add chikv primers from Xavier et al 2023

[ammaraziz]

Primers from: https://pmc.ncbi.nlm.nih.gov/articles/PMC10362057

I am not the author of this, I hope this isn't a problem.

[ammaraziz]

I've done something to the primer.bed, the primer sequences are missing....

[ChrisgKent]

I'll merge if you are happy with the updates!

[ammaraziz]

Hey Chris,

Apologies I pulled the trigger on this PR too quickly. I Need to double check a few things, eg why the primer names are different from the paper.

[ChrisgKent]

Ah yeah. The dev regenerate command for primal-page version: 1.13.2 reformats the bed file. I meant to release a patch to fix that!

artic-network/primal-page#18

[ammaraziz]

Yeah could be that. I was given the bed file by a colleague, I want to double check things first before pulling the trigger.

[ammaraziz]

Hi Chris, I tracked down origin of this primer scheme, the provenance is completely wrong. Please accept my apologies, this primer scheme originated from the primal.zikaproject.org paper. To make matters worse, the primer names have changed in this submission (not a fault of primal-pages, something on our end).

It appears to be different from the existing artic-chikv-ecsa/400/v1.0.0 scheme. They use different a reference and the primer positions are different. I'll rework this pull request.

I think we've also worked up the zika primers from that paper.

Any suggestions on the name of the primer scheme?

[ammaraziz]

Made these changes:

1. Changed name to quick-chikv-esca
2. The amplicon length is marked as 300, but the primer names (and the paper) state 400. When I calculated the length it was closer to 300 than 400 on average.
3. I added both quick-lab and loman-lab because at the time the zika paper was loman lab. I made a judgement call, please correct as you see fit.
4. I added both citations, Xavier et al had 5 (oops 4) more primers which are in this version. The authors state this:

using a sequencing protocol (primers sequences in Supplementary Data 1) based on multiplex PCR-tiling amplicon approach design for MinION nanopore sequencing74

Clear as mud? 😆

I have reverted to a draft version. We've used this scheme to sequence samples. So I want to test the bed/ref to confirm everything is good before proceeding.

[ChrisgKent]

Thank you for doing the research on this!

It would be great if the scheme could be renamed to zibra-

Also for 4. it seems the scheme reported in the supplement of Xavier is identical to the scheme in the quick paper?

[ammaraziz]

It would be great if the scheme could be renamed to zibra-
Done!

Also for 4. it seems the scheme reported in the supplement of Xavier is identical to the scheme in the quick paper?

you are correct... further confusing the situation. I was relying on the github data found here which does not list the primer sets 43 and 44. I used seqkit locate to find the primer location.

I will remove the citation Xavier et al citation.

[ammaraziz]

Ready for review Chris!