SARS-CoV-2 mutation rate remains low with Strain G still dominate among the six strains circulating and with little variability.
In contrast, common influenza variability is at least twice that.
The original Wuhan strain (L strain) is recorded at least as far back as December 2019, and subsequently mutated to the S strain in January 2020. At ~74% of all sequences, Strain G is the most widespread: it mutated into strains GR and GH at the end of February 2020.
Federico Giorgi: “The SARS-CoV-2 coronavirus is presumably already optimized to affect human beings, and this explains its low evolutionary change.”
Day et al (2020) observe zoonotic pathogen are normally “poorly adapted” in shifting hosts (e.g., bats to humans). Yet, Wuhan/Covid seems remarkably stable and optimized to the human host. In particular, Wuhan/Covid is extraordinary in its binding affinity with ACE2 receptors.
Day et al: “For SARS-CoV-2, six amino acids in the receptor binding domain of the spike protein are critical for binding the host target receptor ACE2 and allowing infection
in humans. These critical spike protein residues are not all present in the most closely related coronavirus.”
How Wuhan/Covid acquired that affinity is “impossible to know.”
Day et al.: “SARS-CoV-2 displays a star-like phylogeny with many long-tip branches, as
expected in a growing population. Based on genomic sampling over time, the substitution rate is estimated to be 0.00084 per site per year.”
Daniele Mercatelli, Federico M. Giorgi. Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Frontiers in Microbiology, 2020; 11 DOI: 10.3389/fmicb.2020.01800
Day, T., Gandon, S., Lion, S., & Otto, S. P. (2020). On the evolutionary epidemiology of SARS-CoV-2. Current Biology: CB, 30(15), R849–R857.
NextStrain.org phylogeny: https://nextstrain.org/ncov/global?r=region