Proposal for sublineage of AY.43 with Spike:N501S in Portugal [~60 sequences]

[insapathogenomics]

New lineage proposal – AY.43 with Spike:N501S in Portugal By: Bioinformatics Unit, National Institute of Health Dr Ricardo Jorge (INSA), Portugal

Description Sub-lineage of: AY.43 Earliest sequence: 2021-10-23 Most recent sequence: 2021-11-09 Countries circulating: Portugal

In Portugal, we have been detecting AY.43 sequences with the additional mutations Spike:N501S, ORF8:A51V and N:R195I. The first case was detected on 23 October 2021. Since then, in our weekly national sampling (~500/week), we have been observing an increase in relative frequency and its dissemination through several districts. The low genetic diversity found within this cluster suggests that all cases are likely linked to a single source/introduction.

Genomes Portugal/PT19662/2021 EPI_ISL_6012260 23/10/2021 Portugal Portugal/PT19816/2021 EPI_ISL_6012587 26/10/2021 Portugal Portugal/PT19886/2021 EPI_ISL_6012657 26/10/2021 Portugal Portugal/PT20038/2021 EPI_ISL_6012817 26/10/2021 Portugal Portugal/PT20077/2021 EPI_ISL_6012857 26/10/2021 Portugal Portugal/PT20252/2021 EPI_ISL_6267378 27/10/2021 Portugal Portugal/PT20256/2021 EPI_ISL_6267382 30/10/2021 Portugal Portugal/PT20278/2021 EPI_ISL_6267404 29/10/2021 Portugal Portugal/PT20324/2021 EPI_ISL_6267451 31/10/2021 Portugal Portugal/PT20327/2021 EPI_ISL_6267454 01/11/2021 Portugal Portugal/PT20434/2021 EPI_ISL_6267563 02/11/2021 Portugal Portugal/PT20437/2021 EPI_ISL_6267566 02/11/2021 Portugal Portugal/PT20439/2021 EPI_ISL_6267568 02/11/2021 Portugal Portugal/PT20445/2021 EPI_ISL_6267574 02/11/2021 Portugal Portugal/PT20486/2021 EPI_ISL_6267615 02/11/2021 Portugal Portugal/PT20634/2021 EPI_ISL_6267767 01/11/2021 Portugal Portugal/PT20672/2021 EPI_ISL_6267805 02/11/2021 Portugal Portugal/PT20695/2021 EPI_ISL_6587945 05/11/2021 Portugal Portugal/PT20700/2021 EPI_ISL_6587950 07/11/2021 Portugal Portugal/PT20713/2021 EPI_ISL_6587963 06/11/2021 Portugal Portugal/PT20731/2021 EPI_ISL_6587981 08/11/2021 Portugal Portugal/PT20734/2021 EPI_ISL_6587984 08/11/2021 Portugal Portugal/PT20739/2021 EPI_ISL_6587989 05/11/2021 Portugal Portugal/PT20804/2021 EPI_ISL_6588056 09/11/2021 Portugal Portugal/PT20904/2021 EPI_ISL_6588159 08/11/2021 Portugal Portugal/PT20909/2021 EPI_ISL_6588164 08/11/2021 Portugal Portugal/PT20918/2021 EPI_ISL_6588173 09/11/2021 Portugal Portugal/PT20928/2021 EPI_ISL_6588183 08/11/2021 Portugal Portugal/PT20945/2021 EPI_ISL_6588200 05/11/2021 Portugal Portugal/PT20946/2021 EPI_ISL_6588201 06/11/2021 Portugal Portugal/PT20992/2021 EPI_ISL_6588247 09/11/2021 Portugal Portugal/PT20994/2021 EPI_ISL_6588249 08/11/2021 Portugal Portugal/PT20995/2021 EPI_ISL_6588250 09/11/2021 Portugal Portugal/PT21000/2021 EPI_ISL_6588255 09/11/2021 Portugal Portugal/PT21046/2021 EPI_ISL_6588304 06/11/2021 Portugal Portugal/PT21052/2021 EPI_ISL_6588310 08/11/2021 Portugal Portugal/PT21057/2021 EPI_ISL_6588315 05/11/2021 Portugal Portugal/PT21071/2021 EPI_ISL_6588329 08/11/2021 Portugal Portugal/PT21079/2021 EPI_ISL_6588337 07/11/2021 Portugal Portugal/PT21088/2021 EPI_ISL_6588346 07/11/2021 Portugal Portugal/PT21125/2021 EPI_ISL_6588383 08/11/2021 Portugal Portugal/PT21129/2021 EPI_ISL_6588387 08/11/2021 Portugal Portugal/PT21134/2021 EPI_ISL_6588394 08/11/2021 Portugal Portugal/PT21139/2021 EPI_ISL_6588399 08/11/2021 Portugal Portugal/PT21155/2021 EPI_ISL_6588415 06/11/2021 Portugal Portugal/PT21156/2021 EPI_ISL_6588416 06/11/2021 Portugal Portugal/PT21158/2021 EPI_ISL_6588418 07/11/2021 Portugal Portugal/PT21163/2021 EPI_ISL_6588423 02/11/2021 Portugal Portugal/PT21165/2021 EPI_ISL_6588425 02/11/2021 Portugal Portugal/PT21166/2021 EPI_ISL_6588426 02/11/2021 Portugal Portugal/PT21167/2021 EPI_ISL_6588427 02/11/2021 Portugal Portugal/PT21168/2021 EPI_ISL_6588428 02/11/2021 Portugal Portugal/PT21170/2021 EPI_ISL_6588430 04/11/2021 Portugal Portugal/PT21171/2021 EPI_ISL_6588431 05/11/2021 Portugal Portugal/PT21172/2021 EPI_ISL_6588432 05/11/2021 Portugal Portugal/PT21173/2021 EPI_ISL_6588433 05/11/2021 Portugal Portugal/PT21175/2021 EPI_ISL_6588435 05/11/2021 Portugal Portugal/PT21176/2021 EPI_ISL_6588436 06/11/2021 Portugal

[FedeGueli]

Thank you for proposing it! I noticed it in your super useful weekly report

[corneliusroemer]

There seem to be very few sequences so far, on the order of ~20? Should be monitored but in my eyes too early for designation.

covSpectrum

[insapathogenomics]

There are currently 58 sequences on GISAID as a result of our latest national sampling. We are currently working on our weekly report (to be released tomorrow - https://insaflu.insa.pt/covid19/) where we will provide further details about its dissemination trends.

[corneliusroemer]

Thanks @insapathogenomics. I'm wondering about why you say you have 58 and covSpectrum shows only 17.

When did you add the sequences? Could it be in the last few days, meaning that covSpectrum will get the remaining 40 sequences over the next few days?

[MCB6]

Could it be in the last few days, meaning that covSpectrum will get the remaining 40 sequences over the next few days?

41 of the 58 have been added today

[insapathogenomics]

We do not know the delay between GISAID and covSpectrum update. The complete GISAID accession list of the 58 AY.43+S:N501S sequences is above.

[corneliusroemer]

Ok, so that's the explanation, you added 41 of 58 only today.

[insapathogenomics]

We have now release our short weekly report (https://insaflu.insa.pt/covid19/), highlighting the marked increase in relative frequency of the AY.43+ Spike N501S: 0.2% (week 42), 1.4% (w 43), 7.6% (w 44), 4.9% (w 45, sampling not closed); It was already detected in 13 Districts (from 18 Districts and 2 Archipelagos), since its first detection on 23 October 2021 (i.e., in roughly two weeks). According to this scenario, we believe a new sub-lineage assignment would greatly help monitoring its spread nationally and its eventual circulation abroad.

[FedeGueli]

Quite impressive growth.

@chrisruis @corneliusroemer

[agolsby]

Your recent uploads are now visible on CoV-Spectrum Dr. Jorge, and their model is spitting out a 58-106% transmission advantage.

[MCB6]

did it stop growing? Nothing in this week's uploads from Portugal, and covSpectrum shows the most recent frequency at 3.6% (but with a lot of uncertainty due to low sample count) https://cov-spectrum.ethz.ch/explore/Portugal/AllSamples/AllTimes/variants?aaMutations=S%3AN501S&pangoLineage=AY.43

[MCB6]

511 genomes from Portugal uploaded yesterday. The decline of S:N501S share appears to have continued.

[insapathogenomics]

Just a brief update from Portugal:

• This “AY.43+S:N501S” keeps circulating in Portugal, representing ~4% in our latest national sampling.
• After a brief search of the combination “AY.43 + S_N501S + N_R195I + ORF8_A51V” in the GISAID database, we found recent matches from Switzerland, Belgium, Italy, Spain and Israel:

Virus name Accession ID Collection date hCoV-19/Switzerland/SO-ETHZ-34522806/2021 EPI_ISL_6721802 22/10/2021 hCoV-19/Belgium/ULB-IBC_CV8207975302/2021 EPI_ISL_6812799 19/11/2021 hCoV-19/Italy/LAZ-IFO-11133045/2021 EPI_ISL_6815736 13/11/2021 hCoV-19/Spain/MD-HGUGM-5818715/2021 EPI_ISL_6854457 19/11/2021 hCoV-19/Israel/SMC-7022022/2021 EPI_ISL_6859810 06/11/2021

Taking into account this scenario (i.e., considerable circulation in Portugal and recent detections abroad), we stress that sub-lineage assignment can greatly help monitoring its spread.

[chrisruis]

Thanks @insapathogenomics We've added this as AY.43.5 in v1.2.105 to start on the branch with A23064G (S:N501S)