Methods
Deaths and confirmed cases data from the European CDC
(https://www.ecdc.europa.eu/en/covid-19-pandemic)1,
which is updated daily, was accessed on April 6, 2020. SARS-CoV-2 viral
spike sequences were accessed from the GISAID database
(https://www.gisaid.org) on April 6, 2020. Assuming that a patient
was tested and accounted as a confirmed case 11 days before death, the
case fatality rate (CFR) was calculated from total cases and total
deaths per day in each country, considering an average of 11 days from
hospitalization to death (medRxiv 2020.01.29.20019547). The analysis was
restricted to a time window consisting of the last 8 days from the data
accession date (3/30/2020-4/6/2020). Both the average and median CFR
were calculated for analysis. Standard linear regression was performed
for CFR vs D614 percentage from this data using GraphPad Prism,
including and excluding the data from the United Kingdom, which
exhibited an unusually low number of cases due to an unusually low level
of testing/diagnosis and an unusually high level of death reporting.
For structural analysis of the impact of 614 D/G identity, we used
published
cryo-electron microscopy structures of the SARS-CoV-2 trimeric viral
spike in its “down”, or unliganded, state, wherein the host
angiotensin converting enzyme 2 (ACE-2) binding site is buried and
inaccessible (PDB ID 6VXX), and its “up” state, wherein this host
receptor binding site that is necessary for viral infection is exposed
(PDB ID 6VYB, 6VSB)2,3. A single monomer (chain A) in
the trimer was mutated in silico to G614. For both 614
identities, the neighboring sidechains (10.0 Å) were minimized using the
Biased-Probability Monte Carlo algorithm for 106steps4. Van der Waals energy, vacuum Coulomb
electrostatics, solvation electrostatics, hydrogen bonding, torsional
energy and entropy were calculated for each conformation searched and
the lowest energy conformation was identified. The free energy change
caused by the mutation of D614 to G was then calculated as: ΔΔG =
ΔGG-Mutant – ΔGD-WildType. Thus, a
positive value indicates destabilization of the mutant G relative to the
wild-type D, since ΔG was a negative value for both forms. All
biophysical calculations, molecular modeling and molecular graphics were
performed using ICM-Pro (Molsoft LLC, La Jolla, CA).