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Principal Investigator: Samantha Kathleen Zepeda
Organization: UNIVERSITY OF WASHINGTON
Fiscal Year: 2023
Award: $43,033
Funding agency: National Institute of Allergy and Infectious Diseases
Abstract
The outbreak of SARS-CoV-2 in late 2019 has resulted in the loss of over 6 million lives worldwide. Since then,
there has been an intense focus on the development of vaccines and clinical treatments to increase the
survivability of the disease caused by this virus. However, in nature other diverse sarbecoviruses circulate
which may present future spillover potential and for which these treatments may be ineffective. Clade 3
sarbecoviruses originate in Africa and Europe, outside of the regions considered to be sarbecovirus hotspots in
Southeast Asia. The geographical location and the absence of native human ACE2 utilization from the earliest
viruses discovered in this clade resulted in this clade being discounted. However, we have recently shown that
one member of this clade, BtKY72 from Kenya, has the capacity to gain human ACE2 binding within one
amino acid mutation and cellular entry within two mutations. Furthermore, we demonstrated for the first time
that another member of this clade, Khosta-2 from Russia, can natively bind human ACE2 as a wildtype
sequence. Together, our recent observations indicate the need to develop tools to study and inhibit potential
human infection by this overlooked clade of viruses. Clade 3 may be the origin of a future sarbecovirus
spillover, but current tools might have limited protective capacity due to the genetic divergence between Clade
3 and the prior human sarbecoviruses in the spike protein, the viral surface glycoprotein responsible for
receptor binding and fusion of the viral envelope and the host cell membrane. I hypothesize that all members
of this clade can gain human ACE2 utilization within a couple of mutations in the receptor binding domain of
the spike glycoprotein but that current vaccines and antibody treatments will have reduced efficacy against
clade 3 sarbecoviruses. In Aim 1 of this proposal, I will uncover receptor usage of all current members of clade
3 in Rhinolophus bat species with ranges in Africa, Europe, and Asia identify mutations that enable human
ACE2 binding and cellular entry of these viruses making use of safe non-replicating pseudovirus systems. In
Aim 2, I will establish what clinical tools in terms of vaccines and monoclonal antibody treatments would be
effective at preventing cellular entry of clade 3 sarbecoviruses. Understanding current native receptor usage
combined with a sequence assessment of sarbecoviruses that may be able to coinfect a specific species of
Rhinolophus will give insight into the evolutionary possibilities available to these viruses. In addition,
identification of mutations that enable human ACE2 binding and cellular entry in human cell lines will provide
context on how close these viruses are to achieving this first step necessary for human spillover. Finally, the
assessment of current tools for their effectiveness against clade 3 sarbecoviruses and the structural
characterization of clade 3 spike ectodomains, will give us a head start should these viruses cross the species
barrier in the future.
Terms: <2019 novel corona virus><2019 novel coronavirus><2019-nCoV><ACE2><Africa><African><Amino Acids><Animals><Antibodies><Antibody Therapy><Asia><Assay><Bats><Binding><Bioassay><Biologic Assays><Biological Assay><COVID-19 outbreak><COVID-19 virus><COVID19 outbreak><COVID19 virus><Cell Body><Cell Surface Glycoproteins><Cell membrane><Cells><Chiroptera><Clinical><Clinical Treatment><Clinical Treatment Moab><CoV S protein><CoV glycoprotein S><CoV spike glycoprotein><CoV spike protein><CoV-2><CoV2><Coronaviridae><Coronavirus><Coronavirus glycoprotein S><Coronavirus spike protein><Cryo-electron Microscopy><Cryoelectron Microscopy><Cytoplasmic Membrane><DNA Recombination><Development><Disease><Disorder><Domestic Animals><Effectiveness><Electron Cryomicroscopy><Europe><European><Foundations><Future><Genetic Alteration><Genetic Change><Genetic Differentiation><Genetic Divergence><Genetic Drift><Genetic Recombination><Genetic defect><Geographic Area><Geographic Locations><Geographic Region><Geographical Location><Glycoproteins><Head Start><Head Start Program><Human><Human Cell Line><Infection><Interferometry><Kenya><Knowledge><Location><Membrane Glycoproteins><Modern Man><Molecular Interaction><Monoclonal Antibodies><Mutation><Nature><Neutralization Tests><Plasma Membrane><Proteins><Publications><Reaction Time><Receptor Cell><Receptor Protein><Recombination><Resistance><Response RT><Response Time><Russia><SARS Virus><SARS corona virus><SARS corona virus 2><SARS coronavirus><SARS-Associated Coronavirus><SARS-CO-V2><SARS-COVID-2><SARS-CoV><SARS-CoV-1><SARS-CoV-2><SARS-CoV-2 outbreak><SARS-CoV2><SARS-Related Coronavirus><SARS-associated corona virus 2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related corona virus 2><SARS-related coronavirus 2><SARSCoV2><Sarbecovirus><Scientific Publication><Severe Acute Respiratory Coronavirus><Severe Acute Respiratory Coronavirus 2><Severe Acute Respiratory Distress Syndrome CoV 2><Severe Acute Respiratory Distress Syndrome Corona Virus 2><Severe Acute Respiratory Distress Syndrome Coronavirus 2><Severe Acute Respiratory Syndrome CoV 2><Severe Acute Respiratory Syndrome Virus><Severe Acute Respiratory Syndrome corona virus><Severe Acute Respiratory Syndrome coronavirus><Severe Acute Respiratory Syndrome-associated coronavirus 2><Severe Acute Respiratory Syndrome-related coronavirus 2><Severe acute respiratory syndrome associated corona virus 2><Severe acute respiratory syndrome coronavirus 2><Severe acute respiratory syndrome coronavirus 2 outbreak><Severe acute respiratory syndrome related corona virus 2><Southeast Asia><Southeastern Asia><Structure><Surface Glycoproteins><System><Testing><Time><Transfection><Trees><Tropism><VSV><Vaccination><Vaccine Design><Vaccinee><Vaccines><Validation><Variant><Variation><Vesicular Stomatitis Virus><Vesicular stomatitis Indiana virus><Viral><Viral Diseases><Virus><Virus Diseases><Wuhan coronavirus><Zoonoses><Zoonotic><Zoonotic Infection><aminoacid><angiotensin converting enzyme 2><angiotensin converting enzyme II><antibody based therapies><antibody neutralization test><antibody treatment><antibody-based therapeutics><antibody-based treatment><biophysical analysis><biophysical studies><clinical development><corona virus><coronavirus S protein><coronavirus disease 2019 outbreak><coronavirus disease 2019 virus><coronavirus disease-19 outbreak><coronavirus disease-19 virus><coronavirus spike glycoprotein><cryo-EM><cryoEM><cryogenic electron microscopy><develop a vaccine><develop vaccines><development of a vaccine><developmental><domesticated animal><genome mutation><geographic site><hCoV19><insight><mAbs><member><monoclonal Abs><mutation scanning><mutation screening><nCoV2><outbreak of SARS-CoV-2><pandemic disease preparedness><pandemic planning><pandemic preparedness><pandemic readiness><plasmalemma><polyclonal antibody><prevent><preventing><psychomotor reaction time><receptor><receptor binding><receptor bound><resistant><response><severe acute respiratory syndrome-CoV><tool><tool development><trial regimen><trial treatment><vaccinated individual><vaccinated participant><vaccinated patient><vaccinated person><vaccinated subject><vaccine antibodies><vaccine development><vaccine induced antibodies><vaccine-induced antibodies><validations><viral infection><virus infection><virus-induced disease><zoonotic CoV><zoonotic coronavirus>