primers that will generate an amplicon that will cross from the unique Omicron-like region to the unique Delta-like region and sequence this amplicon to prove its contiguity.

[yexiao-cheng]

Hi @vviala
Thanks for your advice. It would be very helpful if corresponding deep sequencing data were available. But I only found these consensus sequences on GISAID.
It's also worth noting that these sequences were originated from different labs according to GISAID. Given the similar genomic patterns, I think contamination is less likely.

[vviala]

I guess they are all from the same originating lab: Wellcome Sanger Institute for the COVID-19 Genomics UK (COG-UK) Consortium. Only the reads info will helps us out with that

[yexiao-cheng]

Agreed that we need more evidence.

[amniewiadomska]

I see ambiguous bases in at least 2 of these genomes. May be the result of a mixed sequences (either contamination or co-infection).

[LVerdurme]

It could be a sequencing bias in co-infected patients: some parts of the genome are better amplified when they are delta (for example around Spike:400) and lead to a "delta-like" spike protein " in a globally omicron fasta. In Europe, especially in France with the intense circulation of delta and Omicron from December 15 to January 15, we saw a lot of samples like that.

[SVN-PhD]

Raw reads for these strains are here:
hCoV-19/England/ALDP-2F86D33/2021: https://www.ebi.ac.uk/ena/browser/view/SAMEA12081130
hCoV-19/England/QEUH-312A66E/2022: https://www.ebi.ac.uk/ena/browser/view/SAMEA12286794
hCoV-19/England/ALDP-31AE19E/2022: https://www.ebi.ac.uk/ena/browser/view/SAMEA12516829
hCoV-19/England/ALDP-325CFB2/2022: https://www.ebi.ac.uk/ena/browser/view/SAMEA12531205

[SVN-PhD]

UKHSA listed Delta x Omicron as a variant under monitoring/investigation: https://www.gov.uk/government/publications/sars-cov-2-variants-of-public-health-interest/sars-cov-2-variants-of-public-health-interest-11-february-2022

[hsnguyen]

Edit by @corneliusroemer: this comment talks about a different cluster for which an issue has been opened here #437, please continue discussion of the Australian cluster there

We've seen several sequences collected early this year in Queensland, Australia being called Omicron unassigned by Pangolin and show similar patterns: ORF1ab mutations are more like from Delta with high alternate freq. However they're far away from the aforementioned UK sequences (>20 SNPs):

• Australia/QLD5084/2022 (Illumina)
• Australia/QLD39476/2022 (ONT low qual.)
• Australia/QLD37984/2022 (Illumina)
• Australia/QLD0x00C42F/2022 (Illumina)

Not all of them are available on GISAID so here is the FASTA and VCF

A rough analysis based on scorpio haplotype of above 4 UK sequences and these 4 QLD sequences using AY.4 and BA.1 constellations:

suggesting that there're 2 different breakpoints from 2 independent recombinant events for UK and QLD sequences.

The low number of sequences may not strong enough for new lineage atm but will keep update if situation changes.

[hsnguyen]

Edit by @corneliusroemer: this comment talks about a different cluster for which an issue has been opened here #437, please continue discussion of the Australian cluster there

Additional 3 sequences make it 7 for this small cluster.

• Australia/QLD0x00C580/2022
• Australia/QLD5084/2022
• Australia/QLD37717/2022
• Australia/QLD37563/2022
• Australia/QLD39476/2022
• Australia/QLD37984/2022
• Australia/QLD0x00C42F/2022

fasta-sequences.zip

[thomasppeacock]

Just confirming that this cluster is one of the two under monitoring in the UK along with #441

[chrisruis]

Thanks @yexiao-cheng It doesn't look like there's any more genomes from this lineage so will close this for now