I tried to do amplicon sequencing for the RSV virus, I got only 22% coverage, kindly suggest the troubleshooting steps to be done.
Sequencing steps in the nanopore was fine as I got complete coverage for another pathogen (SARS CoV 2) in the same run.
I got 10 lakh reads, out of which only 4000 were binding to RSV, most of them binds to the human genome and other bacteria.
I used 50 sets of primer pairs of 400bp long for 15kb genome size.
I have attached a reference image.