ACE2 binding is an ancestral and evolvable trait of sarbecoviruses.

Tyler N Starr1,2 Samantha K Zepeda3 Alexandra C Walls3 Allison J Greaney4,5 Sergey Alkhovsky6 David Veesler7,8 Jesse D Bloom9,10,11
Affiliations 11 institutions
  1. Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. [email protected].
  2. Howard Hughes Medical Institute, Seattle, WA, USA. [email protected].
  3. Department of Biochemistry, University of Washington, Seattle, WA, USA.
  4. Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  5. Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  6. N.F. Gamleya National Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.
  7. Howard Hughes Medical Institute, Seattle, WA, USA. [email protected].
  8. Department of Biochemistry, University of Washington, Seattle, WA, USA. [email protected].
  9. Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. [email protected].
  10. Howard Hughes Medical Institute, Seattle, WA, USA. [email protected].
  11. Department of Genome Sciences, University of Washington, Seattle, WA, USA. [email protected].

Abstract

Two different sarbecoviruses have caused major human outbreaks in the past two decades1,2. Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the spike receptor-binding domain2-6. However, binding to ACE2 orthologues of humans, bats and other species has been observed only sporadically among the broader diversity of bat sarbecoviruses7-11. Here we use high-throughput assays12 to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades. Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2. Moreover, ACE2 binding is highly evolvable-for many sarbecovirus receptor-binding domains, there are single amino-acid mutations that enable binding to new ACE2 orthologues. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. Our results point to the deep ancestral origin and evolutionary plasticity of ACE2 binding, broadening the range of sarbecoviruses that should be considered to have spillover potential.

Supporting text Virus Host Location
Angiotensin-Converting Enzyme 2 177 Evolution, Molecular 176 SARS-CoV-2 453 Severe acute respiratory syndrome-related coronavirus 78 Spike Glycoprotein, Coronavirus 274 Animals 1948 Binding Sites 89 Chiroptera 371 COVID-19 425 Humans 1440 Protein Binding 193 SARS-CoV-2 variants 86 spike protein, SARS-CoV-2 157

Evidence records

3 total
Functional Mechanism
2 records · 2 evidence types
Evidence type
1 records
OVE5605
Key finding

Bat sarbecoviruses from outside Asia can bind to ACE2.

Virus
Host
Not specified
Location
Not specified
Supporting text

Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2.

Method
high-throughput assays
Receptors
ACE2
Evidence type
1 records
OVE5607
Key finding

The N501Y mutation enhances human ACE2-binding affinity in several SARS-CoV-2 variants but decreases it in SARS-CoV-1.

Virus
Host
Not specified
Location
Not specified
Supporting text

the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern but substantially decreases it for SARS-CoV-1

Genes or proteins
ACE2
Receptors
human ACE2
Mutations
N501Y
Mechanism types
receptor binding
Genomic Evolution
1 records · 1 evidence types
Evidence type
1 records
OVE5608
Key finding

Phylogenetic and comparative sequence analyses showed that ACE2-binding ability is an ancestral trait of sarbecoviruses, later lost in some lineages.

Virus
Host
Not specified
Location
Not specified
Supporting text

We use high-throughput assays to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades.

Genes or proteins
spike receptor-binding domain
Analysis methods
phylogenetic analysis | comparative sequence analysis | evolutionary history reconstruction | high-throughput binding assays