Hi guys, I'm currently will be doing comparative genome analysis of human coronaviruses (including SARS-CoV-2, SARS-CoV and MERS-CoV). I will be including strains of each coronaviruses (along with their reference sequences as well) for my project for multiple sequence alignment. So far from what I knew is that the human coronaviruses strains are not that much, except SARS-CoV-2 strains which have over 10k+ now and I'm not capable to handle so many sequences, so may I ask how do I select the important strains of SARS-CoV-2 only?

I'm lost on how to retrieve sequences for SARS-CoV-2, all the retrieved sequences will be running multiple sequence alignment to identify the patterns and differences among the aligned sequences.

Any recommendations and opinions will be appreciated. Thank you.