OmniVira

Clade-3 Bat Sarbecovirus PRD0038 Reveals Constraints on Coronavirus Emergence and Immune Sensitivity.

Anfal Abdelgadir1 Edgar F Kong2 Ruth J Parsons3,4 Michael L Mallory2 Boyd L Yount2 Trevor Scobey2 John M Powers2 Kendra L Gully2 Lily E Adams1 Robert J Edwards3,5 Katayoun Mansouri3 Priyanka Devkota3 Katarzyna Janowska3 Rasangi Pathirage3 Nicholas J Catanzaro2 Abbey L Biggers2 Jason J Lavinder6 Gregory C Ippolito7 Mark T Heise1,8 Priyamvada Acharya3,4,9 Lisa E Gralinski1,2 Ralph S Baric1,2
Affiliations 9 institutions
  1. Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  2. Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  3. Duke Human Vaccine Institute, Durham, NC, USA.
  4. Duke University, Department of Biochemistry, Durham, NC, USA.
  5. Duke University, Department of Medicine, Durham, NC, USA.
  6. Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
  7. Texas Biomedical Research Institute, San Antonio, TX, USA.
  8. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  9. Duke University, Department of Surgery, Durham, NC, USA.
PMID42427868 DOI10.21203/rs.3.rs-9954172/v1 Year2026 Journal Research square Res Sq Languageeng Statusepublish

Abstract

Zoonotic Sarbecoviruses present a documented threat to global health. Here, we report the recovery of an African clade-3 recombinant Sarbecovirus, PRD0038, and derivatives encoding reporter genes. Cryo-EM structural analyses of rPRD0038 revealed spike glycoprotein sites that facilitate the receptor-binding domain (RBD)-up conformation, enhancing replication in R. affinis but not human ACE2 expressing cells. Host range analysis of rPRD0038 identified civets, rabbits, camels, and cows as potential intermediate hosts, while confirming the lack of human ACE2 usage and replication in primary human airway epithelial cells. Despite significant divergence from SARS-CoV-2, PRD0038 remains susceptible to FDA-approved nucleoside and mPro-targeted antivirals as well as some monoclonal antibodies that target select conserved spike epitopes. Pre-existing SARS-CoV-2 immune memory conferred reduced cross-neutralizing activity against PRD0038. Finally, we present an R. affinis ACE2-expressing mouse model for assessing PRD0038 in vivo replication and pathogenesis, and testing countermeasures. Together, these data illustrate functional and immunological constraints that regulate the emergence potential of clade-3 bat Sarbecoviruses while identifying protective therapeutics.

Supporting text Virus Host Location
antiviral 1 Coronavirus 195 epidemiology 48 PRD0038 1 Sarbecovirus 19 Spike 25

Evidence records

7 total
Zoonotic Surveillance
2 records · 2 evidence types
Evidence type Virus Isolation
1 records
OVE11717 Virus Isolation
Key finding

Infectious African clade-3 recombinant Sarbecovirus PRD0038 was recovered, with additional reporter gene derivatives generated.

Virus
PRD0038 rPRD0038 African clade-3 recombinant Sarbecovirus
Host
Not specified
Location
Not specified
Supporting text

we report the recovery of an African clade-3 recombinant Sarbecovirus, PRD0038, and derivatives encoding reporter genes.

Evidence type Serological Evidence
1 records
OVE11723 Serological Evidence
Key finding

Pre-existing SARS-CoV-2 immune memory showed reduced cross-neutralizing activity against the bat sarbecovirus PRD0038.

Virus
PRD0038 Severe acute respiratory syndrome coronavirus 2
Host
Pre-existing SARS-CoV-2 immune memory Context pending
Location
Not specified
Supporting text

Pre-existing SARS-CoV-2 immune memory conferred reduced cross-neutralizing activity against PRD0038.

Method
cross-neutralization assay
Experimental Infection
3 records · 2 evidence types
Evidence type Pathogenicity Experiment
1 records
OVE11722 Pathogenicity Experiment
Key finding

An R. affinis ACE2-expressing mouse model was used to assess in vivo replication and pathogenesis of PRD0038.

Virus
PRD0038
Host
R. affinis ACE2-expressing mouse Experimental system
Location
Not specified
Supporting text

we present an R. affinis ACE2-expressing mouse model for assessing PRD0038 in vivo replication and pathogenesis, and testing countermeasures.

Method
in vivo mouse infection model
Experimental system
R. affinis ACE2-expressing mouse model
Evidence type Host Range Experiment
2 records
OVE11719 Host Range Experiment
Key finding

Host range testing of rPRD0038 indicated susceptibility of civets, rabbits, camels, and cows as potential intermediates, with no human ACE2 usage and no replication in primary human airway epithelial cells.

Virus
rPRD0038
Host
masked palm civet Paguma larvata Experimental system rabbit Oryctolagus cuniculus Experimental system Camelus Experimental system domestic cattle Bos taurus Experimental system primary human airway epithelial cells Homo sapiens Experimental system human Homo sapiens Experimental system
Location
Not specified
Supporting text

Host range analysis of rPRD0038 identified civets, rabbits, camels, and cows as potential intermediate hosts, while confirming the lack of human ACE2 usage and replication in primary human airway epithelial cells.

Method
host range analysis | receptor usage assay | cell-culture replication assessment
Experimental system
host range analysis including primary human airway epithelial cells and ACE2 receptor usage assays
OVE11720 Host Range Experiment
Key finding

rPRD0038 showed enhanced replication with R. affinis ACE2 but not in human ACE2–expressing cells.

Virus
rPRD0038
Host
intermediate horseshoe bat Rhinolophus affinis Experimental system human ACE2 expressing cells Experimental system
Location
Not specified
Supporting text

Cryo-EM structural analyses of rPRD0038 revealed spike glycoprotein sites that facilitate the receptor-binding domain (RBD)-up conformation, enhancing replication in R. affinis but not human ACE2 expressing cells.

Method
cell-culture replication assay | ACE2 receptor-expression system
Experimental system
cell-culture system comparing replication with R. affinis ACE2 versus human ACE2
Functional Mechanism
2 records · 2 evidence types
Evidence type Receptor Usage
1 records
OVE11718 Receptor Usage
Key finding

rPRD0038 does not use human ACE2 but shows enhanced replication associated with RBD-up spike conformation in Rhinolophus affinis ACE2 systems.

Virus
rPRD0038
Host
intermediate horseshoe bat Rhinolophus affinis Experimental system human ACE2 expressing cells Experimental system primary human airway epithelial cells Homo sapiens Experimental system R. affinis ACE2-expressing mouse Experimental system
Location
Not specified
Supporting text

rPRD0038 revealed spike glycoprotein sites that facilitate the receptor-binding domain (RBD)-up conformation, enhancing replication in R. affinis but not human ACE2 expressing cells. ... confirming the lack of human ACE2 usage and replication in primary human airway epithelial cells.

Method
cryo-EM structural analysis | cell-based replication assays | receptor usage assay in human ACE2 expressing cells | primary human airway epithelial cell replication assay | in vivo R. affinis ACE2-expressing mouse model
Receptors
human ACE2 | R. affinis ACE2
Evidence type Molecular Adaptation
1 records
OVE11721 Molecular Adaptation
Key finding

Spike glycoprotein sites in rPRD0038 that favor the RBD-up conformation enhance replication in Rhinolophus affinis cells but not in human ACE2-expressing cells.

Virus
rPRD0038
Host
Not specified
Location
Not specified
Supporting text

Cryo-EM structural analyses of rPRD0038 revealed spike glycoprotein sites that facilitate the receptor-binding domain (RBD)-up conformation, enhancing replication in R. affinis but not human ACE2 expressing cells.

Genes or proteins
spike glycoprotein | receptor-binding domain (RBD)
Receptors
human ACE2
Host factors
R. affinis ACE2
Mechanism types
host-range expansion | replication adaptation | receptor binding | host entry | tissue tropism