Cecret for Human Norovirus Typing

[ABissonn]

@k-florek @fanninpm @erinyoung @tives82 @DrB-S

I have been using Cecret for all things SARS-CoV-2 and our research lab just started to work up a NGS methodology for Human Norovirus sequencing with primer specific amplification of Group I virus as well as Group II human norovirus samples. I tried to configure the cecret config file for my amplicon of interest, creating both a HuNoV Group I primer and amplicon bedfiles, as well as specific bedfiles for Group II HuNoV. Would anyone be able to walk through my config file and discuss my process with me at their earliest convenience. Our wet-lab approach is to use the same Group I primer pair and Group II primer pair from the Polymerase:Capsid (PC) sanger sequencing amplicon methodology (Citation: Chhabra, Preeti et al., Single-step RT-PCR assay for dual genotyping of GI and GII norovirus strains, Journal of Clinical Virology 134 (2021). The PCR amplification step creates a single 570 bp or 579 bp product that we are then fragmenting using the same Illumina tagmentation DNA Prep library kit that our lab utilizes for the SARS-CoV-2 modified Artic NGS pipeline that we use Cecret with. Thanks.

Adam Bissonnette
Integrated Research and Development Lab
Marshfield Clinic Research Institute
E-Mail: bissonnette.adam@marshfieldresearch.org
Cell: 401-714-1625
Office: 715-221-6762

[erinyoung]

This sounds like a really interesting project! I'll send you an email.