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SARS-CoV-2 viral spike G614 mutation
exhibits higher case fatality rate
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Just today PubMed released a study from NYU backing Korber’s belief that the spike mutation she isolated (D614G) is more pathogenic than the original Chinese virus.
"Based on our results, short-term epidemiologic models of the pandemic aiming to predict the incidence and prevalence of severe disease and fatalities over time, which do not take the G614 percentage of viruses in a
region into account, may be inaccurate. The presence of G614 in a virus detected in a patient may also have prognostic significance.
Recent molecular epidemiology analyses have not evaluated the SARS-CoV-2 viral spike in isolation from the rest of the viral genome. The viral spike protein is relatively invariant, when compared to influenza or HIV,
across worldwide strains, with essentially only one missense variant so far in the viral spike at amino acid position 614 (D/G), despite global spread. We here report that the G614 variant correlated strongly with CFR
during an early time window in the pandemic in a global survey of countries, suggesting that a higher CFR possibly emerging in the USA East Coast or other regions affected later in the pandemic may be at least partly
a consequence of this virus-autonomous factor."
Int J Clin Pract. 2020 May 6. doi: 10.1111/ijcp.13525. [Epub ahead of print]
SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate.
Manuel Becerra-Flores and Timothy Cardozo*
NYU Langone Health
550 First Avenue
New York, NY, USA 10016
Abstract
AIM:
The COVID pandemic is caused by infection with the SARS-CoV-2 virus. The major mutation detected to date in the SARS-CoV-2 viral envelope spike protein, which is responsible for virus attachment to the host and is also the main target for host antibodies, is a mutation of an aspartate (D) at position 614 found frequently in Chinese strains to a glycine (G). We sought to infer health impact of this mutation.
RESULT:
Increased case fatality rate correlated strongly with the proportion of viruses bearing G614 on a country by country basis. The amino acid at position 614 occurs at an internal protein interface of the viral spike, and the presence of G at this position was calculated to destabilize a specific conformation of the viral spike, within which the key host receptor binding site is more accessible.
CONCLUSION:
These results imply that G614 is a more pathogenic strain of SARS-CoV-2, which may influence vaccine design. The prevalence of this form of the virus should also be included in epidemiologic models predicting the COVID-19 health burden and fatality over time in specific regions. Physicians should be aware of this characteristic of the virus to anticipate the clinical course of infection.
Introduction
In December 2019, an outbreak of pneumonia due to a coronavirus was reported in the Wuhan, Hubei
Province by Chinese health officials. On January 11, 2020, the genetic sequence of SARS-CoV-2, the
coronavirus that causes disease, which was named COVID-19, was published. The first outbreak in the United
States of America (USA) was in Washington state on the USA West Coast and was attributed to Chinese origin
of the virus, while recent studies have determined that the most intense outbreak in New York state on the
USA East Coast is from SARS-CoV-2 viruses of European origin. The only significant variation in the SARS-CoV-2
viral envelope spike protein, which executes viral glycoprotein-mediated binding to host cells and subsequent
fusion of virus and host cell membranes, is mutation of an aspartate (D) at position 614 found in nearly all
Chinese strains to a glycine (G) enriched in European strains. To compare case fatality rates (CFRs) of SARSCoV-
2 variants, we calculated a linear regression of global, country-by-country CFR vs country-by-country
G614 percentage and analyzed structural differences of the D to G mutation using published cryo-electron
microscopy 3D structures of the SARS-CoV-2 viral spike.
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 G614
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, or 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 106
steps4. 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).
Results
SARS-CoV-2 viral spike amino acid sequences from strains infecting patients in Europe exhibited a
predominance of glycine at amino acid position 614 in the viral spike (G614), while countries in the Far East
exhibited a high percentage of D614 viral spikes. Based on CFR and SARS-CoV-2 viral spike sequence data
available on April 6, 2020, both the average and median CFR correlate strongly (p < 0.02) with the proportion
of viruses in the same geographic region bearing glycine at position 614 (G614) in the viral spike (Figure 1).
For example, the proportion of recorded viruses in China exhibiting G614 was less than 1% and this country
exhibited the second lowest average or median CFR.
As of the time of writing, the complete daily data necessary to calculate the CFR for US states was not
available, so this correlation could not be plotted for US states, however, the percentage of viruses in each
state exhibiting glycine (G) instead of aspartate (D) at amino acid residue number 614 in the viral spike (S)
protein can be assessed (Table 1), revealing dramatically lower G614 and absolute number of fatalities in
Western USA states.
Modeling of aspartate (D) or glycine (G) at position 614 in the 3D structure of the viral envelope spike trimer
revealed that G is a less stable occupant from a biophysical point of view specifically in the “up” state of the
viral spike, in which the surface of the viral spike that binds human ACE-2 is exposed and accessible to this
host cell surface protein. The “down” or unliganded form shows no or mildly the opposite effect. The model
predicts the G mutation to be destabilizing relative to D for the local area around the amino acid 614 position,
apparently from loss of packing with the side-chain of threonine 859 from the helical core stalk of the viral
spike of an adjacent monomer (Figure 2), creating an unstable cavity in the protein. Cavities in the protein
core or at protein interfaces are well known to destabilize protein tertiary and quaternary structure5. Thus,
the structures predict a higher energy barrier for rearrangement of the viral spikes harboring G614 to their
infectious form (i.e. the conformation of the viral spike that is most optimal for binding host ACE-2, which is
the first animal/human receptor to which the virus binds in order to infect and cause disease).
Discussion
Recent molecular epidemiology analyses have not evaluated the SARS-CoV-2 viral spike in isolation from the
rest of the viral genome. The viral spike protein is relatively invariant, when compared to influenza or HIV,
across worldwide strains, with essentially only one missense variant so far in the viral spike at amino acid
position 614 (D/G), despite global spread. We here report that the G614 variant correlated strongly with CFR
during an early time window in the pandemic in a global survey of countries, suggesting that a higher CFR
possibly emerging in the USA East Coast or other regions affected later in the pandemic may be at least partly
a consequence of this virus-autonomous factor.
Molecular modeling suggests that G614 destabilizes the infectious form of the viral spike protein, thereby
favoring the ground-state, unliganded, “down” SARS-CoV-2 viral forms that would be expected to infect less
readily, due to masking of the host receptor binding site. This suggests that the mechanism by which G614
viruses causes greater fatality is immunologic rather than virologic: namely, that the form that binds the
receptor less well is also better shielded from host immune system attack and/or elicits harmful anti-viralspike
antibodies or other harmful immune responses. Indeed, there are several precedents in other viral
diseases: the viral spikes of both HIV and RSV exhibit unliganded states that do not elicit protective antibodies
via vaccination, and indeed, may elicit antibodies that enhance disease6,7. Furthermore, disease-enhancing,
immunodominant, antibody-targeted epitopes in the SARS viral spike have been definitively identified8, and a
recent report emphasized that key cryptic antibody-targeted neutralization epitopes in the SARS family of
viral spikes are accessible only in the conformation in which the ACE-2 binding site is exposed9.
There are several potential limitations and/or confounding issues in the data we used to calculate country-bycountry
CFR. First, the data assumes unbiased comorbidities, diagnostic testing and fatality reporting, which
were highly variable in prevalence and accuracy across countries during the time window studied. For
example, large volume testing took place in South Korea during the window studied, and the United Kingdom
is an outlier with an unusually high CFR, which weakens the correlation when included (Figure S1). This outlier
may be caused by the unusually low incidence of active cases being reported in the UK during the 2 weeks
under study. Such selection bias is unlikely to be a confounder in this analysis, however, since the same
reporting or incidence bias would have to occur in the same direction and for the same reason across diverse
countries. Social distancing measures have been implemented in a highly variable fashion across the
countries studied in this report, but the case fatality rate should be unaffected by social distancing, as it does
not affect the clinical course of viral disease, only acquisition of virus. Measuring this correlation at this early
time point in a limited window in the pandemic may be optimal to detect this correlation and avoid the
confounder of successful medical treatment that may artificially reduce the organic CFR risk of the virus.
Based on our results, short-term epidemiologic models of the pandemic aiming to predict the incidence and
prevalence of severe disease and fatalities over time, which do not take the G614 percentage of viruses in a
region into account, may be inaccurate. The presence of G614 in a virus detected in a patient may also have
prognostic significance.
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