1
|
Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2. eLife 2024; 13:RP94836. [PMID: 38941236 PMCID: PMC11213569 DOI: 10.7554/elife.94836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
Collapse
Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaUnited States
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaUnited States
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaUnited States
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaUnited States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaUnited States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaUnited States
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of HealthBethesdaUnited States
| |
Collapse
|
2
|
Ives CM, Nguyen L, Fogarty CA, Harbison AM, Durocher Y, Klassen J, Fadda E. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife 2024; 13:RP95708. [PMID: 38864493 PMCID: PMC11168744 DOI: 10.7554/elife.95708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work, we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated by N-glycosylation at N343 and how this glycan's structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2), and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of the N-glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha, and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.
Collapse
Affiliation(s)
- Callum M Ives
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | - Linh Nguyen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Carl A Fogarty
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | | | - Yves Durocher
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council CanadaQuébecCanada
- Département de Biochimie et Médecine Moléculaire, Université de MontréalQuébecCanada
| | - John Klassen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Elisa Fadda
- School of Biological Sciences, University of SouthamptonSouthamptonUnited Kingdom
| |
Collapse
|
3
|
Rojas Chávez RA, Fili M, Han C, Rahman SA, Bicar IGL, Gregory S, Helverson A, Hu G, Darbro BW, Das J, Brown GD, Haim H. Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. PLoS Comput Biol 2024; 20:e1012215. [PMID: 38857308 PMCID: PMC11192331 DOI: 10.1371/journal.pcbi.1012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/21/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.
Collapse
Affiliation(s)
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Syed A. Rahman
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Isaiah G. L. Bicar
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Sullivan Gregory
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Benjamin W. Darbro
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States of America
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Grant D. Brown
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| |
Collapse
|
4
|
Fountain-Jones NM, Vanhaeften R, Williamson J, Maskell J, Chua ILJ, Charleston M, Cooley L. Effect of molnupiravir on SARS-CoV-2 evolution in immunocompromised patients: a retrospective observational study. THE LANCET. MICROBE 2024; 5:e452-e458. [PMID: 38527471 DOI: 10.1016/s2666-5247(23)00393-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 03/27/2024]
Abstract
INTRODUCTION Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 outcomes, but the extended effects of these drugs on viral evolution in patients with chronic infections remain uncertain. This study investigates how molnupiravir affects SARS-CoV-2 evolution in immunocompromised patients with prolonged infections. METHODS The study included five immunocompromised patients treated with molnupiravir and four patients not treated with molnupiravir (two immunocompromised and two non-immunocompromised). We selected patients who had been infected by similar SARS-CoV-2 variants and with high-quality genomes across timepoints to allow comparison between groups. Throat and nasopharyngeal samples were collected in patients up to 44 days post treatment and were sequenced using tiled amplicon sequencing followed by variant calling. The UShER pipeline and University of California Santa Cruz genome viewer provided insights into the global context of variants. Treated and untreated patients were compared, and mutation profiles were visualised to understand the impact of molnupiravir on viral evolution. FINDINGS Patients treated with molnupiravir showed a large increase in low-to-mid-frequency variants in as little as 10 days after treatment, whereas no such change was observed in untreated patients. Some of these variants became fixed in the viral population, including non-synonymous mutations in the spike protein. The variants were distributed across the genome and included unique mutations not commonly found in global omicron genomes. Notably, G-to-A and C-to-T mutations dominated the mutational profile of treated patients, persisting up to 44 days post treatment. INTERPRETATION Molnupiravir treatment in immunocompromised patients led to the accumulation of a distinctive pattern of mutations beyond the recommended 5 days of treatment. Treated patients maintained persistent PCR positivity for the duration of monitoring, indicating clear potential for transmission and subsequent emergence of novel variants. FUNDING Australian Research Council.
Collapse
Affiliation(s)
- Nicholas M Fountain-Jones
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia; School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia.
| | | | - Jan Williamson
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Janelle Maskell
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia
| | - I-Ly J Chua
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael Charleston
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Louise Cooley
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia; School of Medicine, University of Tasmania, Hobart, TAS, Australia
| |
Collapse
|
5
|
Gruber CEM, Tucci FG, Giombini E, Mazzotta V, Spezia PG, Rueca M, Mastrorosa I, Fabeni L, Berno G, Butera O, Rosati S, Specchiarello E, Carletti F, Focosi D, Nicastri E, Girardi E, Antinori A, Maggi F. Molnupiravir increases SARS-CoV-2 genome diversity and complexity: A case-control cohort study. J Med Virol 2024; 96:e29642. [PMID: 38708812 DOI: 10.1002/jmv.29642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
Molnupiravir, an oral direct-acting antiviral effective in vitro against SARS-CoV-2, has been largely employed during the COVID-19 pandemic, since December 2021. After marketing and widespread usage, a progressive increase in SARS-CoV-2 lineages characterized by a higher transition/transversion ratio, a characteristic signature of molnupiravir action, appeared in the Global Initiative on Sharing All Influenza Data (GISAID) and International Nucleotide Sequence Database Collaboration (INSDC) databases. Here, we assessed the drug effects by SARS-CoV-2 whole-genome sequencing on 38 molnupiravir-treated persistently positive COVID-19 outpatients tested before and after treatment. Seventeen tixagevimab/cilgavimab-treated outpatients served as controls. Mutational analyses confirmed that SARS-CoV-2 exhibits an increased transition/transversion ratio seven days after initiation of molnupiravir. Moreover we observed an increased G->A ratio compared to controls, which was not related to apolipoprotein B mRNAediting enzyme, catalytic polypeptide-like (APOBEC) activity. In addition, we demonstrated for the first time an increased diversity and complexity of the viral quasispecies.
Collapse
Affiliation(s)
| | | | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Pietro Giorgio Spezia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ilaria Mastrorosa
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ornella Butera
- Laboratory of Microbiology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Silvia Rosati
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Eliana Specchiarello
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Fabrizio Carletti
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Emanuele Nicastri
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases "L. Spallanzani"-IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| |
Collapse
|
6
|
Liukang C, Zhao J, Tian J, Huang M, Liang R, Zhao Y, Zhang G. Deciphering infected cell types, hub gene networks and cell-cell communication in infectious bronchitis virus via single-cell RNA sequencing. PLoS Pathog 2024; 20:e1012232. [PMID: 38743760 PMCID: PMC11125504 DOI: 10.1371/journal.ppat.1012232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/24/2024] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Infectious bronchitis virus (IBV) is a coronavirus that infects chickens, which exhibits a broad tropism for epithelial cells, infecting the tracheal mucosal epithelium, intestinal mucosal epithelium, and renal tubular epithelial cells. Utilizing single-cell RNA sequencing (scRNA-seq), we systematically examined cells in renal, bursal, and tracheal tissues following IBV infection and identified tissue-specific molecular markers expressed in distinct cell types. We evaluated the expression of viral RNA in diverse cellular populations and subsequently ascertained that distal tubules and collecting ducts within the kidney, bursal mucosal epithelial cells, and follicle-associated epithelial cells exhibit susceptibility to IBV infection through immunofluorescence. Furthermore, our findings revealed an upregulation in the transcription of proinflammatory cytokines IL18 and IL1B in renal macrophages as well as increased expression of apoptosis-related gene STAT in distal tubules and collecting duct cells upon IBV infection leading to renal damage. Cell-to-cell communication unveiled potential interactions between diverse cell types, as well as upregulated signaling pathways and key sender-receiver cell populations after IBV infection. Integrating single-cell data from all tissues, we applied weighted gene co-expression network analysis (WGCNA) to identify gene modules that are specifically expressed in different cell populations. Based on the WGCNA results, we identified seven immune-related gene modules and determined the differential expression pattern of module genes, as well as the hub genes within these modules. Our comprehensive data provides valuable insights into the pathogenesis of IBV as well as avian antiviral immunology.
Collapse
Affiliation(s)
- Chengyin Liukang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiaxin Tian
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Min Huang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rong Liang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Ye Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| |
Collapse
|
7
|
Selvavinayagam ST, Sankar S, Yong YK, Murugesan A, Suvaithenamudhan S, Hemashree K, Rajeshkumar M, Kumaresan A, Pandey RP, Shanmugam S, Arthydevi P, Kumar MS, Gopalan N, Kannan M, Cheedarla N, Tan HY, Zhang Y, Larsson M, Balakrishnan P, Velu V, Byrareddy SN, Shankar EM, Raju S. Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305882. [PMID: 38699322 PMCID: PMC11065016 DOI: 10.1101/2024.04.16.24305882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In December 2023, we observed a notable shift in the COVID-19 landscape, when the JN.1 emerged as a predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive samples, followed by sequence analysis. Mutations within the spike protein sequences were analyzed and compared with the previous lineages and sublineages of SARS-CoV-2, to identify the potential impact of these unique mutations on protein structure and possible functionality. Several unique and dynamic mutations were identified herein. Our data provides key insights into the emergence of newer variants of SARS-CoV-2 in our region and highlights the need for robust and sustained genomic surveillance of SARS-CoV-2.
Collapse
|
8
|
Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
Collapse
Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| |
Collapse
|
9
|
Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568093. [PMID: 38045241 PMCID: PMC10690151 DOI: 10.1101/2023.11.21.568093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
Collapse
Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
10
|
Bernauer H, Maier J, Bannert N, Ivanusic D. tANCHOR cell-based ELISA approach as a surrogate for antigen-coated plates to monitor specific IgG directed to the SARS-CoV-2 receptor-binding domain. Biol Methods Protoc 2024; 9:bpae001. [PMID: 38332985 PMCID: PMC10850845 DOI: 10.1093/biomethods/bpae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
Enzyme-linked immunosorbent assay (ELISA) systems use plates coated with peptides or expressed and purified proteins to monitor immunoglobulins derived from patient serum. However, there is currently no easy, flexible, and fast adaptive ELISA-based system for testing antibodies directed against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. In this study, we utilized the tANCHOR protein display system that provides a cell surface decorated with the receptor-binding domain (RBD) to monitor specific antibodies derived from SARS-CoV-2 convalescent and vaccinated individuals directed against it. To test sera from vaccinees or convalescent individuals, only the RBD coding sequence needs to be cloned in the tANCHOR vector system and transfected into HeLa cells. Time-consuming protein expression, isolation, and purification followed by coating assay plates are not necessary. With this technique, the immune evasion of new SARS-CoV-2 variants from current vaccination regimes can be examined quickly and reliably.
Collapse
Affiliation(s)
| | - Josef Maier
- ATG:biosynthetics GmbH, 79249 Merzhausen, Germany
| | - Norbert Bannert
- Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| | - Daniel Ivanusic
- Sexually Transmitted Bacterial Pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| |
Collapse
|
11
|
McGaughran A, Dhami MK, Parvizi E, Vaughan AL, Gleeson DM, Hodgins KA, Rollins LA, Tepolt CK, Turner KG, Atsawawaranunt K, Battlay P, Congrains C, Crottini A, Dennis TPW, Lange C, Liu XP, Matheson P, North HL, Popovic I, Rius M, Santure AW, Stuart KC, Tan HZ, Wang C, Wilson J. Genomic Tools in Biological Invasions: Current State and Future Frontiers. Genome Biol Evol 2024; 16:evad230. [PMID: 38109935 PMCID: PMC10776249 DOI: 10.1093/gbe/evad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.
Collapse
Affiliation(s)
- Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Dianne M Gleeson
- Centre for Conservation Ecology and Genomics, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Lee A Rollins
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Kathryn G Turner
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Kamolphat Atsawawaranunt
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Carlos Congrains
- Entomology Section, Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
- US Department of Agriculture-Agricultural Research Service, Daniel K. Inouye US Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169–007, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tristan P W Dennis
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claudia Lange
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Henry L North
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Iva Popovic
- School of the Environment, University of Queensland, Brisbane, QLD, Australia
| | - Marc Rius
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc, Blanes, Spain
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg 2006, South Africa
| | - Anna W Santure
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Katarina C Stuart
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Hui Zhen Tan
- School of Biological Sciences, Waipapa Taumata Rau/University of Auckland, Auckland, New Zealand
| | - Cui Wang
- The Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| |
Collapse
|
12
|
Lamb KD, Luka MM, Saathoff M, Orton RJ, Phan MVT, Cotten M, Yuan K, Robertson DL. Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Comput Biol 2024; 20:e1011795. [PMID: 38271457 PMCID: PMC10868779 DOI: 10.1371/journal.pcbi.1011795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/15/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to more efficient human infection since the emergence of this new human coronavirus in late 2019. Here, we use machine learning models to identify shared signatures, i.e., common underlying mutational processes and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and virus properties were associated with the waves of regional SARS-CoV-2 reported infection numbers and this impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity and the effectiveness of government stringency. To assess underlying evolutionary change, we used non-negative matrix factorisation and observed three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 1, 2 and 3 were biased to C→T, T→C/A→G and G→T point mutations. We hypothesise assignments of these mutational signatures to the host antiviral molecules APOBEC, ADAR and ROS respectively. We observe a shift amidst the pandemic in relative mutational signature activity from predominantly Signature 1 changes to an increasingly high proportion of changes consistent with Signature 2. This could represent changes in how the virus and the host immune response interact and indicates how SARS-CoV-2 may continue to generate variation in the future. Linkage of the detected mutational signatures to the VOC-defining amino acids substitutions indicates the majority of SARS-CoV-2's evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.
Collapse
Affiliation(s)
- Kieran D. Lamb
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Martha M. Luka
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Megan Saathoff
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - Richard J. Orton
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| | - My V. T. Phan
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
| | - Matthew Cotten
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- College of Health Solutions, Arizona State University, Phoenix, Arizona, United States of America
- Complex Adaptive Systems Initiative, Arizona State University, Scottsdale, Arizona, United States of America
| | - Ke Yuan
- School of Computing Science, University of Glasgow, Glasgow, Scotland, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Cancer Research UK Scotland Institute, Glasgow, Scotland, United Kingdom
| | - David L. Robertson
- Medical Research Council - University of Glasgow Centre for Virus Research, School of Infection and Immunity, Glasgow, Scotland, United Kingdom
| |
Collapse
|
13
|
Schuck P, Zhao H. Diversity of short linear interaction motifs in SARS-CoV-2 nucleocapsid protein. mBio 2023; 14:e0238823. [PMID: 38018991 PMCID: PMC10746173 DOI: 10.1128/mbio.02388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Short linear motifs (SLiMs) are 3-10 amino acid long binding motifs in intrinsically disordered protein regions (IDRs) that serve as ubiquitous protein-protein interaction modules in eukaryotic cells. Through molecular mimicry, viruses hijack these sequence motifs to control host cellular processes. It is thought that the small size of SLiMs and the high mutation frequencies of viral IDRs allow rapid host adaptation. However, a salient characteristic of RNA viruses, due to high replication errors, is their obligate existence as mutant swarms. Taking advantage of the uniquely large genomic database of SARS-CoV-2, here, we analyze the role of sequence diversity in the presentation of SLiMs, focusing on the highly abundant, multi-functional nucleocapsid protein. We find that motif mimicry is a highly dynamic process that produces an abundance of motifs transiently present in subsets of mutant species. This diversity allows the virus to efficiently explore eukaryotic motifs and evolve the host-virus interface.
Collapse
Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
14
|
Sanderson T, Hisner R, Donovan-Banfield I, Hartman H, Løchen A, Peacock TP, Ruis C. A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes. Nature 2023; 623:594-600. [PMID: 37748513 PMCID: PMC10651478 DOI: 10.1038/s41586-023-06649-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Molnupiravir, an antiviral medication widely used against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), acts by inducing mutations in the virus genome during replication. Most random mutations are likely to be deleterious to the virus and many will be lethal; thus, molnupiravir-induced elevated mutation rates reduce viral load1,2. However, if some patients treated with molnupiravir do not fully clear the SARS-CoV-2 infections, there could be the potential for onward transmission of molnupiravir-mutated viruses. Here we show that SARS-CoV-2 sequencing databases contain extensive evidence of molnupiravir mutagenesis. Using a systematic approach, we find that a specific class of long phylogenetic branches, distinguished by a high proportion of G-to-A and C-to-T mutations, are found almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age groups with widespread use of the drug. We identify a mutational spectrum, with preferred nucleotide contexts, from viruses in patients known to have been treated with molnupiravir and show that its signature matches that seen in these long branches, in some cases with onward transmission of molnupiravir-derived lineages. Finally, we analyse treatment records to confirm a direct association between these high G-to-A branches and the use of molnupiravir.
Collapse
Affiliation(s)
| | - Ryan Hisner
- Department of Bioinformatics, University of Cape Town, Cape Town, South Africa
| | - I'ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health and Care Research, Liverpool, UK
| | | | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- The Pirbright Institute, Pirbright, UK
| | - Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
15
|
Beichman AC, Robinson J, Lin M, Moreno-Estrada A, Nigenda-Morales S, Harris K. Evolution of the Mutation Spectrum Across a Mammalian Phylogeny. Mol Biol Evol 2023; 40:msad213. [PMID: 37770035 PMCID: PMC10566577 DOI: 10.1093/molbev/msad213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023] Open
Abstract
Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
Collapse
Affiliation(s)
- Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Meixi Lin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Advanced Genomics Unit (UGA-LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Sergio Nigenda-Morales
- Department of Biological Sciences, California State University, San Marcos, San Marcos, CA, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
| |
Collapse
|
16
|
Bloom JD, Neher RA. Fitness effects of mutations to SARS-CoV-2 proteins. Virus Evol 2023; 9:vead055. [PMID: 37727875 PMCID: PMC10506532 DOI: 10.1093/ve/vead055] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/21/2023] Open
Abstract
Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here, we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
Collapse
Affiliation(s)
- Jesse D Bloom
- Basic Sciences and Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Richard A Neher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel 4056, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerl
| |
Collapse
|
17
|
Beichman AC, Robinson J, Lin M, Moreno-Estrada A, Nigenda-Morales S, Harris K. "Evolution of the mutation spectrum across a mammalian phylogeny". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543114. [PMID: 37398383 PMCID: PMC10312511 DOI: 10.1101/2023.05.31.543114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Little is known about how the spectrum and etiology of germline mutagenesis might vary among mammalian species. To shed light on this mystery, we quantify variation in mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k -mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clocklike mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these clocklike signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the mutation spectrum's phylogenetic signal when fit to non-context-dependent mutation spectrum data in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
Collapse
Affiliation(s)
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Meixi Lin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Advanced Genomics Unit (UGA-LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Sergio Nigenda-Morales
- Department of Biological Sciences, California State University, San Marcos, San Marcos CA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle WA
| |
Collapse
|