In my lab we study cancer evolution rather than pathogens so I’m no virology expert but since we use the same kind of data (sequencing) and the same kind of methods (i.e. Bayesian phylogenomics, coalescent theory, parameter inference from phylogenies, phylogeography, etc) of genomic epidemiology, I took the time to collate some old and new papers describing methods and tools relevant to COVID-19 genomic data analyses. Hope this is useful:
Good old Bayesian phylogenomics applied to the latest COVID-19 genomes:
Fantastic and prophetic review about genomic epidemiology during viral outbreaks:
Estimating biological parameters from phylogenetic trees (applicable to viral genomes) with Bayesian inference and coalescent:
Some interesting phylogeography
If somebody finds themselves stuck in front of a paywall, please let me know I will share the PDFs.