1
|
Chambers MJ, Scobell SB, Sadhu MJ. Systematic genetic characterization of the human PKR kinase domain highlights its functional malleability to escape a viral substrate mimic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596416. [PMID: 38903081 PMCID: PMC11188142 DOI: 10.1101/2024.05.29.596416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that inhibit PKR by interacting with the same binding surface as eIF2α. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3 from vaccinia virus. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.
Collapse
Affiliation(s)
- Michael J Chambers
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Microbiology & Immunology, Georgetown University, Washington DC, USA
| | - Sophia B Scobell
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Meru J Sadhu
- Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
2
|
Shukla N, Roelle SM, Snell JC, DelSignore O, Bruchez AM, Matreyek KA. Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage. PLoS Pathog 2024; 20:e1012044. [PMID: 38768238 PMCID: PMC11142672 DOI: 10.1371/journal.ppat.1012044] [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: 02/12/2024] [Revised: 05/31/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.
Collapse
Affiliation(s)
- Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Sarah M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - John C. Snell
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Olivia DelSignore
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anna M. Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| |
Collapse
|
3
|
Shukla N, Roelle SM, Snell JC, DelSignore O, Bruchez AM, Matreyek KA. Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580056. [PMID: 38405739 PMCID: PMC10888787 DOI: 10.1101/2024.02.13.580056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.
Collapse
Affiliation(s)
- Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Sarah M Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - John C Snell
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Olivia DelSignore
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Anna M Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kenneth A Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
4
|
Tada T, Minnee J, Landau NR. Vectored immunoprophylaxis and treatment of SARS-CoV-2 infection in a preclinical model. Proc Natl Acad Sci U S A 2023; 120:e2303509120. [PMID: 37252952 PMCID: PMC10266030 DOI: 10.1073/pnas.2303509120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Vectored immunoprophylaxis was first developed as a means of establishing engineered immunity to HIV using an adenoassociated viral vector expressing a broadly neutralizing antibody. We applied this concept to establish long-term prophylaxis against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a mouse model using adenoassociated virus and lentiviral vectors expressing a high-affinity angiotensin-converting enzyme 2 (ACE2) decoy. Administration of decoy-expressing (adenoassociated virus) AAV2.retro and AAV6.2 vectors by intranasal instillation or intramuscular injection protected mice against high-titered SARS-CoV-2 infection. AAV and lentiviral vectored immunoprophylaxis was durable and was active against SARS-CoV-2 Omicron subvariants. The AAV vectors were also effective therapeutically when administered postinfection. Vectored immunoprophylaxis could be of value for immunocompromised individuals for whom vaccination is not practical and as a means to rapidly establish protection from infection. Unlike monoclonal antibody therapy, the approach is expected to remain active despite continued evolution viral variants.
Collapse
Affiliation(s)
- Takuya Tada
- Department of Microbiology, New York University (NYU) Grossman School of Medicine, New York, NY10016
| | - Julia Minnee
- Department of Microbiology, New York University (NYU) Grossman School of Medicine, New York, NY10016
| | - Nathaniel R. Landau
- Department of Microbiology, New York University (NYU) Grossman School of Medicine, New York, NY10016
| |
Collapse
|
5
|
Interactions between Humans and Dogs during the COVID-19 Pandemic: Recent Updates and Future Perspectives. Animals (Basel) 2023; 13:ani13030524. [PMID: 36766413 PMCID: PMC9913536 DOI: 10.3390/ani13030524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
COVID-19 is one of the deadliest epidemics. This pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but the role of dogs in spreading the disease in human society is poorly understood. This review sheds light on the limited susceptibility of dogs to COVID-19 infections which is likely attributed to the relatively low levels of angiotensin-converting enzyme 2 (ACE2) in the respiratory tract and the phylogenetic distance of ACE2 in dogs from the human ACE2 receptor. The low levels of ACE2 affect the binding affinity between spike and ACE2 proteins resulting in it being uncommon for dogs to spread the disease. To demonstrate the role of dogs in spreading COVID-19, we reviewed the epidemiological studies and prevalence of SARS-CoV-2 in dogs. Additionally, we discussed the use of detection dogs as a rapid and reliable method for effectively discriminating between SARS-CoV-2 infected and non-infected individuals using different types of samples (secretions, saliva, and sweat). We considered the available information on COVID-19 in the human-dog interfaces involving the possibility of transmission of COVID-19 to dogs by infected individuals and vice versa, the human-dog behavior changes, and the importance of preventive measures because the risk of transmission by domestic dogs remains a concern.
Collapse
|
6
|
Tada T, Dcosta BM, Minnee J, Landau NR. Vectored Immunoprophylaxis and Treatment of SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523649. [PMID: 36711584 PMCID: PMC9882093 DOI: 10.1101/2023.01.11.523649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Vectored immunoprophylaxis was first developed as a means to establish engineered immunity to HIV through the use of an adeno-associated viral vector expressing a broadly neutralizing antibody. We have applied this concept to establish long-term prophylaxis against SARS-CoV-2 by adeno-associated and lentiviral vectors expressing a high affinity ACE2 decoy receptor. Administration of decoy-expressing AAV vectors based on AAV2.retro and AAV6.2 by intranasal instillation or intramuscular injection protected mice against high-titered SARS-CoV-2 infection. AAV and lentiviral vectored immunoprophylaxis was durable and active against recent SARS-CoV-2 Omicron subvariants. The AAV vectors were also effective when administered up to 24 hours post-infection. Vectored immunoprophylaxis could be of value for immunocompromised individuals for whom vaccination is not practical and as a means to rapidly establish protection from infection. Unlike monoclonal antibody therapy, the approach is expected to remain active despite continued evolution viral variants.
Collapse
|
7
|
Duman N, Tuncel G, Bisgin A, Bozdogan ST, Sag SO, Gul S, Kiraz A, Balta B, Erdogan M, Uyanik B, Canbek S, Ata P, Geckinli BB, Arslan Ates E, Alavanda C, Yesim Ozdemir S, Sezer O, Ozgon GO, Gurkan H, Guler K, Boga I, Kaya N, Alemdar A, Sayan M, Dundar M, Ergoren MC, Temel SG. Analysis of ACE2 and TMPRSS2 coding variants as a risk factor for SARS-CoV-2 from 946 whole-exome sequencing data in the Turkish population. J Med Virol 2022; 94:5225-5243. [PMID: 35811452 PMCID: PMC9349697 DOI: 10.1002/jmv.27976] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/14/2022] [Accepted: 07/02/2022] [Indexed: 12/15/2022]
Abstract
Heterogeneity in symptoms associated with COVID-19 in infected patients remains unclear. ACE2 and TMPRSS2 gene variants are considered possible risk factors for COVID-19. In this study, a retrospective comparative genome analysis of the ACE2 and TMPRSS2 variants from 946 whole-exome sequencing data was conducted. Allele frequencies of all variants were calculated and filtered to remove variants with allele frequencies lower than 0.003 and to prioritize functional coding variants. The majority of detected variants were intronic, only two ACE2 and three TMPRSS2 nonsynonymous variants were detected in the analyzed cohort. The main ACE2 variants that putatively have a protective or susceptibility effect on SARS-CoV-2 have not yet been determined in the Turkish population. The Turkish genetic makeup likely lacks any ACE2 variant that increases susceptibility to SARS-CoV-2 infection. TMPRSS2 rs75603675 and rs12329760 variants that were previously defined as common variants that have different allele frequencies among populations and may have a role in SARS-CoV-2 attachment to host cells were determined in the population. Overall, these data will contribute to the formation of a national variation database and may also contribute to further studies of ACE2 and TMPRSS2 in the Turkish population and differences in SARS-CoV-2 infection among other populations.
Collapse
Affiliation(s)
- Nilgun Duman
- Department of Medical Genetics, Faculty of MedicineBezmialem Vakif UniversityIstanbulTurkey
| | - Gulten Tuncel
- DESAM Research InstituteNear East UniversityNicosiaCyprus
| | - Atil Bisgin
- Department of Medical Genetics, Faculty of MedicineÇukurova UniversityAdanaTurkey,AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center)Cukurova UniversityAdanaTurkey
| | - Sevcan Tug Bozdogan
- Department of Medical Genetics, Faculty of MedicineÇukurova UniversityAdanaTurkey,AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center)Cukurova UniversityAdanaTurkey
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Seref Gul
- Department of Biology, Biotechnology Division, Faculty of SciencesIstanbul UniversityIstanbulTurkey
| | - Aslihan Kiraz
- Department of Medical GeneticsKayseri Education and Research State HospitalKayseriTurkey
| | - Burhan Balta
- Department of Medical GeneticsKayseri Education and Research State HospitalKayseriTurkey
| | - Murat Erdogan
- Department of Medical GeneticsKayseri Education and Research State HospitalKayseriTurkey
| | - Bulent Uyanik
- Department of Medical GeneticsIstanbul Bakırkoy Dr. Sadi Konuk Education and Research HospitalIstanbulTurkey
| | - Sezin Canbek
- Department of Medical GeneticsUmraniye City HospitalIstanbulTurkey
| | - Pinar Ata
- Department of Medical Genetics, Faculty of MedicineMarmara UniversityIstanbulTurkey
| | | | - Esra Arslan Ates
- Department of Medical Genetics, Faculty of MedicineMarmara UniversityIstanbulTurkey
| | - Ceren Alavanda
- Department of Medical Genetics, Faculty of MedicineMarmara UniversityIstanbulTurkey
| | - Sevda Yesim Ozdemir
- Department of Medical Genetics, Faculty of MedicineUskudar UniversityİstanbulTurkey
| | - Ozlem Sezer
- Department of Medical GeneticsSamsun Education and Research HospitalSamsunTurkey
| | | | - Hakan Gurkan
- Department of Medical Genetics, Faculty of MedicineTrakya UniversityEdirneTurkey
| | - Kubra Guler
- Mikrogen Genetic Diagnostic CenterAnkaraTurkey
| | - Ibrahim Boga
- Department of Medical Genetics, Faculty of MedicineÇukurova UniversityAdanaTurkey,AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center)Cukurova UniversityAdanaTurkey
| | - Niyazi Kaya
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Adem Alemdar
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Murat Sayan
- DESAM Research InstituteNear East UniversityNicosiaCyprus,PCR Unit, Kocaeli University Education and Research HospitalKocaeliTurkey
| | - Munis Dundar
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTurkey
| | - Mahmut Cerkez Ergoren
- DESAM Research InstituteNear East UniversityNicosiaCyprus,Department of Medical Genetics, Faculty of MedicineNear East UniversityNicosiaCyprus
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey,Department of Medical Genetics, Faculty of MedicineNear East UniversityNicosiaCyprus,Department of Histology and Embryology, Faculty of MedicineBursa Uludag UniversityBursaTurkey,Department of Translational Medicine, Institute of Health SciencesBursa Uludag UniversityBursaTurkey
| |
Collapse
|
8
|
Warren CJ, Yu S, Peters DK, Barbachano-Guerrero A, Yang Q, Burris BL, Worwa G, Huang IC, Wilkerson GK, Goldberg TL, Kuhn JH, Sawyer SL. Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans. Cell 2022; 185:3980-3991.e18. [PMID: 36182704 PMCID: PMC9588614 DOI: 10.1016/j.cell.2022.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/22/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023]
Abstract
Simian arteriviruses are endemic in some African primates and can cause fatal hemorrhagic fevers when they cross into primate hosts of new species. We find that CD163 acts as an intracellular receptor for simian hemorrhagic fever virus (SHFV; a simian arterivirus), a rare mode of virus entry that is shared with other hemorrhagic fever-causing viruses (e.g., Ebola and Lassa viruses). Further, SHFV enters and replicates in human monocytes, indicating full functionality of all of the human cellular proteins required for viral replication. Thus, simian arteriviruses in nature may not require major adaptations to the human host. Given that at least three distinct simian arteriviruses have caused fatal infections in captive macaques after host-switching, and that humans are immunologically naive to this family of viruses, development of serology tests for human surveillance should be a priority.
Collapse
Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Shuiqing Yu
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Douglas K Peters
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Bridget L Burris
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Gabriella Worwa
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - I-Chueh Huang
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Gregory K Wilkerson
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA.
| |
Collapse
|
9
|
Beeraka NM, Sukocheva OA, Lukina E, Liu J, Fan R. Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Rev Med Virol 2022; 32:e2346. [PMID: 35416390 PMCID: PMC9111059 DOI: 10.1002/rmv.2346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/28/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
Collapse
Affiliation(s)
- Narasimha M. Beeraka
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
- Department of Human AnatomyI.M. Sechenov First Moscow State Medical University (Sechenov University)MoscowRussian Federation
| | - Olga A. Sukocheva
- Discipline of Health SciencesCollege of Nursing and Health SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Elena Lukina
- Discipline of BiologyCollege of SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Junqi Liu
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| | - Ruitai Fan
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| |
Collapse
|
10
|
Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19. Proc Natl Acad Sci U S A 2022; 119:e2206610119. [PMID: 35947637 PMCID: PMC9436378 DOI: 10.1073/pnas.2206610119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a coronavirus that spilled over from the bat reservoir. However, the host genetic determinants that drive SARS-CoV-2 susceptibility and COVID-19 severity are largely unknown. Understanding how cellular proteins interacting with SARS-CoV-2 have evolved in primates and bats is of primary importance to decipher differences in the infection outcome between humans and the viral reservoir in bats. Here, we performed comparative functional genetic analyses of hundreds of SARS-CoV-2-interacting proteins to study virus–host interface adaptation over millions of years, pointing to genes similarly—or differentially—engaged in evolutionary arms races and that may be at the basis of in vivo pathogenic differences. The coronavirus disease 19 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a coronavirus that spilled over from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus–host interfaces. We performed high-throughput evolutionary analyses of 334 SARS-CoV-2-interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates, and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus–host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus–host arms race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified adaptations involved in SARS-CoV-2 infection in bats and primates, enlightening modern genetic determinants of virus susceptibility and severity.
Collapse
|
11
|
Frank HK, Enard D, Boyd SD. Exceptional diversity and selection pressure on coronavirus host receptors in bats compared to other mammals. Proc Biol Sci 2022; 289:20220193. [PMID: 35892217 PMCID: PMC9326293 DOI: 10.1098/rspb.2022.0193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/30/2022] [Indexed: 12/25/2022] Open
Abstract
Pandemics originating from non-human animals highlight the need to understand how natural hosts have evolved in response to emerging human pathogens and which groups may be susceptible to infection and/or potential reservoirs to mitigate public health and conservation concerns. Multiple zoonotic coronaviruses, such as severe acute respiratory syndrome-associated coronavirus (SARS-CoV), SARS-CoV-2 and Middle Eastern respiratory syndrome-associated coronavirus (MERS-CoV), are hypothesized to have evolved in bats. We investigate angiotensin-converting enzyme 2 (ACE2), the host protein bound by SARS-CoV and SARS-CoV-2, and dipeptidyl-peptidase 4 (DPP4 or CD26), the host protein bound by MERS-CoV, in the largest bat datasets to date. Both the ACE2 and DPP4 genes are under strong selection pressure in bats, more so than in other mammals, and in residues that contact viruses. Additionally, mammalian groups vary in their similarity to humans in residues that contact SARS-CoV, SARS-CoV-2 and MERS-CoV, and increased similarity to humans in binding residues is broadly predictive of susceptibility to SARS-CoV-2. This work augments our understanding of the relationship between coronaviruses and mammals, particularly bats, provides taxonomically diverse data for studies of how host proteins are bound by coronaviruses and can inform surveillance, conservation and public health efforts.
Collapse
Affiliation(s)
- Hannah K. Frank
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
12
|
Roelle SM, Shukla N, Pham AT, Bruchez AM, Matreyek KA. Expanded ACE2 dependencies of diverse SARS-like coronavirus receptor binding domains. PLoS Biol 2022; 20:e3001738. [PMID: 35895696 PMCID: PMC9359572 DOI: 10.1371/journal.pbio.3001738] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 08/08/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
Viral spillover from animal reservoirs can trigger public health crises and cripple the world economy. Knowing which viruses are primed for zoonotic transmission can focus surveillance efforts and mitigation strategies for future pandemics. Successful engagement of receptor protein orthologs is necessary during cross-species transmission. The clade 1 sarbecoviruses including Severe Acute Respiratory Syndrome-related Coronavirus (SARS-CoV) and SARS-CoV-2 enter cells via engagement of angiotensin converting enzyme-2 (ACE2), while the receptor for clade 2 and clade 3 remains largely uncharacterized. We developed a mixed cell pseudotyped virus infection assay to determine whether various clades 2 and 3 sarbecovirus spike proteins can enter HEK 293T cells expressing human or Rhinolophus horseshoe bat ACE2 proteins. The receptor binding domains from BtKY72 and Khosta-2 used human ACE2 for entry, while BtKY72 and Khosta-1 exhibited widespread use of diverse rhinolophid ACE2s. A lysine at ACE2 position 31 appeared to be a major determinant of the inability of these RBDs to use a certain ACE2 sequence. The ACE2 protein from Rhinolophus alcyone engaged all known clade 3 and clade 1 receptor binding domains. We observed little use of Rhinolophus ACE2 orthologs by the clade 2 viruses, supporting the likely use of a separate, unknown receptor. Our results suggest that clade 3 sarbecoviruses from Africa and Europe use Rhinolophus ACE2 for entry, and their spike proteins appear primed to contribute to zoonosis under the right conditions. Knowing which viruses are primed for zoonotic transmission can focus surveillance efforts and mitigation strategies for future pandemics. This study shows that SARS-like coronaviruses identified in bats from Europe and Africa can use a range of horseshoe bat ACE2s for entry. In addition, viruses found in Russia and Kenya also have the ability to at least weakly use human ACE2.
Collapse
Affiliation(s)
- Sarah M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anh T. Pham
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anna M. Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail:
| |
Collapse
|
13
|
Merkel OM. Can pulmonary RNA delivery improve our pandemic preparedness? J Control Release 2022; 345:549-556. [PMID: 35358609 PMCID: PMC8958776 DOI: 10.1016/j.jconrel.2022.03.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/20/2022] [Indexed: 12/17/2022]
Abstract
The coronavirus pandemic has changed our perception of RNA medicines, and RNA vaccines have revolutionized our pandemic preparedness. But are we indeed prepared for the next variant or the next emerging virus? How can we prepare? And what does the role of inhaled antiviral RNA play in this regard? When the pandemic started, I rerouted much of the ongoing inhaled RNA delivery research in my group towards the inhibition and treatment of respiratory viral infections. Two years later, I have taken the literature, past and ongoing clinical trials into consideration and have gained new insights based on our collaborative research which I will discuss in this oration.
Collapse
|
14
|
Cobb RR, Nkolola J, Gilchuk P, Chandrashekar A, Yu J, House RV, Earnhart CG, Dorsey NM, Hopkins SA, Snow DM, Chen RE, VanBlargan LA, Hechenblaickner M, Hoppe B, Collins L, Tomic MT, Nonet GH, Hackett K, Slaughter JC, Lewis MG, Andersen H, Cook A, Diamond MS, Carnahan RH, Barouch DH, Crowe JE. A combination of two human neutralizing antibodies prevents SARS-CoV-2 infection in cynomolgus macaques. MED 2022; 3:188-203.e4. [PMID: 35132398 PMCID: PMC8810411 DOI: 10.1016/j.medj.2022.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human monoclonal antibody (mAb) treatments are promising for COVID-19 prevention or therapy. The pre-exposure prophylactic efficacy of neutralizing antibodies that are engineered with mutations to extend their persistence in human serum and the neutralizing antibody titer in serum required for protection against SARS-CoV-2 infection remain poorly characterized. METHODS The Fc region of two neutralizing mAbs (COV2-2130 and COV2-2381) targeting non-overlapping epitopes on the receptor binding domain of SARS-CoV-2 spike protein was engineered to extend their persistence in humans and reduce interactions with Fc gamma receptors. We assessed protection by individual antibodies or a combination of the two antibodies (designated ADM03820) given prophylactically by an intravenous or intramuscular route in a non-human primate (NHP) model of SARS-CoV-2 infection. FINDINGS Passive transfer of individual mAbs or ADM03820 conferred virological protection in the NHP respiratory tract in a dose-dependent manner, and ADM03820 potently neutralized SARS-CoV-2 variants of concern in vitro. We defined a protective serum-neutralizing antibody titer and concentration in NHPs for passively transferred human antibodies that acted by direct viral neutralization. CONCLUSIONS In summary, we demonstrate that neutralizing antibodies with extended half-life and lacking Fc-mediated effector functions are efficient for pre-exposure prophylaxis of SARS-CoV-2 infection in NHPs. These results support clinical development of ADM03820 for COVID-19 prevention. FUNDING This research was supported by a contract from the JPEO-CBRND (W911QY-20-9-003, 20-05); the Joint Sciences and Technology Office and Joint Program Executive Office (MCDC-16-01-002 JSTO, JPEO); a DARPA grant (HR0011-18-2-0001); an NIH grant (R01 AI157155); and the 2019 Future Insight Prize from Merck KGaA.
Collapse
Affiliation(s)
- Ronald R Cobb
- Ology Bioservices, Process Development and Manufacturing, Alachua, FL 32615, USA
| | - Joseph Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Christopher G Earnhart
- Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense, US Department of Defense, Frederick, MD 21703, USA
| | - Nicole M Dorsey
- Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense, US Department of Defense, Frederick, MD 21703, USA
| | | | | | - Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Brian Hoppe
- Ology Bioservices, Process Development and Manufacturing, Alachua, FL 32615, USA
| | - Laura Collins
- Ology Bioservices, Process Development and Manufacturing, Alachua, FL 32615, USA
| | - Milan T Tomic
- Research and Development, Ology Bioservices, Inc., Alameda 94501, CA, USA
| | - Genevieve H Nonet
- Research and Development, Ology Bioservices, Inc., Alameda 94501, CA, USA
| | | | - James C Slaughter
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | | | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| |
Collapse
|
15
|
Starr TN, Zepeda SK, Walls AC, Greaney AJ, Alkhovsky S, Veesler D, Bloom JD. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 2022; 603:913-918. [PMID: 35114688 PMCID: PMC8967715 DOI: 10.1038/s41586-022-04464-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022]
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.
Collapse
Affiliation(s)
- Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sergey Alkhovsky
- N.F. Gamleya National Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - David Veesler
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| |
Collapse
|
16
|
Castiglione GM, Zhou L, Xu Z, Neiman Z, Hung CF, Duh EJ. Evolutionary pathways to SARS-CoV-2 resistance are opened and closed by epistasis acting on ACE2. PLoS Biol 2021; 19:e3001510. [PMID: 34932561 PMCID: PMC8730403 DOI: 10.1371/journal.pbio.3001510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 01/05/2022] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infects a broader range of mammalian species than previously predicted, binding a diversity of angiotensin converting enzyme 2 (ACE2) orthologs despite extensive sequence divergence. Within this sequence degeneracy, we identify a rare sequence combination capable of conferring SARS-CoV-2 resistance. We demonstrate that this sequence was likely unattainable during human evolution due to deleterious effects on ACE2 carboxypeptidase activity, which has vasodilatory and cardioprotective functions in vivo. Across the 25 ACE2 sites implicated in viral binding, we identify 6 amino acid substitutions unique to mouse-one of the only known mammalian species resistant to SARS-CoV-2. Substituting human variants at these positions is sufficient to confer binding of the SARS-CoV-2 S protein to mouse ACE2, facilitating cellular infection. Conversely, substituting mouse variants into either human or dog ACE2 abolishes viral binding, diminishing cellular infection. However, these same substitutions decrease human ACE2 activity by 50% and are predicted as pathogenic, consistent with the extreme rarity of human polymorphisms at these sites. This trade-off can be avoided, however, depending on genetic background; if substituted simultaneously, these same mutations have no deleterious effect on dog ACE2 nor that of the rodent ancestor estimated to exist 70 million years ago. This genetic contingency (epistasis) may have therefore opened the road to resistance for some species, while making humans susceptible to viruses that use these ACE2 surfaces for binding, as does SARS-CoV-2.
Collapse
Affiliation(s)
- Gianni M. Castiglione
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lingli Zhou
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Zhenhua Xu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Zachary Neiman
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Chien-Fu Hung
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elia J. Duh
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| |
Collapse
|
17
|
Buratto D, Saxena A, Ji Q, Yang G, Pantano S, Zonta F. Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations. Front Immunol 2021; 12:730099. [PMID: 34858396 PMCID: PMC8632240 DOI: 10.3389/fimmu.2021.730099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 infects humans and causes Coronavirus disease 2019 (COVID-19). The S1 domain of the spike glycoprotein of SARS-CoV-2 binds to human angiotensin-converting enzyme 2 (hACE2) via its receptor-binding domain, while the S2 domain facilitates fusion between the virus and the host cell membrane for entry. The spike glycoprotein of circulating SARS-CoV-2 genomes is a mutation hotspot. Some mutations may affect the binding affinity for hACE2, while others may modulate S-glycoprotein expression, or they could result in a virus that can escape from antibodies generated by infection with the original variant or by vaccination. Since a large number of variants are emerging, it is of vital importance to be able to rapidly assess their characteristics: while changes of binding affinity alone do not always cause direct advantages for the virus, they still can provide important insights on where the evolutionary pressure is directed. Here, we propose a simple and cost-effective computational protocol based on Molecular Dynamics simulations to rapidly screen the ability of mutated spike protein to bind to the hACE2 receptor and selected neutralizing biomolecules. Our results show that it is possible to achieve rapid and reliable predictions of binding affinities. A similar approach can be used to perform preliminary screenings of the potential effects of S-RBD mutations, helping to prioritize the more time-consuming and expensive experimental work.
Collapse
Affiliation(s)
- Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Abhishek Saxena
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Sergio Pantano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| |
Collapse
|
18
|
King SB, Singh M. Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections. PLoS Comput Biol 2021; 17:e1009560. [PMID: 34793437 PMCID: PMC8601562 DOI: 10.1371/journal.pcbi.1009560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.
Collapse
Affiliation(s)
- Sean B. King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
19
|
Carey CM, Apple SE, Hilbert ZA, Kay MS, Elde NC. Diarrheal pathogens trigger rapid evolution of the guanylate cyclase-C signaling axis in bats. Cell Host Microbe 2021; 29:1342-1350.e5. [PMID: 34358433 PMCID: PMC8429143 DOI: 10.1016/j.chom.2021.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 05/06/2021] [Accepted: 07/13/2021] [Indexed: 12/21/2022]
Abstract
The pathogenesis of infectious diarrheal diseases is largely attributed to enterotoxins that cause dehydration by disrupting intestinal water absorption. We investigated patterns of genetic variation in mammalian guanylate cyclase-C (GC-C), an intestinal receptor targeted by bacterially encoded heat-stable enterotoxins (STa), to determine how host species adapt in response to diarrheal infections. Our phylogenetic and functional analysis of GC-C supports long-standing evolutionary conflict with diarrheal bacteria in primates and bats, with highly variable susceptibility to STa across species. In bats, we further show that GC-C diversification has sparked compensatory mutations in the endogenous uroguanylin ligand, suggesting an unusual scenario of pathogen-driven evolution of an entire signaling axis. Together, these findings suggest that conflicts with diarrheal pathogens have had far-reaching impacts on the evolution of mammalian gut physiology.
Collapse
Affiliation(s)
- Clayton M Carey
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Sarah E Apple
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Zoë A Hilbert
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael S Kay
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nels C Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
| |
Collapse
|
20
|
Karnik M, Beeraka NM, Uthaiah CA, Nataraj SM, Bettadapura ADS, Aliev G, Madhunapantula SV. A Review on SARS-CoV-2-Induced Neuroinflammation, Neurodevelopmental Complications, and Recent Updates on the Vaccine Development. Mol Neurobiol 2021; 58:4535-4563. [PMID: 34089508 PMCID: PMC8179092 DOI: 10.1007/s12035-021-02399-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/19/2021] [Indexed: 02/08/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a devastating viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The incidence and mortality of COVID-19 patients have been increasing at an alarming rate. The mortality is much higher in older individuals, especially the ones suffering from respiratory distress, cardiac abnormalities, renal diseases, diabetes, and hypertension. Existing evidence demonstrated that SARS-CoV-2 makes its entry into human cells through angiotensin-converting enzyme 2 (ACE-2) followed by the uptake of virions through cathepsin L or transmembrane protease serine 2 (TMPRSS2). SARS-CoV-2-mediated abnormalities in particular cardiovascular and neurological ones and the damaged coagulation systems require extensive research to develop better therapeutic modalities. As SARS-CoV-2 uses its S-protein to enter into the host cells of several organs, the S-protein of the virus is considered as the ideal target to develop a potential vaccine. In this review, we have attempted to highlight the landmark discoveries that lead to the development of various vaccines that are currently under different stages of clinical progression. Besides, a brief account of various drug candidates that are being tested to mitigate the burden of COVID-19 was also covered. Further, in a dedicated section, the impact of SARS-CoV-2 infection on neuronal inflammation and neuronal disorders was discussed. In summary, it is expected that the content covered in this article help to understand the pathophysiology of COVID-19 and the impact on neuronal complications induced by SARS-CoV-2 infection while providing an update on the vaccine development.
Collapse
Affiliation(s)
- Medha Karnik
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India
| | - Narasimha M Beeraka
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India
- Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, bld. 2, Moscow, 119991, Russia
| | - Chinnappa A Uthaiah
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India
| | - Suma M Nataraj
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India
| | - Anjali Devi S Bettadapura
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India
| | - Gjumrakch Aliev
- Sechenov First Moscow State Medical University (Sechenov University), St. Trubetskaya, 8, bld. 2, Moscow, 119991, Russia
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, Moscow Region, 142432, Russia
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russia
- GALLY International Research Institute, 7733 Louis Pasteur Drive, San Antonio, TX, #330, USA
| | - SubbaRao V Madhunapantula
- Center of Excellence in Molecular Biology and Regenerative Medicine (CEMR), Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India.
- Special Interest Group in Cancer Biology and Cancer Stem Cells (SIG-CBCSC), JSS Medical College, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India.
| |
Collapse
|
21
|
An overview of SARS-COV-2 epidemiology, mutant variants, vaccines, and management strategies. J Infect Public Health 2021; 14:1299-1312. [PMID: 34429257 PMCID: PMC8366110 DOI: 10.1016/j.jiph.2021.08.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background Over the last two decades, humanity has observed the extraordinary anomaly caused by novel, weird coronavirus strains, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). As the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus has made its entry into the world, it has dramatically affected life in every domain by continuously producing new variants. The vaccine development is an ongoing process, although some vaccines got marketed. The big challenge is now whether the vaccine candidates can provide long-lasting protection or prevention against mutant variants. Methods The information was gathered from various journals, electronic searches via Internet-based information such as PubMed, Google Scholar, Science Direct, online electronic journals, WHO landscape, world meters, WHO website, and News. Results This review will present and discuss some coronavirus disease 19 (COVID-19) related aspects including: the pathophysiology, epidemiology, mutant variants vaccine candidates, vaccine efficacy, and management strategies. Due to the high death rate, continuous spread, an inadequate workforce, lack of required therapeutics, and incomplete understanding of the viral strain, it becomes crucial to build the knowledge of its biological characteristics and make available the rapid diagnostic and vital therapeutic machinery for the combat and management of an infection. Conclusion The data summarizes current research on the COVID 19 infection and therapeutic interventions, which will direct future decision-making on the effort-worthy phases of the COVID 19 and the development of critical therapeutics. The only possible solution is the vaccine development targeting against all variant strains to halt its progress; the identified theoretical and practical knowledge can eliminate the gaps to improve a better understanding of the novel coronavirus structure and its design of a vaccine. In addition, to that the long-lasting protection is another challenging objective that need to be looked into.
Collapse
|
22
|
Pervasive positive selection on virus receptors driven by host-virus conflicts in mammals. J Virol 2021; 95:e0102921. [PMID: 34319153 DOI: 10.1128/jvi.01029-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses hijack cellular proteins known as viral receptors to initiate their infection. Viral receptors are subject to two conflicting directional forces, namely negative selection to maintain their cellular function and positive selection resulted from everchanging host-virus arms race. Much remains unclear how viral receptors evolved in mammals, and whether viral receptors from different mammal groups experienced different strength of natural selection. Here, we perform evolutionary analyses of 92 viral receptors in five major orders of mammals, including Carnivora, Cetartiodactyla, Chiroptera, Primates, and Rodentia. In all the five mammal orders, signals of positive selection are detected for a high proportion of viral receptors (from 41% in Carnivora to 65% in Rodentia). Many positively selected residues overlap host-virus interaction interface. Compared with control genes, we find viral receptors underwent elevated rate of adaptive evolution in all the five mammal orders, suggesting that host-virus conflicts are the main driver of the adaptive evolution of viral receptors in mammals. Interestingly, the overall strength of natural selection acting on viral receptors driven by host-virus arms race is largely homogenous and correlated among different mammal orders with bats and rodents, zoonosis reservoirs of importance, unexceptional. Taken together, our findings indicate host-virus conflicts have driven the elevated rate of adaptive evolution in viral receptors across mammals, and might have important implications in zoonosis surveillance and prediction. Importance Viral receptors are cellular proteins hijacked by viruses to help their infections. A complete picture on the evolution of viral receptors in mammals is still lacking. Here, we perform a comprehensive evolutionary analysis of the evolution of 92 viral receptors in five mammal orders, including Carnivora, Cetartiodactyla, Chiroptera, Primates, and Rodentia. We find that positive selection pervasively occurred during the evolution of viral receptors, and viral receptors exhibit at an elevated rate of adaptive evolution than control genes in all the five mammal orders, suggesting host-virus conflicts are a major driver of the adaptive evolution of viral receptors. Interestingly, the strength of positive selection acting on viral receptors is similar among the five mammal orders. Our study might have important implications in understanding the evolution of host-virus interaction.
Collapse
|
23
|
Wang W, Han GZ. Ancient Adaptative Evolution of ACE2 in East Asians. Genome Biol Evol 2021; 13:6327689. [PMID: 34302465 PMCID: PMC8369073 DOI: 10.1093/gbe/evab173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing an unprecedented challenge to global public health. SARS-CoV-2 and several other coronaviruses utilize angiotensin-converting enzyme 2 (ACE2) as their entry receptors. The ACE2 gene has been found to experience episodic positive selection across mammals. However, much remains unknown about how the ACE2 gene evolved in human populations. Here, we use population genetics approaches to investigate the evolution of the ACE2 gene in 26 human populations sampled globally. We find the ACE2 gene exhibits an extremely low nucleotide diversity in the East Asian populations. Strong signals of selective sweep are detected in the East Asian populations, but not in the other human populations. The selective sweep in ACE2 is estimated to begin in East Asian populations ∼23,600 years ago. Our study provides novel insights into the evolution of the ACE2 gene within human populations.
Collapse
Affiliation(s)
- Wenqiang Wang
- College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Jiangsu, China
| |
Collapse
|
24
|
Etienne EE, Nunna BB, Talukder N, Wang Y, Lee ES. COVID-19 Biomarkers and Advanced Sensing Technologies for Point-of-Care (POC) Diagnosis. Bioengineering (Basel) 2021; 8:98. [PMID: 34356205 PMCID: PMC8301167 DOI: 10.3390/bioengineering8070098] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19, also known as SARS-CoV-2 is a novel, respiratory virus currently plaguing humanity. Genetically, at its core, it is a single-strand positive-sense RNA virus. It is a beta-type Coronavirus and is distinct in its structure and binding mechanism compared to other types of coronaviruses. Testing for the virus remains a challenge due to the small market available for at-home detection. Currently, there are three main types of tests for biomarker detection: viral, antigen and antibody. Reverse Transcription-Polymerase Chain Reaction (RT-PCR) remains the gold standard for viral testing. However, the lack of quantitative detection and turnaround time for results are drawbacks. This manuscript focuses on recent advances in COVID-19 detection that have lower limits of detection and faster response times than RT-PCR testing. The advancements in sensing platforms have amplified the detection levels and provided real-time results for SARS-CoV-2 spike protein detection with limits as low as 1 fg/mL in the Graphene Field Effect Transistor (FET) sensor. Additionally, using multiple biomarkers, detection levels can achieve a specificity and sensitivity level comparable to that of PCR testing. Proper biomarker selection coupled with nano sensing detection platforms are key in the widespread use of Point of Care (POC) diagnosis in COVID-19 detection.
Collapse
Affiliation(s)
- Ernst Emmanuel Etienne
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| | - Bharath Babu Nunna
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
- Division of Engineering in Medicine, Department of Medicine, Brigham, and Women’s Hospital, Harvard Medical School, Harvard University, Cambridge, MA 02139, USA
| | - Niladri Talukder
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| | - Yudong Wang
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| | - Eon Soo Lee
- Advanced Energy Systems and Microdevices Laboratory, Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA; (E.E.E.); (B.B.N.); (N.T.); (Y.W.)
| |
Collapse
|
25
|
Shukla N, Roelle SM, Suzart VG, Bruchez AM, Matreyek KA. Mutants of human ACE2 differentially promote SARS-CoV and SARS-CoV-2 spike mediated infection. PLoS Pathog 2021; 17:e1009715. [PMID: 34270613 PMCID: PMC8284657 DOI: 10.1371/journal.ppat.1009715] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/15/2021] [Indexed: 01/10/2023] Open
Abstract
SARS-CoV and SARS-CoV-2 encode spike proteins that bind human ACE2 on the cell surface to enter target cells during infection. A small fraction of humans encode variants of ACE2, thus altering the biochemical properties at the protein interaction interface. These and other ACE2 coding mutants can reveal how the spike proteins of each virus may differentially engage the ACE2 protein surface during infection. We created an engineered HEK 293T cell line for facile stable transgenic modification, and expressed the major human ACE2 allele or 28 of its missense mutants, 24 of which are possible through single nucleotide changes from the human reference sequence. Infection with SARS-CoV or SARS-CoV-2 spike pseudotyped lentiviruses revealed that high ACE2 cell-surface expression could mask the effects of impaired binding during infection. Drastically reducing ACE2 cell surface expression revealed a range of infection efficiencies across the panel of mutants. Our infection results revealed a non-linear relationship between soluble SARS-CoV-2 RBD binding to ACE2 and pseudovirus infection, supporting a major role for binding avidity during entry. While ACE2 mutants D355N, R357A, and R357T abrogated entry by both SARS-CoV and SARS-CoV-2 spike proteins, the Y41A mutant inhibited SARS-CoV entry much more than SARS-CoV-2, suggesting differential utilization of the ACE2 side-chains within the largely overlapping interaction surfaces utilized by the two CoV spike proteins. These effects correlated well with cytopathic effects observed during SARS-CoV-2 replication in ACE2-mutant cells. The panel of ACE2 mutants also revealed altered ACE2 surface dependencies by the N501Y spike variant, including a near-complete utilization of the K353D ACE2 variant, despite decreased infection mediated by the parental SARS-CoV-2 spike. Our results clarify the relationship between ACE2 abundance, binding, and infection, for various SARS-like coronavirus spike proteins and their mutants, and inform our understanding for how changes to ACE2 sequence may correspond with different susceptibilities to infection.
Collapse
Affiliation(s)
- Nidhi Shukla
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Sarah M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Vinicius G. Suzart
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Anna M. Bruchez
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| |
Collapse
|
26
|
Ozbalci D. A tale of two diseases: Sarcoidosis, COVID-19 and new therapeutic options with dual RAS inhibition and tetanus-diphtheria vaccine. Med Hypotheses 2021; 152:110619. [PMID: 34102600 PMCID: PMC8168307 DOI: 10.1016/j.mehy.2021.110619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/25/2021] [Accepted: 05/30/2021] [Indexed: 01/08/2023]
Abstract
Sars Cov-2, the pathogen which belongs to the beta coronavirus family that is responsible for COVID-19, uses Angiotensin Converting Enzyme 2 (ACE2) as a receptor, which is responsible for controlling the actions of renin-angiotensin system (RAS). Sars Cov-2 - ACE2 binding leads to a RAS mediated immune response, which targets especially lungs to form ARDS, which in turn, is the most important cause of mortality in COVID-19. CD8+ T cell response dominates over CD4+ T cell response and natural killer cell dysfunction also leads to CD4+ cell dysfunction in COVID-19; this immune dysregulation leads to inappropriate (ARDS) and inadequate (low or quickly waning antibodies) responses to the disease and unfortunately, prepares the patients for re-infections. The peripheral anergy seen in chronic sarcoidosis has much resemblance to COVID-19; CD8+ T cell accumulation is also responsible for inadequate reaction to tuberculin and antigenic stimulus. This article, based on the similarity of COVID-19 and sarcoidosis, discusses a combination of the therapeutic strategy of the tetanus-diphtheria vaccine and dual RAS inhibition, alongside with hydroxychloroquine and antiviral agents, as a solution to overcome the problems described above.
Collapse
Affiliation(s)
- Demircan Ozbalci
- Suleyman Demirel University School of Medicine, Department of Hematology, Dogu Yerleskesi Cunur, Isparta, Turkey.
| |
Collapse
|
27
|
Dharmaraj S, Ashokkumar V, Hariharan S, Manibharathi A, Show PL, Chong CT, Ngamcharussrivichai C. The COVID-19 pandemic face mask waste: A blooming threat to the marine environment. CHEMOSPHERE 2021; 272:129601. [PMID: 33497928 PMCID: PMC7836388 DOI: 10.1016/j.chemosphere.2021.129601] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/25/2020] [Accepted: 01/06/2021] [Indexed: 05/18/2023]
Abstract
Recently, the COVID-19 disease spread has emerged as a worldwide pandemic and cause severe threats to humanity. The World Health Organisation (WHO) releases guidelines to help the countries to reduce the spread of this virus to the public, like wearing masks, hand hygiene, social distancing, shutting down all types of public transports, etc. These conditions led to a worldwide economic fall drastically, and on the other hand, indirect environmental benefits like global air quality improvement and decreased water pollution are also pictured. Currently, use of face masks is part of a comprehensive package of the prevention and control measures that can limit the spread of COVID-19 since there is no clinically proven drugs or vaccine available for COVID-19. Mostly, face masks are made of petroleum-based non-renewable polymers that are non-biodegradable, hazardous to the environment and create health issues. This study demonstrates the extensive use of the face mask and how it affects human health and the marine ecosystem. It has become a great challenge for the government sectors to impose strict regulations for the proper disposal of the masks as medical waste by the public. Neglecting the seriousness of this issue may lead to the release of large tonnes of micro-plastics to the landfill as well as to the marine environment where mostly end-up and thereby affecting their fauna and flora population vastly. Besides, this study highlights the COVID-19 spread, its evolutionary importance, taxonomy, genomic structure, transmission to humans, prevention, and treatment.
Collapse
Affiliation(s)
- Selvakumar Dharmaraj
- Department of Marine Biotechnology, Academy of Maritime Education and Training [AMET] (Deemed to be University), Chennai 603112, Tamil Nadu, India
| | - Veeramuthu Ashokkumar
- Center of Excellence in Catalysis for Bioenergy and Renewable Chemicals (CBRC), Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Sneha Hariharan
- Department of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Akila Manibharathi
- PG and Research Department of Biotechnology, Mohamed Sathak College of Arts and Science, Sholinganallur 600116, Tamil Nadu, India
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Cheng Tung Chong
- China-UK Low Carbon College, Shanghai Jiao Tong University, Lingang, Shanghai, 201306, China
| | - Chawalit Ngamcharussrivichai
- Center of Excellence in Catalysis for Bioenergy and Renewable Chemicals (CBRC), Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Center of Excellence on Petrochemical and Materials Technology (PETROMAT), Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.
| |
Collapse
|
28
|
Olarte-Castillo XA, Dos Remédios JF, Heeger F, Hofer H, Karl S, Greenwood AD, East ML. The virus-host interface: Molecular interactions of Alphacoronavirus-1 variants from wild and domestic hosts with mammalian aminopeptidase N. Mol Ecol 2021; 30:2607-2625. [PMID: 33786949 PMCID: PMC8251223 DOI: 10.1111/mec.15910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022]
Abstract
The Alphacoronavirus‐1 species include viruses that infect numerous mammalian species. To better understand the wide host range of these viruses, better knowledge on the molecular determinants of virus–host cell entry mechanisms in wildlife hosts is essential. We investigated Alphacoronavirus‐1 infection in carnivores using long‐term data on Serengeti spotted hyenas (Crocuta crocuta) and molecular analyses guided by the tertiary structure of the viral spike (S) attachment protein's interface with the host receptor aminopeptidase N (APN). We sequenced the complete 3′‐end region of the genome of nine variants from wild African carnivores, plus the APN gene of 15 wild carnivore species. Our results revealed two outbreaks of Alphacoronavirus‐1 infection in spotted hyenas associated with genetically distinct canine coronavirus type II (CCoVII) variants. Within the receptor binding domain (RBD) of the S gene the residues that directly bind to the APN receptor were conserved in all variants studied, even those infecting phylogenetically diverse host taxa. We identified a variable region within RBD located next to a region that directly interacts with the APN receptor. Two residues within this variable region were under positive selection in hyena variants, indicating that both sites were associated with adaptation of CCoVII to spotted hyena APN. Analysis of APN sequences revealed that most residues that interact with the S protein are conserved in wild carnivores, whereas some adjacent residues are highly variable. Of the variable residues, four that are critical for virus–host binding were under positive selection and may modulate the efficiency of virus attachment to carnivore APN.
Collapse
Affiliation(s)
- Ximena A Olarte-Castillo
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,ZIBI Interdisciplinary Center for Infection Biology and Immunity, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Felix Heeger
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Stephan Karl
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Marion L East
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,ZIBI Interdisciplinary Center for Infection Biology and Immunity, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
29
|
Smaoui MR, Yahyaoui H. Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Sci Rep 2021; 11:9166. [PMID: 33911163 PMCID: PMC8080587 DOI: 10.1038/s41598-021-88696-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
The interaction between the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein and the ACE2 enzyme is believed to be the entry point of the virus into various cells in the body, including the lungs, heart, liver, and kidneys. The current focus of several therapeutic design efforts explores attempts at affecting the binding potential between the two proteins to limit the activity of the virus and disease progression. In this work, we analyze the stability of the spike protein under all possible single-point mutations in the RBD and computationally explore mutations that can affect the binding with the ACE2 enzyme. We unravel the mutation landscape of the receptor region and assess the toxicity potential of single and multi-point mutations, generating insights for future vaccine efforts on mutations that might further stabilize the spike protein and increase its infectivity. We developed a tool, called SpikeMutator, to construct full atomic protein structures of the mutant spike proteins and shared a database of 3800 single-point mutant structures. We analyzed the recent 65,000 reported spike sequences across the globe and observed the emergence of stable multi-point mutant structures. Using the landscape, we searched through 7.5 million possible 2-point mutation combinations and report that the (R355D K424E) mutation produces one of the strongest spike proteins that therapeutic efforts should investigate for the sake of developing effective vaccines.
Collapse
Affiliation(s)
| | - Hamdi Yahyaoui
- Computer Science Department, Kuwait University, Kuwait, State of Kuwait
| |
Collapse
|
30
|
Judd EN, Gilchrist AR, Meyerson NR, Sawyer SL. Positive natural selection in primate genes of the type I interferon response. BMC Ecol Evol 2021; 21:65. [PMID: 33902453 PMCID: PMC8074226 DOI: 10.1186/s12862-021-01783-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses are locked in an evolutionary arms race for dominance of the Type I interferon pathway. As a result, many genes in interferon pathways have experienced positive natural selection in favor of new allelic forms that can better recognize viruses or escape viral antagonists. Here, we performed a holistic analysis of selective pressures acting on genes in the Type I interferon family. We initially hypothesized that the genes responsible for inducing the production of interferon would be antagonized more heavily by viruses than genes that are turned on as a result of interferon. Our logic was that viruses would have greater effect if they worked upstream of the production of interferon molecules because, once interferon is produced, hundreds of interferon-stimulated proteins would activate and the virus would need to counteract them one-by-one.
Results We curated multiple sequence alignments of primate orthologs for 131 genes active in interferon production and signaling (herein, “induction” genes), 100 interferon-stimulated genes, and 100 randomly chosen genes. We analyzed each multiple sequence alignment for the signatures of recurrent positive selection. Counter to our hypothesis, we found the interferon-stimulated genes, and not interferon induction genes, are evolving significantly more rapidly than a random set of genes. Interferon induction genes evolve in a way that is indistinguishable from a matched set of random genes (22% and 18% of genes bear signatures of positive selection, respectively). In contrast, interferon-stimulated genes evolve differently, with 33% of genes evolving under positive selection and containing a significantly higher fraction of codons that have experienced selection for recurrent replacement of the encoded amino acid. Conclusion Viruses may antagonize individual products of the interferon response more often than trying to neutralize the system altogether.
Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01783-z.
Collapse
Affiliation(s)
- Elena N Judd
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Alison R Gilchrist
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Nicholas R Meyerson
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA
| | - Sara L Sawyer
- Department of Molecular, Cellular and Developmental Biology; BioFrontiers Institute, University of Colorado Boulder, Boulder, USA.
| |
Collapse
|
31
|
Suryamohan K, Diwanji D, Stawiski EW, Gupta R, Miersch S, Liu J, Chen C, Jiang YP, Fellouse FA, Sathirapongsasuti JF, Albers PK, Deepak T, Saberianfar R, Ratan A, Washburn G, Mis M, Santhosh D, Somasekar S, Hiranjith GH, Vargas D, Mohan S, Phalke S, Kuriakose B, Antony A, Ustav M, Schuster SC, Sidhu S, Junutula JR, Jura N, Seshagiri S. Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. Commun Biol 2021; 4:475. [PMID: 33846513 PMCID: PMC8041869 DOI: 10.1038/s42003-021-02030-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/23/2021] [Indexed: 01/07/2023] Open
Abstract
COVID-19 is a respiratory illness caused by a novel coronavirus called SARS-CoV-2. The viral spike (S) protein engages the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells with ~10-15-fold higher affinity compared to SARS-CoV S-protein, making it highly infectious. Here, we assessed if ACE2 polymorphisms can alter host susceptibility to SARS-CoV-2 by affecting this interaction. We analyzed over 290,000 samples representing >400 population groups from public genomic datasets and identified multiple ACE2 protein-altering variants. Using reported structural data, we identified natural ACE2 variants that could potentially affect virus-host interaction and thereby alter host susceptibility. These include variants S19P, I21V, E23K, K26R, T27A, N64K, T92I, Q102P and H378R that were predicted to increase susceptibility, while variants K31R, N33I, H34R, E35K, E37K, D38V, Y50F, N51S, M62V, K68E, F72V, Y83H, G326E, G352V, D355N, Q388L and D509Y were predicted to be protective variants that show decreased binding to S-protein. Using biochemical assays, we confirmed that K31R and E37K had decreased affinity, and K26R and T92I variants showed increased affinity for S-protein when compared to wildtype ACE2. Consistent with this, soluble ACE2 K26R and T92I were more effective in blocking entry of S-protein pseudotyped virus suggesting that ACE2 variants can modulate susceptibility to SARS-CoV-2.
Collapse
Affiliation(s)
- Kushal Suryamohan
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Eric W Stawiski
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Ravi Gupta
- MedGenome Labs Ltd., Bangalore, Karnataka, India
| | - Shane Miersch
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jiang Liu
- ModMab Therapeutics, Foster City, CA, USA
| | - Chao Chen
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Frederic A Fellouse
- ModMab Therapeutics, Accelerator for Donnelly Collaboration, University of Toronto, Toronto, ON, Canada
| | | | | | | | - Reza Saberianfar
- ModMab Therapeutics, Accelerator for Donnelly Collaboration, University of Toronto, Toronto, ON, Canada
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gavin Washburn
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Monika Mis
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | | | | | - G H Hiranjith
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Sangeetha Mohan
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | - Sameer Phalke
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | | | - Aju Antony
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | - Mart Ustav
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sachdev Sidhu
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| | - Somasekar Seshagiri
- ModMab Therapeutics, Foster City, CA, USA.
- SciGenom Research Foundation, Bangalore, Karnataka, India.
| |
Collapse
|
32
|
Jain S, Abrham E, Khan MN, Mathur R. An Account of Immune Senescence in the Clinical Pathophysiology of COVID-19 Infection in Aging. Aging Dis 2021; 12:662-670. [PMID: 33815889 PMCID: PMC7990370 DOI: 10.14336/ad.2020.1019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Worldwide COVID-19 infection poses an enormous risk to public health and an alarming global socioeconomic burden. The impact of the COVID-19 pandemic on individuals with underlying health conditions as well as on the elderly population is extensive and effective strategies are needed to understand the mechanism behind it. Cellular senescence defines as an irreversible cell cycle arrest due to DNA damage leading to accumulation of senescent cells in the elderly population and may result in worsening of COVID-19 mediated increased mortality. However, whether this variation in senescence levels, in different aged populations, translation to COVID-19 infection is unknown. The spike protein of SARS-CoV-2 has been recently identified to be responsible for inducing pathogenic signals, although a clear understanding of how the host receptor interacts with SARS-CoV-2 protein and mediates the immune responses is not clear. In this review, we address the epidemiology of SARS-CoV-2 and the cellular senescence responding immune response to pathogenic SARS-CoV-2. We provide a prospective summary of what to expect and how to brace the possible immunological strategy to protect against COVID-19 infection. The review majorly explores an underline mechanism of how senescent cells trigger a hyperimmune inflammatory response and cause high mortality in aging people could serve as a potential aid to alleviate the treatment for elderly battling COVID-19 infection.
Collapse
Affiliation(s)
- Shilpi Jain
- 1Department of Geriatrics, University of North Dakota, Grand Forks, North Dakota 58202, USA
| | - Eden Abrham
- 1Department of Geriatrics, University of North Dakota, Grand Forks, North Dakota 58202, USA
| | - M Nadeem Khan
- 2Department of Biomedical Science, University of North Dakota, Grand Forks, North Dakota 58202, USA
| | - Ramkumar Mathur
- 1Department of Geriatrics, University of North Dakota, Grand Forks, North Dakota 58202, USA
| |
Collapse
|
33
|
Russell RM, Bibollet-Ruche F, Liu W, Sherrill-Mix S, Li Y, Connell J, Loy DE, Trimboli S, Smith AG, Avitto AN, Gondim MVP, Plenderleith LJ, Wetzel KS, Collman RG, Ayouba A, Esteban A, Peeters M, Kohler WJ, Miller RA, François-Souquiere S, Switzer WM, Hirsch VM, Marx PA, Piel AK, Stewart FA, Georgiev AV, Sommer V, Bertolani P, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH. CD4 receptor diversity represents an ancient protection mechanism against primate lentiviruses. Proc Natl Acad Sci U S A 2021; 118:e2025914118. [PMID: 33771926 PMCID: PMC8020793 DOI: 10.1073/pnas.2025914118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Infection with human and simian immunodeficiency viruses (HIV/SIV) requires binding of the viral envelope glycoprotein (Env) to the host protein CD4 on the surface of immune cells. Although invariant in humans, the Env binding domain of the chimpanzee CD4 is highly polymorphic, with nine coding variants circulating in wild populations. Here, we show that within-species CD4 diversity is not unique to chimpanzees but found in many African primate species. Characterizing the outermost (D1) domain of the CD4 protein in over 500 monkeys and apes, we found polymorphic residues in 24 of 29 primate species, with as many as 11 different coding variants identified within a single species. D1 domain amino acid replacements affected SIV Env-mediated cell entry in a single-round infection assay, restricting infection in a strain- and allele-specific fashion. Several identical CD4 polymorphisms, including the addition of N-linked glycosylation sites, were found in primate species from different genera, providing striking examples of parallel evolution. Moreover, seven different guenons (Cercopithecus spp.) shared multiple distinct D1 domain variants, pointing to long-term trans-specific polymorphism. These data indicate that the HIV/SIV Env binding region of the primate CD4 protein is highly variable, both within and between species, and suggest that this diversity has been maintained by balancing selection for millions of years, at least in part to confer protection against primate lentiviruses. Although long-term SIV-infected species have evolved specific mechanisms to avoid disease progression, primate lentiviruses are intrinsically pathogenic and have left their mark on the host genome.
Collapse
Affiliation(s)
- Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jesse Connell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Dorothy E Loy
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Stephanie Trimboli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew G Smith
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexa N Avitto
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection, and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Katherine S Wetzel
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ahidjo Ayouba
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Amandine Esteban
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - William J Kohler
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Richard A Miller
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | | | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329
| | - Vanessa M Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892
| | - Preston A Marx
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70118
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433
| | - Alex K Piel
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
| | - Fiona A Stewart
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Volker Sommer
- Department of Anthropology, University College London, WC1H 0BW London, United Kingdom
| | - Paco Bertolani
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, CB2 1QH Cambridge, United Kingdom
| | - John A Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - Terese B Hart
- Lukuru Wildlife Research Foundation, Tshuapa-Lomami-Lualaba Project, BP 2012, Kinshasa, Democratic Republic of the Congo
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection, and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
34
|
Shojaee A, Vahedian-Azimi A, Faizi F, Rahimi-Bashar F, Shahriary A, Galeh HEG, Nehrir B, Guest PC, Sahebkar A. Relationship Between COVID-19 and Angiotensin-Converting Enzyme 2: A Scoping Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1321:53-68. [PMID: 33656713 DOI: 10.1007/978-3-030-59261-5_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Following the outbreaks of SARS-CoV in 2002 and MERS-CoV in 2012, the COVID-19 pandemic caused by the SARS-CoV-2 virus has become an increasing threat to human health around the world. Numerous studies have shown that SARS-CoV-2 appears similar to the SARS-CoV as it uses angiotensin converting enzyme 2 (ACE2) as a receptor to gain entry into cells. The main aims of this scoping review were to identify the primary hosts of coronaviruses, the relationship between the receptor binding domain of coronaviruses and ACE2, the organ specificity of ACE2 expression compared with clinical manifestations of the disease, and to determine if this information can be used in the development of novel treatment approaches for the COVID-19 pandemic.
Collapse
Affiliation(s)
- Asma Shojaee
- Student Research Committee, Nursing Faculty, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amir Vahedian-Azimi
- Trauma Research Center, Nursing Faculty, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Fakhrudin Faizi
- Atherosclerosis research center, Nursing Faculty, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Farshid Rahimi-Bashar
- Anesthesia and Critical Care Department, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Batool Nehrir
- Health Management Research Center, Nursing Faculty, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Amirhossein Sahebkar
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran. .,Polish Mother's Memorial Hospital Research Institute (PMMHRI), Lodz, Poland. .,Halal Research Center of IRI, FDA, Tehran, Iran.
| |
Collapse
|
35
|
Al-Mulla F, Mohammad A, Al Madhoun A, Haddad D, Ali H, Eaaswarkhanth M, John SE, Nizam R, Channanath A, Abu-Farha M, Ahmad R, Abubaker J, Thanaraj TA. ACE2 and FURIN variants are potential predictors of SARS-CoV-2 outcome: A time to implement precision medicine against COVID-19. Heliyon 2021; 7:e06133. [PMID: 33532652 PMCID: PMC7843038 DOI: 10.1016/j.heliyon.2021.e06133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/23/2020] [Accepted: 01/26/2021] [Indexed: 01/08/2023] Open
Abstract
The severity of the new COVID-19 pandemic caused by the SARS-CoV-2 virus is strikingly variable in different global populations. SARS-CoV-2 uses ACE2 as a cell receptor, TMPRSS2 protease, and FURIN peptidase to invade human cells. Here, we investigated 1,378 whole-exome sequences of individuals from the Middle Eastern populations (Kuwait, Qatar, and Iran) to explore natural variations in the ACE2, TMPRSS2, and FURIN genes. We identified two activating variants (K26R and N720D) in the ACE2 gene that are more common in Europeans than in the Middle Eastern, East Asian, and African populations. We postulate that K26R can activate ACE2 and facilitate binding to S-protein RBD while N720D enhances TMPRSS2 cutting and, ultimately, viral entry. We also detected deleterious variants in FURIN that are frequent in the Middle Eastern but not in the European populations. This study highlights specific genetic variations in the ACE2 and FURIN genes that may explain SARS-CoV-2 clinical disparity. We showed structural evidence of the functionality of these activating variants that increase the SARS-CoV-2 aggressiveness. Finally, our data illustrate a significant correlation between ACE2 variants identified in people from Middle Eastern origins that can be further explored to explain the variation in COVID-19 infection and mortality rates globally.
Collapse
Affiliation(s)
- Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Ashraf Al Madhoun
- Department of Animal and Imaging Core Facilities, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Dania Haddad
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Hamad Ali
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait
| | | | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Mohamed Abu-Farha
- Department of Special Services Facilities, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheed Ahmad
- Department of Immunology & Microbiology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | | |
Collapse
|
36
|
Xavier LL, Neves PFR, Paz LV, Neves LT, Bagatini PB, Timmers LFSM, Rasia-Filho AA, Mestriner RG, Wieck A. Does Angiotensin II Peak in Response to SARS-CoV-2? Front Immunol 2021; 11:577875. [PMID: 33519802 PMCID: PMC7842149 DOI: 10.3389/fimmu.2020.577875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
Human infection by the SARS-CoV-2 is causing the current COVID-19 pandemic. With the growing numbers of cases and deaths, there is an urgent need to explore pathophysiological hypotheses in an attempt to better understand the factors determining the course of the disease. Here, we hypothesize that COVID-19 severity and its symptoms could be related to transmembrane and soluble Angiotensin-converting enzyme 2 (tACE2 and sACE2); Angiotensin II (ANG II); Angiotensin 1-7 (ANG 1-7) and angiotensin receptor 1 (AT1R) activation levels. Additionally, we hypothesize that an early peak in ANG II and ADAM-17 might represent a physiological attempt to reduce viral infection via tACE2. This viewpoint presents: (1) a brief introduction regarding the renin-angiotensin-aldosterone system (RAAS), detailing its receptors, molecular synthesis, and degradation routes; (2) a description of the proposed early changes in the RAAS in response to SARS-CoV-2 infection, including biological scenarios for the best and worst prognoses; and (3) the physiological pathways and reasoning for changes in the RAAS following SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Léder Leal Xavier
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Paula Fernanda Ribas Neves
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Lisiê Valeria Paz
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Laura Tartari Neves
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Pamela Brambilla Bagatini
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Luís Fernando Saraiva Macedo Timmers
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Programa de Pós-Graduação em Ciências Médicas (PPGCM), Universidade do Vale do Taquari-UNIVATES, Lajeado, Brazil
| | - Alberto Antônio Rasia-Filho
- Departamento de Ciências Básicas da Saúde/Fisiologia, Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
| | - Régis Gemerasca Mestriner
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Andrea Wieck
- Laboratório de Biologia Celular e Tecidual, Programa de Pós-Graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| |
Collapse
|
37
|
Melin AD, Janiak MC, Marrone F, Arora PS, Higham JP. Comparative ACE2 variation and primate COVID-19 risk. Commun Biol 2020; 3:641. [PMID: 33110195 PMCID: PMC7591510 DOI: 10.1038/s42003-020-01370-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 has caused over a million human deaths and massive global disruption. The viral infection may also represent a threat to our closest living relatives, nonhuman primates. The contact surface of the host cell receptor, ACE2, displays amino acid residues that are critical for virus recognition, and variations at these critical residues modulate infection susceptibility. Infection studies have shown that some primate species develop COVID-19-like symptoms; however, the susceptibility of most primates is unknown. Here, we show that all apes and African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at critical contact residues, and protein modeling predicts that these differences should greatly reduce SARS-CoV-2 binding affinity. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, and some lemurs, are likely to be highly susceptible to SARS-CoV-2. Urgent actions have been undertaken to limit the exposure of great apes to humans, and similar efforts may be necessary for many other primate species. Amanda Melin et al. compare variation in 29 primate species at 12 amino acid residue sites coded by the ACE2 gene and show that apes and African and Asian monkeys exhibit the same set of twelve key amino acid residues as human ACE2. These results suggest that these primates are likely to be susceptible to SARS-CoV-2, whereas ACE2 gene sequences and protein-protein interaction models suggest reduced susceptibility for platyrrhines, tarsiers, lorisoids, and some lemurs.
Collapse
Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada. .,Department of Medical Genetics, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr, NW, Calgary, AB, T2N 4N1, Canada.
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr, NW, Calgary, AB, T2N 4N1, Canada
| | - Frank Marrone
- Department of Chemistry, New York University, 100 Washington Square East, 10th Floor, New York, NY, 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, 10th Floor, New York, NY, 10003, USA
| | - James P Higham
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA. .,New York Consortium in Evolutionary Primatology, New York, NY, USA.
| |
Collapse
|
38
|
Zamora-Ledezma C, C. DFC, Medina E, Sinche F, Santiago Vispo N, Dahoumane SA, Alexis F. Biomedical Science to Tackle the COVID-19 Pandemic: Current Status and Future Perspectives. Molecules 2020; 25:E4620. [PMID: 33050601 PMCID: PMC7587204 DOI: 10.3390/molecules25204620] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
The coronavirus infectious disease (COVID-19) pandemic emerged at the end of 2019, and was caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which has resulted in an unprecedented health and economic crisis worldwide. One key aspect, compared to other recent pandemics, is the level of urgency, which has started a race for finding adequate answers. Solutions for efficient prevention approaches, rapid, reliable, and high throughput diagnostics, monitoring, and safe therapies are needed. Research across the world has been directed to fight against COVID-19. Biomedical science has been presented as a possible area for combating the SARS-CoV-2 virus due to the unique challenges raised by the pandemic, as reported by epidemiologists, immunologists, and medical doctors, including COVID-19's survival, symptoms, protein surface composition, and infection mechanisms. While the current knowledge about the SARS-CoV-2 virus is still limited, various (old and new) biomedical approaches have been developed and tested. Here, we review the current status and future perspectives of biomedical science in the context of COVID-19, including nanotechnology, prevention through vaccine engineering, diagnostic, monitoring, and therapy. This review is aimed at discussing the current impact of biomedical science in healthcare for the management of COVID-19, as well as some challenges to be addressed.
Collapse
Affiliation(s)
- Camilo Zamora-Ledezma
- School of Physical Sciences and Nanotechnology, Yachay Tech University, Urcuquí 100650, Ecuador;
| | - David F. Clavijo C.
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100650, Ecuador; (D.F.C.C.); (F.S.); (N.S.V.); (F.A.)
| | - Ernesto Medina
- School of Physical Sciences and Nanotechnology, Yachay Tech University, Urcuquí 100650, Ecuador;
| | - Federico Sinche
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100650, Ecuador; (D.F.C.C.); (F.S.); (N.S.V.); (F.A.)
| | - Nelson Santiago Vispo
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100650, Ecuador; (D.F.C.C.); (F.S.); (N.S.V.); (F.A.)
| | - Si Amar Dahoumane
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100650, Ecuador; (D.F.C.C.); (F.S.); (N.S.V.); (F.A.)
| | - Frank Alexis
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100650, Ecuador; (D.F.C.C.); (F.S.); (N.S.V.); (F.A.)
| |
Collapse
|
39
|
Fernandes JD, Hinrichs AS, Clawson H, Gonzalez JN, Lee BT, Nassar LR, Raney BJ, Rosenbloom KR, Nerli S, Rao AA, Schmelter D, Fyfe A, Maulding N, Zweig AS, Lowe TM, Ares M, Corbet-Detig R, Kent WJ, Haussler D, Haeussler M. The UCSC SARS-CoV-2 Genome Browser. Nat Genet 2020; 52:991-998. [PMID: 32908258 PMCID: PMC8016453 DOI: 10.1038/s41588-020-0700-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background: Researchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into “annotation tracks” where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis. Results: The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html ) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day. Conclusions: We invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at genome-www@soe.ucsc.edu with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.
Collapse
Affiliation(s)
- Jason D Fernandes
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Hiram Clawson
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Brian T Lee
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Luis R Nassar
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Brian J Raney
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Kate R Rosenbloom
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Santrupti Nerli
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Arjun A Rao
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Schmelter
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alastair Fyfe
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nathan Maulding
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ann S Zweig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russ Corbet-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - W James Kent
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
| | | |
Collapse
|
40
|
Evolutionary Arms Race between Virus and Host Drives Genetic Diversity in Bat Severe Acute Respiratory Syndrome-Related Coronavirus Spike Genes. J Virol 2020; 94:JVI.00902-20. [PMID: 32699095 PMCID: PMC7527062 DOI: 10.1128/jvi.00902-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/17/2020] [Indexed: 01/03/2023] Open
Abstract
Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoVs in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS-CoV and SARSr-CoV infection but with different binding affinities to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity for spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease. The Chinese horseshoe bat (Rhinolophus sinicus), reservoir host of severe acute respiratory syndrome coronavirus (SARS-CoV), carries many bat SARS-related CoVs (SARSr-CoVs) with high genetic diversity, particularly in the spike gene. Despite these variations, some bat SARSr-CoVs can utilize the orthologs of the human SARS-CoV receptor, angiotensin-converting enzyme 2 (ACE2), for entry. It is speculated that the interaction between bat ACE2 and SARSr-CoV spike proteins drives diversity. Here, we identified a series of R. sinicus ACE2 variants with some polymorphic sites involved in the interaction with the SARS-CoV spike protein. Pseudoviruses or SARSr-CoVs carrying different spike proteins showed different infection efficiencies in cells transiently expressing bat ACE2 variants. Consistent results were observed by binding affinity assays between SARS-CoV and SARSr-CoV spike proteins and receptor molecules from bats and humans. All tested bat SARSr-CoV spike proteins had a higher binding affinity to human ACE2 than to bat ACE2, although they showed a 10-fold lower binding affinity to human ACE2 compared with that of their SARS-CoV counterpart. Structure modeling revealed that the difference in binding affinity between spike and ACE2 might be caused by the alteration of some key residues in the interface of these two molecules. Molecular evolution analysis indicates that some key residues were under positive selection. These results suggest that the SARSr-CoV spike protein and R. sinicus ACE2 may have coevolved over time and experienced selection pressure from each other, triggering the evolutionary arms race dynamics. IMPORTANCE Evolutionary arms race dynamics shape the diversity of viruses and their receptors. Identification of key residues which are involved in interspecies transmission is important to predict potential pathogen spillover from wildlife to humans. Previously, we have identified genetically diverse SARSr-CoVs in Chinese horseshoe bats. Here, we show the highly polymorphic ACE2 in Chinese horseshoe bat populations. These ACE2 variants support SARS-CoV and SARSr-CoV infection but with different binding affinities to different spike proteins. The higher binding affinity of SARSr-CoV spike to human ACE2 suggests that these viruses have the capacity for spillover to humans. The positive selection of residues at the interface between ACE2 and SARSr-CoV spike protein suggests long-term and ongoing coevolutionary dynamics between them. Continued surveillance of this group of viruses in bats is necessary for the prevention of the next SARS-like disease.
Collapse
|
41
|
Rangel HR, Ortega JT, Maksoud S, Pujol FH, Serrano ML. SARS-CoV-2 host tropism: An in silico analysis of the main cellular factors. Virus Res 2020; 289:198154. [PMID: 32918944 PMCID: PMC7480320 DOI: 10.1016/j.virusres.2020.198154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
The role in host selectivity of ACE2, Tmprss2 and GPR78 in SARS-CoV-2 was explored. Differences in the SARS-CoV-2 RBD binding mode with ACE2 of secondary hosts could be associated with host permissiveness. Nafamostat could be considered a good inhibitor of mammalian hosts TMPRSS2 proteins. In silico studies confirm that the spike protein could interact with GRP78 in studied mammalian hosts. TMPRSS2 and GRP78 do not seem to play a role in host selectivity.
Recent reports have shown that small and big felines could be infected by SARS-CoV-2, while other animals, like swines and mice, are apparently not susceptible to this infection. These findings raise the question of the role of cell factors associated with early stages of the viral infection in host selectivity. The cellular receptor for SARS-CoV-2 is the Angiotensin Converting Enzyme (ACE2). Transmembrane protease serine 2 (TMPRSS2) has been shown to prime the viral spike for its interaction with its receptor. GRP78 has also been proposed as a possible co-receptor. In this study, we used several bioinformatics approaches to bring clues in the interaction of ACE2, TMPRSS2, and GRP78 with SARS-CoV-2. We selected several mammalian hosts that could play a key role in viral spread by acting as secondary hosts (cats, dogs, pigs, mice, and ferrets) and evaluated their predicted permissiveness by in silico analysis. Results showed that ionic pairs (salt bridges, N–O pair, and long-range interactions) produced between ACE2 and the viral spike has an essential function in the host interaction. On the other hand, TMPRSS2 and GRP78 are proteins with high homology in all the evaluated hosts. Thus, these proteins do not seem to play a role in host selectivity, suggesting that other factors may play a role in the non-permissivity in some of these hosts. These proteins represent however interesting cell targets that could be explored in order to control the virus replication in humans and in the intermediary hosts.
Collapse
Affiliation(s)
- H R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - J T Ortega
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - S Maksoud
- Department of Neurology and Experimental Therapeutics and Molecular Imaging Laboratory, Massachusetts General Hospital, MA 02129, USA
| | - F H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - M L Serrano
- Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas 1041-A, Venezuela.
| |
Collapse
|
42
|
Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci U S A 2020. [DOI: 10.1073/pnas.2010146117 'a=0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Significance
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a major pandemic that threatens millions of human lives and the global economy. We identified a large number of mammals that can potentially be infected by SARS-CoV-2 via their ACE2 proteins. This can assist the identification of intermediate hosts for SARS-CoV-2 and hence reduce the opportunity for a future outbreak of COVID-19. Among the species we found with the highest risk for SARS-CoV-2 infection are wildlife and endangered species. These species represent an opportunity for spillover of SARS-CoV-2 from humans to other susceptible animals. Given the limited infectivity data for the species studied, we urge caution not to overinterpret the predictions of the present study.
Collapse
|
43
|
Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci U S A 2020; 117:22311-22322. [PMID: 32826334 PMCID: PMC7486773 DOI: 10.1073/pnas.2010146117] [Citation(s) in RCA: 426] [Impact Index Per Article: 106.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
Collapse
Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, CA 95616
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kathleen C Keough
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, Quantitative Biosciences Consortium, University of California, San Francisco, CA 94117
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158
| | - Corrie A Painter
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Nicole S Persky
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Marco Corbo
- The Genome Center, University of California, Davis, CA 95616
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Andreas R Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
- College of Science, Tibet University, Lhasa 850000, China
| | | | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158
- Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California, San Francisco, CA 94158
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027
- Department of Evolution, Behavior, and Ecology, Division of Biology, University of California San Diego, La Jolla, CA 92093
| | - Martin T Nweeia
- Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115
- School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106
- Marine Mammal Program, Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Elinor K Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA 95616;
- Department of Evolution and Ecology, University of California, Davis, CA 95616
- John Muir Institute for the Environment, University of California, Davis, CA 95616
| |
Collapse
|
44
|
Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, King NP, Veesler D, Bloom JD. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell 2020; 182:1295-1310.e20. [PMID: 32841599 PMCID: PMC7418704 DOI: 10.1016/j.cell.2020.08.012] [Citation(s) in RCA: 1362] [Impact Index Per Article: 340.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and is a major determinant of host range and a dominant target of neutralizing antibodies. Here, we experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity-enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
Collapse
Affiliation(s)
- Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Sarah K Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
| |
Collapse
|
45
|
Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors. J Virol 2020; 94:JVI.00684-20. [PMID: 32493827 DOI: 10.1128/jvi.00684-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/01/2020] [Indexed: 02/02/2023] Open
Abstract
Viral receptors are the cell surface proteins that are hijacked by viruses to initialize their infections. Viral receptors are subject to two conflicting directional forces, namely, negative selection due to functional constraints and positive selection due to host-virus arms races. It remains largely obscure whether negative pleiotropy limits the rate of adaptation in viral receptors. Here, we perform evolutionary analyses of 96 viral receptor genes in primates and find that 41 out of 96 viral receptors experienced adaptive evolution. Many positively selected residues in viral receptors are located at the virus-receptor interfaces. Compared with control proteins, viral receptors exhibit significantly elevated rate of adaptation. Further analyses of genetic polymorphisms in human populations reveal signals of positive selection and balancing selection for 53 and 5 viral receptors, respectively. Moreover, we find that 49 viral receptors experienced different selection pressures in different human populations, indicating that viruses represent an important driver of local adaptation in humans. Our findings suggest that diverse viruses, many of which have not been known to infect nonhuman primates, have maintained antagonistic associations with primates for millions of years, and the host-virus conflicts drive accelerated adaptive evolution in viral receptors.IMPORTANCE Viruses hijack cellular proteins, termed viral receptors, to assist their entry into host cells. While viral receptors experience negative selection to maintain their normal functions, they also undergo positive selection due to an everlasting evolutionary arms race between viruses and hosts. A complete picture on how viral receptors evolve under two conflicting forces is still lacking. In this study, we systematically analyzed the evolution of 96 viral receptors in primates and human populations. We found around half of viral receptors underwent adaptive evolution and exhibit significantly elevated rates of adaptation compared to control genes in primates. We also found signals of past natural selection for 58 viral receptors in human populations. Interestingly, 49 viral receptors experienced different selection pressures in different human populations, indicating that viruses represent an important driver of local adaptation in humans. Our results suggest that host-virus arms races drive accelerated adaptive evolution in viral receptors.
Collapse
|
46
|
Melin AD, Janiak MC, Marrone F, Arora PS, Higham JP. Comparative ACE2 variation and primate COVID-19 risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.09.034967. [PMID: 32511330 PMCID: PMC7239060 DOI: 10.1101/2020.04.09.034967] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The emergence of the novel coronavirus SARS-CoV-2, which in humans is highly infectious and leads to the potentially fatal disease COVID-19, has caused hundreds of thousands of deaths and huge global disruption. The viral infection may also represent an existential threat to our closest living relatives, the nonhuman primates, many of which are endangered and often reduced to small populations. The virus engages the host cell receptor, angiotensin-converting enzyme-2 (ACE2), through the receptor binding domain (RBD) on the spike protein. The contact surface of ACE2 displays amino acid residues that are critical for virus recognition, and variations at these critical residues are likely to modulate infection susceptibility across species. While infection studies are emerging and have shown that some primates, such as rhesus macaques and vervet monkeys, develop COVID-19-like symptoms when exposed to the virus, the susceptibility of many other nonhuman primates is unknown. Here, we show that all apes, including chimpanzees, bonobos, gorillas, and orangutans, and all African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at significant contact residues, and protein modeling predicts that these differences should greatly reduce the binding affinity of the ACE2 for the virus, hence moderating their susceptibility for infection. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, as well as some lemurs are all likely to be highly susceptible to SARS-CoV-2, representing a critical threat to their survival. Urgent actions have been undertaken to limit the exposure of Great Apes to humans, and similar efforts may be necessary for many other primate species.
Collapse
Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, CA
- Department of Medical Genetics, University of Calgary, CA
- Alberta Children's Hospital Research Institute, University of Calgary, CA
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, CA
- Alberta Children's Hospital Research Institute, University of Calgary, CA
| | | | | | - James P Higham
- Department of Anthropology, New York University, US
- New York Consortium in Evolutionary Primatology, New York, US
| |
Collapse
|
47
|
Mathavarajah S, Dellaire G. Lions, tigers and kittens too: ACE2 and susceptibility to COVID-19. Evol Med Public Health 2020; 2020:109-113. [PMID: 32974030 PMCID: PMC7337683 DOI: 10.1093/emph/eoaa021] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) has been reported to infect domesticated animals in a species-specific manner, where cats were susceptible but not dogs. Using the recently published crystal structure of the SARS-CoV-2 spike protein complexed with the human host cell receptor angiotensin converting enzyme 2 (ACE2), we characterized the structure and evolution of ACE2 in several of these species and identify a single interacting amino acid residue conserved between human and Felidae ACE2 but not in Canidae that correlates with virus susceptibility. Using computational analyses we describe how this site likely affects ACE2 targeting by the virus. Thus, we highlight how evolution-based approaches can be used to form hypotheses and study animal transmission of such viruses in the future.
Collapse
Affiliation(s)
- Sabateeshan Mathavarajah
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
48
|
Transferrin Binding Protein B and Transferrin Binding Protein A2 Expand the Transferrin Recognition Range of Histophilus somni. J Bacteriol 2020; 202:JB.00177-20. [PMID: 32366593 DOI: 10.1128/jb.00177-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/24/2020] [Indexed: 01/04/2023] Open
Abstract
The bacterial bipartite transferrin receptor is an iron acquisition system that several important human and animal pathogens require for survival. It consists of the TonB-dependent transporter transferrin binding protein A (TbpA) and the surface lipoprotein transferrin binding protein B (TbpB). Curiously, the Tbps are only found in host-specific pathogens and are themselves host specific, meaning that they will bind to the transferrin of their host species but not to the transferrins of other animal species. While this phenomenon has long been established, neither the steps in the evolutionary process that led to this exquisite adaptation for the host nor the steps that could alter it are known. We sought to gain insight into these processes by studying Tbp specificity in Histophilus somni, an economically important pathogen of cattle. A past study showed that whole cells of H. somni specifically bind bovine transferrin but not transferrin from sheep and goats, two bovids whose transferrins share 93% amino acid sequence identity with bovine transferrin. To our surprise, we found that H. somni can use sheep and goat transferrins as iron sources for growth and that HsTbpB, but not HsTbpA, has detectable affinity for sheep and goat transferrins. Furthermore, a third transferrin binding protein found in H. somni, HsTbpA2, also showed affinity for sheep and goat transferrins. Our results suggest that H. somni TbpB and TbpA2 may contribute to broadening the host transferrin recognition range of H. somni IMPORTANCE Host-restricted pathogens infect a single host species or a narrow range of host species. Histophilus somni, a pathogen that incurs severe economic losses for the cattle industry, infects cattle, sheep, and goats but not other mammals. The transferrin binding proteins, TbpA and TbpB, are thought to be a key iron acquisition system in H. somni; however, despite their importance, H. somni TbpA and TbpB were previously shown to be cattle transferrin specific. In our study, we find that H. somni TbpB and another little-studied Tbp, TbpA2, bind sheep and goat transferrins, as well as bovine transferrin. Our results suggest that TbpB and TbpA2 may allow for host range expansion and provide a mechanism for how host specificity in Tbp-encoding pathogens can be altered.
Collapse
|
49
|
Starr TN, Greaney AJ, Hilton SK, Crawford KH, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, Veesler D, Bloom JD. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.17.157982. [PMID: 32587970 PMCID: PMC7310626 DOI: 10.1101/2020.06.17.157982] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.
Collapse
Affiliation(s)
- Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Co-first authors
| | - Allison J. Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
- Co-first authors
| | - Sarah K. Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katharine H.D. Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Lead Contact
| |
Collapse
|
50
|
Alanagreh L, Alzoughool F, Atoum M. The Human Coronavirus Disease COVID-19: Its Origin, Characteristics, and Insights into Potential Drugs and Its Mechanisms. Pathogens 2020; 9:E331. [PMID: 32365466 PMCID: PMC7280997 DOI: 10.3390/pathogens9050331] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
The emerging coronavirus disease (COVID-19) swept across the world, affecting more than 200 countries and territories. Genomic analysis suggests that the COVID-19 virus originated in bats and transmitted to humans through unknown intermediate hosts in the Wuhan seafood market, China, in December of 2019. This virus belongs to the Betacoronavirus group, the same group of the 2003 severe acute respiratory syndrome coronavirus (SARS-CoV), and for the similarity, it was named SARS-CoV-2. Given the lack of registered clinical therapies or vaccines, many physicians and scientists are investigating previously used clinical drugs for COVID-19 treatment. In this review, we aim to provide an overview of the CoVs origin, pathogenicity, and genomic structure, with a focus on SARS-CoV-2. Besides, we summarize the recently investigated drugs that constitute an option for COVID-19 treatment.
Collapse
Affiliation(s)
- Lo’ai Alanagreh
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | | | | |
Collapse
|