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\begin{document}

\title{COVID-19: Structural Predictions of Viral Success}



\author[1]{Richard Stein}%
\author[2]{Lauren M. Young}%
\affil[1]{New York University Tandon School of Engineering}%
\affil[2]{University of Chicago}%


\vspace{-1em}



  
  \date{April 29, 2024}


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Since the beginning of the 21\textsuperscript{st} century, three
coronaviruses have crossed the species barrier and caused serious human
disease: severe acute respiratory syndrome coronavirus (SARS-CoV) in
November 2002 {[}1, 2{]}, Middle-East respiratory syndrome coronavirus
(MERS-CoV) in 2012 {[}3, 4{]}, and SARS-CoV-2 in 2019 {[}5, 6{]}.
SARS-CoV-2 {[}7{]}, initially called 2019-nCoV, is the etiological agent
of COVID-19, a highly contagious infectious illness that was first
reported in December 2019 in Wuhan, China and subsequently spread
globally {[}8{]}. As of May 24, 2020, COVID-19 has caused
\textgreater{}5,370,000 infections and \textgreater{}343,000 deaths
worldwide {[}9{]}.

Unfortunately, nearly 20 years after the SARS outbreak, and despite many
attempts for vaccines and therapeutic agents directed against SARS and
MERS, no approved prophylactics or therapeutics exist. As a result, the
management of COVID-19 largely relies on supportive care {[}10, 11{]}
and on hopes surrounding compounds that appeared promising against
previous coronaviruses {[}12, 13{]}. This lost opportunity, in itself,
offers a valuable lesson for current and future outbreaks, and the need
for new experimental rationales to accelerate discovery.

The cellular entry of coronaviruses is fairly conserved across members
of the \emph{Coronaviridae} family and is mediated by the transmembrane
spike (S) glycoprotein {[}14{]}, a homotrimer {[}15, 16{]} that is often
heavily glycosylated {[}17{]} and protrudes from the viral surface. Each
of the three monomers of the spike glycoprotein consists of two
functional subunits, S1, involved in membrane attachment, and S2,
required for membrane fusion {[}15, 18{]}. In many coronaviruses, the
spike glycoprotein is cleaved at the S1/S2 interface by host cell
proteases {[}19{]}. Within the S1 domain, the receptor binding domain
(RBD) attaches to the cellular receptor, which in the case of both
SARS-CoV and SARS-CoV-2 is the angiotensin-converting enzyme 2 (ACE2)
{[}19-21{]}. Another cleavage site, S2', is located within S2 {[}17,
19{]}. The spike glycoproteins of SARS-CoV and SARS-CoV-2 share 76\%
identity at the amino acid level {[}22, 23{]}, although biophysical
assays indicate that SARS-CoV-2 binds their common receptor, ACE2, with
a 10-20 fold higher affinity than SARS--CoV {[}14{]}.

As we contemplate the dynamics of COVID-19 and the development of
prophylactic and therapeutic interventions, one of the key
considerations is the emergence and potential relevance of viral
mutations. In the short time since the pandemic started, several
missense mutations have been observed in various SARS-CoV-2 isolates
{[}24{]}. One of these, the 23403A\textgreater{}G variant, substitutes
the aspartic acid at position 614 of the viral spike glycoprotein with
glycine (D614G), and is frequently documented in European countries but
rarely observed in China {[}25{]}.

In the current issue of the \emph{IJCP} , Becerra-Flores and Cardozo
interrogate the impact of this mutation on pathogenicity and offer a
structural correlate for their findings {[}26{]}. Their analysis
includes confirmed COVID-19 cases and deaths as reported by the European
CDC during the first week of April 2020 and examines the viral spike
genomic sequences deposited in the GISAID database over that period,
correlating the prevalence of the D614G mutation with fatality rates in
the same regions. The authors then use cryo-electron microscopy data
and\emph{in silico} mutagenesis of this key residue to predict
conformational preferences of the two variants of the spike protein.

The analysis indicates that viruses isolated from European patients
predominantly expressed a glycine at position 614 of the spike
glycoprotein, while a high percentage of the isolates collected from Far
East patients favored aspartic acid at the same position. The proportion
of viral isolates having a glycine at this position significantly
correlated with higher average and median case fatality rates across
geographic areas. Interestingly, their data also imply a rationale for
divergence in the behavior of the disease between the East and West
coasts of the United States, based upon the provenance of the viral
`founders' in these regions, from the European and Asian variants,
respectively.

Surprisingly, the authors' molecular modeling indicates that the
presence of a glycine at position 614 \emph{diminishes} binding to the
cellular receptor when replacing the aspartic acid at that residue,
mainly by reducing the spike protein's occupancy of the ``up'' or
liganded state, when it is most amenable to receptor interaction. While
seemingly counterintuitive, this finding opens at least two fascinating
scenarios. As the authors hypothesize, a spike glycoprotein that harbors
glycine at this position might be better protected from immune
recognition, elicit the production of harmful antibodies, flood the host
with ineffective antibodies, or some combination of all three. A delay
in immune recognition may impact viral transmission by delaying
symptomatic presentation or allowing unfettered infection without
effective immune response. An aberrant response, suited to the viral
conformation at large but not the infective conformation, could equally
allow for an increased---but poorly targeted---inflammatory cascade. The
possibility of a harmful immune response is particularly thought
provoking, as antibody-dependent enhancement, the phenomenon by which
antibodies facilitate viral entry into host cells that do not
necessarily have viral receptors {[}27, 28{]}, has been reported for
many viruses, including coronaviruses {[}27, 29{]}, dengue virus {[}30,
31{]}, feline infectious peritonitis virus {[}32{]} , Ebola virus
{[}33{]}, and HIV {[}34{]}. Another possibility, not mutually exclusive,
is that the D614G mutation creates or exposes a novel cleavage site in
the spike glycoprotein.

Delving into these molecular mechanisms with confirmatory \emph{in
vitro} studies will hopefully reap the benefits of decades of scientific
strides while simultaneously highlighting deficiencies in key areas that
can guide our approach to the current pandemic. One of the immediate
questions involves the impact of this and other mutations on vaccine
efficiency and the potential need to develop multiple candidate vaccines
that cover a range of epitopes and their variants. In all likelihood,
there is a lengthy and tortuous road ahead, but characterizing
significant variants will allow us to better understand many elusive
aspects of this virus' success -- the latent/incubation period, immune
evasion and hyper-response, variable receptor binding, replication
dynamics, and organ-specific pathogenesis---and discover host
vulnerabilities that mutations such as D614G seem to exploit.

The D614G mutation appears to become more common as the pandemic unfolds
{[}35{]}. That this phenomenon is simply the result of a founder effect
is possible but unlikely, and rather may be explained by this variant's
selective advantage allowing more efficient spread. Whether this
advantage is conferred by infectivity, immune evasion, or
pathogenicity---or some combination of these---is yet to be understood.
Interestingly, this mutation is now known to travel simultaneously with
other mutations, including one that affects the RNA-dependent RNA
polymerase, with implications for proofreading, replication efficiency
(and thus viral titer), and the emergence of drug-resistant viral
phenotypes {[}36{]}.

Addressing these molecular questions relies heavily on widespread
efforts to assemble accurate and comprehensive data on population
infection rates and mortality, and frequent sampling of the genotypes of
circulating isolates on a global basis. So far, this feat has been
challenging and continued deficiencies will translate into missed
singular opportunities to link molecular findings with population-level
consequences, ultimately leaving us less prepared to address both this
and future pandemics.

The valuable and timely experimental strategy used by Becerra-Flores and
Cardozo serves as an important analytic model that should be employed
routinely to understand the `molecular strategy' of this virus in the
context of the evolving pandemic. This approach will also prove to be an
indispensable instrument if also employed routinely at the onset of
future outbreaks, which are all but guaranteed in the coming years,
given the only recently appreciated ease of global spread of viruses in
the modern world. In summary, this set of tools allows us to perform
active surveillance, monitor the emergence of deleterious mutations
prior to their widespread distribution, and use informed \emph{in
silico} and structural data to make informed decisions guiding molecular
research and epidemic preparedness.

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