Abstract: Molecular Biology and Evolution, 2025, 42, 1–21
https://doi.org/10.1093/molbev/msaf211
Advance access publication 15 October 2025
Discoveries
MBE
Importance of De Novo Gene Evolution to Emerging Viral
Threats: The ORF10 Strain-Restricted Orphan Gene of
SARS-CoV-2 Promotes Pathogenesis
1
Bioinformatics and Computational Biology Program, Genetics Program, Iowa State University, Ames, IA 50011, USA
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
3
Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia,
PA 19104, USA
4
COVID-19 International Research Team, Medford, MA 02155, USA
5
Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda,
MD 20892, USA
6
Blue Marble Space Institute of Science, Seattle, WA 98104, USA
7
Guarnieri Research Group LLC, Philadelphia, PA 19146, USA
8
Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
9
Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
10
Department of Biology and Chemistry, Cornell College, Mount Vernon, IA 52314, USA
11
Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
12
Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA 30310-1495, USA
13
Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
14
Van Andel Research Institute, Grand Rapids, MI 49503, USA
15
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
16
Center for Space Biomedicine, McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh,
Pittsburgh, PA 15219, USA
17
Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
18
Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
2
*Corresponding authors: E-mails: res2025@med.cornell.edu; mash@iastate.edu.
Associate editor: Anne-Ruxandra Carvunis
Abstract
Orphan genes, which encode species-specific proteins, are common but are rarely investigated. The SARS-CoV-2 orphan gene, ORF10, has been
understudied; in vitro work suggests it may modulate innate immunity. Whether ORF10 influences COVID-19 outcomes in humans remained
unknown. Here, analyzing millions of SARS-CoV-2 genomes, we find ORF10 sequences are identical to ancestral Wuhan-Hu-1 haplotype. In all
variants of concern, <5% of genomes carry any ORF10 mutation. Despite limited statistical power due to the sparsity of mutated sequences,
four ORF10 mutations were associated with less severe clinical outcomes in COVID-19 patients: three affect protein structure, one alters
RNA structural dynamics. No mutations were linked to increased severity. ORF10 transcript levels in humans and human models are
conditionally discordant from other SARS-CoV-2 genes. ORF10 expression in A549 and 293T cells significantly perturbs oxidative
phosphorylation gene expression, disrupts immune gene networks, and shifts expression of 14 novel human transcripts. ORF10 is present in
multiple Betacoronavirus pandemicum strains, but absent from SARS-CoV-1-like strains. We propose that this strain-restricted orphan gene
contributes to severe COVID-19 in humans, with implications for..
DOI record:
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"abstract": "<jats:title>Abstract</jats:title>\n <jats:p>Orphan genes, which encode species-specific proteins, are common but are rarely investigated. The SARS-CoV-2 orphan gene, ORF10, has been understudied; in vitro work suggests it may modulate innate immunity. Whether ORF10 influences COVID-19 outcomes in humans remained unknown. Here, analyzing millions of SARS-CoV-2 genomes, we find ORF10 sequences are identical to ancestral Wuhan-Hu-1 haplotype. In all variants of concern, &lt;5% of genomes carry any ORF10 mutation. Despite limited statistical power due to the sparsity of mutated sequences, four ORF10 mutations were associated with less severe clinical outcomes in COVID-19 patients: three affect protein structure, one alters RNA structural dynamics. No mutations were linked to increased severity. ORF10 transcript levels in humans and human models are conditionally discordant from other SARS-CoV-2 genes. ORF10 expression in A549 and 293T cells significantly perturbs oxidative phosphorylation gene expression, disrupts immune gene networks, and shifts expression of 14 novel human transcripts. ORF10 is present in multiple Betacoronavirus pandemicum strains, but absent from SARS-CoV-1-like strains. We propose that this strain-restricted orphan gene contributes to severe COVID-19 in humans, with implications for future therapeutic strategies. These findings underscore the importance of studying recently evolved, potentially overlooked, viral orphan genes as a standard approach in pandemic preparedness.</jats:p>",
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