A point for your consideration. you can bring in ambiguities in the primer and make it specific and non-specific to just one target at the same time by keeping the seeding region of the primer stable.

Sarath Reghunathan

You mean degenerate primer design? I already got a plan for degenerate primer design, but I don't know the odds of the detection and what about complex infection.

Dear Raul Riesco

Thank you for the answer. It really helps me. But it seems to be easier for individual because there won't be too many pathogens. Targets may be not too much in each clinical specimen. However, your suggestion deserves to be considered seriously.

Dear Raul Riesco ,

Thank you very much for the discussion!

Are you referring to WHO list of pandemic pathogens?

Yes. It is clear that there are limitations of this approach. I approve "it is not feasible to design a reaction for ALL pathogens + accessory genes" now. Is it worthy if we can capture 80% of pathogen accessions or achieve 80% accuracy of the diagnoses?

Why do yo need to diagnose for 8 diseases if you are only considering 2? (think that with more targets, more false positives).

It’s hard for doctors to identify pathogen because the clinical symptoms caused by infection are always similar. However, we can combine primers for pandemic pathogens beforehand. In such situation (8 diseases), we can get information like [√ × √ × × × × × ] or [√ × × × × × √ × ] by target next generation sequencing, the working primers are patient-dependent. It would be helpful for clinical diagnoses. Additionally, it is uncommon for a person to be infected with more than 2 pathogens at the same time.

Are there any cross positives with common pathogens?

I don't know, but can we avoid it? like pathogen specific primer?

Mutation in virus is quickly, but can we design primers in the conserved region to maintain a high accuracy?