This is reasonably idiomatic Python and 10x faster than the implementation in the original post:

  with open("orthocoronavirinae.fasta") as f:
      text = ''.join((line.rstrip() for line in f.readlines() if not line.startswith('>')))
      gc = text.count('G') + text.count('C')
      total = len(text)

Or if you want to be explicit, this is just as fast (and might scale better for particularly long genomes):

  gc = 0
  total = 0
  
  with open("orthocoronavirinae.fasta") as f:
      for line in f.readlines():
          if not line.startswith('>'):
              line = line.rstrip()
              gc += line.count('C') + line.count('G')
              total += len(line)

I didn't test Nim but the author reports Nim is 30x faster than his Python implementation, so mine would be about 3x slower than his Nim.