As bioinformatician which never worked before analyzing virus sequences, I'd like to know which current challenges exists in the analysis of SARS-CoV-2, in any of the stages: 1) detection & diagnosis 2) In prevention and 3) In treatment & therapeutics.
I saw the people at Nextrain did an impressive phylogenetics analysis for Genomic epidemiology. The group behind artic-network setup a plataform for nanopore analysis of sequences. And there are other APIs for example for geovisualization.
But there's a typical "the standard workflow for a virus strain"? What is the current "bottleneck" in bioinformatics for analyzing COVID-19 sequences? It's about finding better primer design sets? It's "Low-level RNA detection" like scRNA-seq analysis or dPCR over and nothing to do there? RNA modification analysis? Transcriptome data enrichment? High-Throughput (HT) SELEX? Do they do a Network analysis or Integrative analysis?
As you can see I am a little bit (completely) lost in this virology for bioinformatics. But would love to read some guidelance from an expert.