New mutation from wastewater sample

[pratibha-kadam]

Hello,
I am working in surveillance of wastewater samples and I have this doubt about defining the new mutation from the wastewater samples.
is it possible to define a new mutation from a wastewater samples ?? Coz I believe new predominant variants are early detected using wastewater samples so, similarly can we define a new mutation which stabilized with the time is a new mutation which observed in the population.

Thanks
Pratibha

[aineniamh]

Hi @pratibha-kadam, do you mean lineage rather than mutation?

pangolin was developed for full genome sequences from a sample with little or no mixture. If your wastewater sample has a majority variant, the consensus you generate from that should be able to have a sensible pangolin assignment, but if you have a lot of lineages circulating and the sample is very mixed, I would be very cautious using pangolin to assign lineages to genome sequences. Similarly if you've very short segments and not complete genomes, pangolin may produce inaccurate results. Hedgehog operates from just the spike protein and combines lineages into sets that can be assigned, but again it's not designed to be used against wastewater data.

[pratibha-kadam]

Thanks @aineniamh

But my question is about mutation only? I know pangolin is used to determine the lineages. But, just for the clarify from the experts like you, is it possible to say that new mutation is found in the wastewater sample based on the stability of the new mutation with the time?