The COVID-19 CG (covidcg.org) browser was built to enable scientists and professionals to systematically analyze millions of SARS-CoV-2 virus genomes and metadata in the GISAID database. Users can visualize lineages and mutations while filtering by location, date range, gene, and mutation of interest. Since its launch in August 2020, COVID-19 CG has been used by scientists to develop diagnostics for new variants and analyze mutations that may potentially impact therapeutic antibodies or small molecules. Here, we describe new features on the site and the new Lineage Reports page, which can be used to identify mutations unique to each SARS-CoV-2 variant, map these mutations onto protein structures of interest, and locate each lineage on a phylogenetic tree. We showcase these new features using three case studies in which users can use COVID-19 CG to (1) determine whether prominent variants may have mutations that could impact protease inhibitors, (2) assess whether the Omicron variant may have spike receptor-binding domain mutations that could affect antibody binding, and (3) evaluate whether commonly used diagnostics are useful for testing patient samples from different regions.