I made a script to retrieve all of the recorded full-length human lung infecting coronaviruses in genbank (virus variation database, ncbi). After trimming out all of the really small files or those that didnt work, I'm left with ~200 fasta files to work with. What are some analyses I can run with the new COVID-19 genome? I made a blast database and ran some blastn queries but I'm wondering what bioinformatic analyses are typically run on novel viruses? 

My blastn query of word size 7 had a few hits but I am wondering how to interpret these results and what to do with that data.

This is just for fun/educational. I don't have much experience with viruses or comparative genomics. 

Thanks
Since you selected these strains (which are similar) there is not much of a point in doing BLAST analysis. Instead, you can start doing a multiple sequence alignment with the sequences. If you are serious about learning then there are command line version of `MAFTT`, `T-COFFEE`, `Clustal` , `MUSCLE`. You will also find web front-ends for these tools (if you search around). A multiple sequence alignment gives you an idea of relationship of the sequences to each other. This can then be used to infer possible evolutionary relationships among the genomes. 

`MEGA` is [user friendly software][1] that has a GUI for doing above analysis. They have a [pretty good online][2] manual as well.


  [1]: https://www.megasoftware.net/
  [2]: https://www.megasoftware.net/web_help_10/index.htm#t=Preface.htm