1
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Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
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2
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Bai H, Zhang X, Gong T, Ma J, Zhang P, Cai Z, Ren D, Zhang C. A systematic mutation analysis of 13 major SARS-CoV-2 variants. Virus Res 2024; 345:199392. [PMID: 38729218 PMCID: PMC11112362 DOI: 10.1016/j.virusres.2024.199392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
SARS-CoV-2 evolves constantly with various novel mutations. Due to their enhanced infectivity, transmissibility and immune evasion, a comprehensive understanding of the association between these mutations and the respective functional changes is crucial. However, previous mutation studies of major SARS-CoV-2 variants remain limited. Here, we performed systematic analyses of full-length amino acids mutation, phylogenetic features, protein physicochemical properties, molecular dynamics and immune escape as well as pseudotype virus infection assays among thirteen major SARS-CoV-2 variants. We found that Omicron exhibited the most abundant and complex mutation sites, higher indices of hydrophobicity and flexibility than other variants. The results of molecular dynamics simulation suggest that Omicron has the highest number of hydrogen bonds and strongest binding free energy between the S protein and ACE2 receptor. Furthermore, we revealed 10 immune escape sites in 13 major variants, some of them were reported previously, but four of which (i.e. 339/373/477/496) are first reported to be specific to Omicron, whereas 462 is specific to Epslion. The infectivity of these variants was confirmed by the pseudotype virus infection assays. Our findings may help us understand the functional consequences of the mutations within various variants and the underlying mechanisms of the immune escapes conferred by the S proteins.
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Affiliation(s)
- Han Bai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Xuan Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Junpeng Ma
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Peng Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China
| | - Zeqiong Cai
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Doudou Ren
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China
| | - Chengsheng Zhang
- The MED-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Building 21, Western China Science and Technology Innovation Harbor, Xi'an 710000, China; Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang 330006, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China.
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3
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Shempela DM, Chambaro HM, Sikalima J, Cham F, Njuguna M, Morrison L, Mudenda S, Chanda D, Kasanga M, Daka V, Kwenda G, Musonda K, Munsaka S, Chilengi R, Sichinga K, Simulundu E. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study. Int J Mol Sci 2024; 25:6338. [PMID: 38928045 PMCID: PMC11203853 DOI: 10.3390/ijms25126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.
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Affiliation(s)
| | - Herman M. Chambaro
- Virology Unit, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka 10101, Zambia;
| | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Fatim Cham
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Michael Njuguna
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Linden Morrison
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Duncan Chanda
- University Teaching Hospital, Ministry of Health, Lusaka 10101, Zambia;
| | - Maisa Kasanga
- Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
| | - Victor Daka
- Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia;
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Karen Sichinga
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Macha Research Trust, Choma 20100, Zambia
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4
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Wu H, Fujioka Y, Sakaguchi S, Suzuki Y, Nakano T. Morphological analysis for two types of viral particles in vacuoles of SARS-CoV-2-infected cells. Med Mol Morphol 2024; 57:124-135. [PMID: 38393367 DOI: 10.1007/s00795-024-00381-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
In this study, we analyzed the morphological structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human cells. We identified the two types of viral particles present within the vacuoles of infected cells. Using transmission electron microscopy, we observed that SARS-CoV-2 particles exhibited both low- and high-electron-density structures, which was further confirmed through three-dimensional reconstruction using electron tomography. The budding of these particles was exclusively observed within these vacuoles. Intriguingly, viral particles with low-electron-density structures were confined to vacuoles, whereas those with high-electron-density structures were found in vacuoles and on the cell membrane surface of infected cells. Notably, high-electron-density particles found within vacuoles exhibited the same morphology as those outside the infected cells. This observation suggests that the two types of viral particles identified in this study had different maturation status. Our findings provide valuable insights into the molecular details of SARS-CoV-2 particles, contributing to our understanding of the virus.
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Affiliation(s)
- Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan.
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
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5
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Ullah S, Ullah A, Waqas M, Halim SA, Pasha AR, Shafiq Z, Mali SN, Jawarkar RD, Khan A, Khalid A, Abdalla AN, Kashtoh H, Al-Harrasi A. Structural, dynamic behaviour, in-vitro and computational investigations of Schiff's bases of 1,3-diphenyl urea derivatives against SARS-CoV-2 spike protein. Sci Rep 2024; 14:12588. [PMID: 38822113 PMCID: PMC11143201 DOI: 10.1038/s41598-024-63345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/28/2024] [Indexed: 06/02/2024] Open
Abstract
The COVID-19 has had a significant influence on people's lives across the world. The viral genome has undergone numerous unanticipated changes that have given rise to new varieties, raising alarm on a global scale. Bioactive phytochemicals derived from nature and synthetic sources possess lot of potential as pathogenic virus inhibitors. The goal of the recent study is to report new inhibitors of Schiff bases of 1,3-dipheny urea derivatives against SARS COV-2 spike protein through in-vitro and in-silico approach. Total 14 compounds were evaluated, surprisingly, all the compounds showed strong inhibition with inhibitory values between 79.60% and 96.00% inhibition. Here, compounds 3a (96.00%), 3d (89.60%), 3e (84.30%), 3f (86.20%), 3g (88.30%), 3h (86.80%), 3k (82.10%), 3l (90.10%), 3m (93.49%), 3n (85.64%), and 3o (81.79%) exhibited high inhibitory potential against SARS COV-2 spike protein. While 3c also showed significant inhibitory potential with 79.60% inhibition. The molecular docking of these compounds revealed excellent fitting of molecules in the spike protein receptor binding domain (RBD) with good interactions with the key residues of RBD and docking scores ranging from - 4.73 to - 5.60 kcal/mol. Furthermore, molecular dynamics simulation for 150 ns indicated a strong stability of a complex 3a:6MOJ. These findings obtained from the in-vitro and in-silico study reflect higher potency of the Schiff bases of 1,3-diphenyl urea derivatives. Furthermore, also highlight their medicinal importance for the treatment of SARS COV-2 infection. Therefore, these small molecules could be a possible drug candidate.
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Affiliation(s)
- Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Anam Rubbab Pasha
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, 60800, Pakistan.
| | - Suraj N Mali
- School of Pharmacy, D.Y. Patil University (Deemed to be University), Sector 7, Nerul, Navi Mumbai, 400706, India
| | - Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr. Rajendra Gode Institute of Pharmacy, University Mardi Road, Amravati, 444603, India
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, 45142, Jazan, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Hamdy Kashtoh
- Department of Biotechnology, Yeungnam University, Gyeongsan, 38541, Gyeongbuk, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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6
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Rojas Chávez RA, Fili M, Han C, Rahman SA, Bicar IGL, Gregory S, Helverson A, Hu G, Darbro BW, Das J, Brown GD, Haim H. Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. PLoS Comput Biol 2024; 20:e1012215. [PMID: 38857308 PMCID: PMC11192331 DOI: 10.1371/journal.pcbi.1012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/21/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.
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Affiliation(s)
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Syed A. Rahman
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Isaiah G. L. Bicar
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Sullivan Gregory
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Benjamin W. Darbro
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States of America
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Grant D. Brown
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
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7
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Khurana MP, Scheidwasser-Clow N, Penn MJ, Bhatt S, Duchêne DA. The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference. Syst Biol 2024; 73:235-246. [PMID: 38153910 PMCID: PMC11129600 DOI: 10.1093/sysbio/syad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 12/30/2023] Open
Abstract
Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.
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Affiliation(s)
- Mark P Khurana
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Neil Scheidwasser-Clow
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Matthew J Penn
- Department of Statistics, University of Oxford, OX1 3LB, Oxford, UK
| | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1352 Copenhagen, Denmark
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, SW7 2AZ, London, UK
| | - David A Duchêne
- Centre for Evolutionary Hologenomics, University of Copenhagen, 1352 Copenhagen, Denmark
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8
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Iglesias-Caballero M, Mas V, Vázquez-Morón S, Vázquez M, Camarero-Serrano S, Cano O, Palomo C, Ruano MJ, Cano-Gómez C, Infantes-Lorenzo JA, Campoy A, Agüero M, Pozo F, Casas I. Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms. Int J Mol Sci 2024; 25:5499. [PMID: 38791536 PMCID: PMC11122236 DOI: 10.3390/ijms25105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.
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Affiliation(s)
- María Iglesias-Caballero
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Vicente Mas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sonia Vázquez-Morón
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Mónica Vázquez
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Sara Camarero-Serrano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Olga Cano
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Concepción Palomo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - María José Ruano
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Cristina Cano-Gómez
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - José Antonio Infantes-Lorenzo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
| | - Albert Campoy
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Montserrat Agüero
- Central Laboratory of Veterinarian (LCV), Ministry of Agriculture, Fisheries and Food, 28110 Algete, Madrid, Spain; (M.J.R.); (C.C.-G.); (M.A.)
| | - Francisco Pozo
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Inmaculada Casas
- Reference and Research Laboratory for Respiratory Virus, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), 28220 Majadahonda, Madrid, Spain; (V.M.); (S.V.-M.); (F.P.)
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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9
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Balasco N, Damaggio G, Esposito L, Colonna V, Vitagliano L. A comprehensive analysis of SARS-CoV-2 missense mutations indicates that all possible amino acid replacements in the viral proteins occurred within the first two-and-a-half years of the pandemic. Int J Biol Macromol 2024; 266:131054. [PMID: 38522702 DOI: 10.1016/j.ijbiomac.2024.131054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
The surveillance of COVID-19 pandemic has led to the determination of millions of genome sequences of the SARS-CoV-2 virus, with the accumulation of a wealth of information never collected before for an infectious disease. Exploring the information retrieved from the GISAID database reporting at that time >13 million genome sequences, we classified the 141,639 unique missense mutations detected in the first two-and-a-half years (up to October 2022) of the pandemic. Notably, our analysis indicates that 98.2 % of all possible conservative amino acid replacements occurred. Even non-conservative mutations were highly represented (73.9 %). For a significant number of residues (3 %), all possible replacements with the other nineteen amino acids have been observed. These observations strongly indicate that, in this time interval, the virus explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain and that those that are not observed severely affect SARS-CoV-2 integrity. The implications of the present findings go well beyond the structural biology of SARS-CoV-2 as the huge amount of information here collected and classified may be valuable for the elucidation of the sequence-structure-function relationships in proteins.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Dep. Chemistry, Sapienza University of Rome, Rome, Italy.
| | - Gianluca Damaggio
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, Milan, Italy; University of Naples Federico II, Naples, Italy
| | | | - Vincenza Colonna
- Institute of Genetics and Biophysics, CNR, Naples, Italy; Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
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10
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Morel M, Zhukova A, Lemoine F, Gascuel O. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor. Genome Biol Evol 2024; 16:evae040. [PMID: 38451738 PMCID: PMC10986858 DOI: 10.1093/gbe/evae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets.
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Affiliation(s)
- Marie Morel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Université Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, 69100, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, CNR Virus Des Infections Respiratoires, Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut de Systématique, Evolution, Biodiversité (UMR 7205—CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), Paris, France
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11
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Álvarez-Herrera M, Sevilla J, Ruiz-Rodriguez P, Vergara A, Vila J, Cano-Jiménez P, González-Candelas F, Comas I, Coscollá M. VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evol 2024; 10:veae018. [PMID: 38510921 PMCID: PMC10953798 DOI: 10.1093/ve/veae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/02/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.
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Affiliation(s)
- Miguel Álvarez-Herrera
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Jordi Sevilla
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Paula Ruiz-Rodriguez
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Pablo Cano-Jiménez
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Mireia Coscollá
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
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12
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O’Connor K, Weissenbacher D, Elyaderani A, Lautenbach E, Scotch M, Gonzalez-Hernandez G. Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.07.14.23292681. [PMID: 37503241 PMCID: PMC10371180 DOI: 10.1101/2023.07.14.23292681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background There has been an unprecedented effort to sequence the SARS-CoV-2 virus and examine its molecular evolution. This has been facilitated by the availability of publicly accessible databases, the Global Initiative on Sharing All Influenza Data (GISAID) and GenBank, which collectively hold millions of SARS-CoV-2 sequence records. Genomic epidemiology, however, seeks to go beyond phylogenetic analysis by linking genetic information to patient characteristics and disease outcomes, enabling a comprehensive understanding of transmission dynamics and disease impact.While these repositories include fields reflecting patient-related metadata for a given sequence, inclusion of these demographic and clinical details is scarce. The extent to which patient-related metadata is reported in published sequencing studies and its quality remains largely unexplored. Methods The NIH's LitCovid collection will be used for automated classification of articles reporting having deposited SARS-CoV-2 sequences in public repositories, while an independent search will be conducted in PubMed for validation. Data extraction will be conducted using Covidence. The extracted data will be synthesized and summarized to quantify the availability of patient metadata in the published literature of SARS-CoV-2 sequencing studies. For the bibliometric analysis, relevant data points, such as author affiliations and citation metrics will be extracted. Discussion This scoping review will report on the extent and types of patient-related metadata reported in genomic viral sequencing studies of SARS-CoV-2, identify gaps in this reporting, and make recommendations for improving the quality and consistency of reporting in this area. The bibliometric analysis will uncover trends and patterns in the reporting of patient-related metadata, including differences in reporting based on study types or geographic regions. Co-occurrence networks of author keywords will also be presented. The insights gained from this study may help improve the quality and consistency of reporting patient metadata, enhancing the utility of sequence metadata and facilitating future research on infectious diseases.
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Affiliation(s)
- Karen O’Connor
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Davy Weissenbacher
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Amir Elyaderani
- Biodesign Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Ebbing Lautenbach
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
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13
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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14
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Ullah A, Ullah S, Halim SA, Waqas M, Ali B, Ataya FS, El-Sabbagh NM, Batiha GES, Avula SK, Csuk R, Khan A, Al-Harrasi A. Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques. Sci Rep 2024; 14:3590. [PMID: 38351259 PMCID: PMC10864406 DOI: 10.1038/s41598-024-53911-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 appeared as a highly contagious disease after its outbreak in December 2019 by the virus, named SARS-CoV-2. The threat, which originated in Wuhan, China, swiftly became an international emergency. Among different genomic products, spike protein of virus plays a crucial role in the initiation of the infection by binding to the human lung cells, therefore, SARS-CoV-2's spike protein is a promising therapeutic target. Using a combination of a structure-based virtual screening and biochemical assay, this study seeks possible therapeutic candidates that specifically target the viral spike protein. A database of ~ 850 naturally derived compounds was screened against SARS-CoV-2 spike protein to find natural inhibitors. Using virtual screening and inhibitory experiments, we identified acetyl 11-keto-boswellic acid (AKBA) as a promising molecule for spike protein, which encouraged us to scan the rest of AKBA derivatives in our in-house database via 2D-similarity searching. Later 19 compounds with > 85% similarity with AKBA were selected and docked with receptor binding domain (RBD) of spike protein. Those hits declared significant interactions at the RBD interface, best possess and excellent drug-likeness and pharmacokinetics properties with high gastrointestinal absorption (GIA) without toxicity and allergenicity. Our in-silico observations were eventually validated by in vitro bioassay, interestingly, 10 compounds (A3, A4, C3, C6A, C6B, C6C, C6E, C6H, C6I, and C6J) displayed significant inhibitory ability with good percent inhibition (range: > 72-90). The compounds C3 (90.00%), C6E (91.00%), C6C (87.20%), and C6D (86.23%) demonstrated excellent anti-SARS CoV-2 spike protein activities. The docking interaction of high percent inhibition of inhibitor compounds C3 and C6E was confirmed by MD Simulation. In the molecular dynamics simulation, we observed the stable dynamics of spike protein inhibitor complexes and the influence of inhibitor binding on the protein's conformational arrangements. The binding free energy ΔGTOTAL of C3 (-38.0 ± 0.08 kcal/mol) and C6E (-41.98 ± 0.08 kcal/mol) respectively indicate a strong binding affinity to Spike protein active pocket. These findings demonstrate that these molecules particularly inhibit the function of spike protein and, therefore have the potential to be evaluated as drug candidates against SARS-CoV-2.
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Affiliation(s)
- Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Basharat Ali
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, Islamabad, Pakistan
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia
| | - Nasser M El-Sabbagh
- Department of Veterinary Pharmacology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Satya Kumar Avula
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Rene Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120, Halle (Saale), Germany
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
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15
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Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr 2024; 12:e0265423. [PMID: 38197644 PMCID: PMC10846092 DOI: 10.1128/spectrum.02654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
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Affiliation(s)
- Shubhangi Gupta
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Deepanshu Gupta
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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16
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Hasan MM, Saha CK, Hamidullah Mehedi HM, Chakma K, Salauddin A, Hossain MS, Sharmen F, Rafiqul Islam SM, Tanni AA, Yasmin F, Akash A, Hossain ME, Miah M, Biswas SK, Sultana N, Mannan A. Genetic determinants of SARS-CoV-2 and the clinical outcome of COVID-19 in Southern Bangladesh. Immun Inflamm Dis 2024; 12:e1171. [PMID: 38415978 PMCID: PMC10845815 DOI: 10.1002/iid3.1171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/13/2023] [Accepted: 01/21/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic has had a severe impact on population health. The genetic determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in southern Bangladesh are not well understood. METHODS This study aimed to determine the genomic variation in SARS-CoV-2 genomes that have evolved over 2 years of the pandemic in southern Bangladesh and their association with disease outcomes and virulence of this virus. We investigated demographic variables, disease outcomes of COVID-19 patients and genomic features of SARS-CoV-2. RESULTS We observed that the disease severity was significantly higher in adults (85.3%) than in children (14.7%), because the expression of angiotensin-converting enzyme-2 (ACE-2) diminishes with ageing that causes differences in innate and adaptive immunity. The clade GK (n = 66) was remarkable between June 2021 and January 2022. Because of the mutation burden, another clade, GRA started a newly separated clustering in December 2021. The burden was significantly higher in GRA (1.5-fold) highlighted in mild symptoms of COVID-19 patients than in other clades (GH, GK, and GR). Mutations were accumulated mainly in S (22.15 mutations per segment) and ORF1ab segments. Missense (67.5%) and synonymous (18.31%) mutations were highly noticed in adult patients with mild cases rather than severe cases, especially in ORF1ab segments. Moreover, we observed many unique mutations in S protein in mild cases compared to severe, and homology modeling revealed that those might cause more folding in the protein's alpha helix and beta sheets. CONCLUSION Our study identifies some risk factors such as age comorbidities (diabetes, hypertension, and renal disease) that are associated with severe COVID-19, providing valuable insight regarding prioritizing vaccination for high-risk individuals and allocating health care and resources. The findings of this work outlined the knowledge and mutational basis of SARS-CoV-2 for the next treatment steps. Further studies are needed to confirm the effects of structural and functional proteins of SARS-CoV-2 in detail for monitoring the emergence of new variants in future.
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Affiliation(s)
- Md. Mahbub Hasan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | | | | | - Kallyan Chakma
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Asma Salauddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
- International Centre for Diarrhoeal Disease ResearchBangladesh (icddr,b)DhakaBangladesh
| | - Md. Shakhawat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Farjana Sharmen
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - S. M. Rafiqul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Afroza Akter Tanni
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Farhana Yasmin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | - Al‐Shahriar Akash
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
| | | | - Mojnu Miah
- International Centre for Diarrhoeal Disease ResearchBangladesh (icddr,b)DhakaBangladesh
| | - Sanjoy Kanti Biswas
- Department of MicrobiologyChattogram Maa‐O‐Shishu HospitalChattogramBangladesh
| | - Nahid Sultana
- Department of MicrobiologyChattogram Maa‐O‐Shishu HospitalChattogramBangladesh
| | - Adnan Mannan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological SciencesUniversity of ChittagongChattogramBangladesh
- Next Generation Sequencing, Research and Innovation Laboratory Chittagong (NRICh), Biotechnology Research and Innovation Center (BRIC)University of ChittagongChattogramBangladesh
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17
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Ling-Hu T, Simons LM, Dean TJ, Rios-Guzman E, Caputo MT, Alisoltani A, Qi C, Malczynski M, Blanke T, Jennings LJ, Ison MG, Achenbach CJ, Larkin PM, Kaul KL, Lorenzo-Redondo R, Ozer EA, Hultquist JF. Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes. Cell Rep Med 2024; 5:101361. [PMID: 38232695 PMCID: PMC10829796 DOI: 10.1016/j.xcrm.2023.101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the coronavirus disease 2019 (COVID-19) pandemic, but the impact of these variants on disease severity has remained unclear. In this single-center, retrospective cohort study, we examined the association between SARS-CoV-2 clade and patient outcome over a two-year period in Chicago, Illinois. Between March 2020 and March 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients and outpatients alongside linked clinical and demographic metadata, of which 2,114 were processed for viral whole-genome sequencing. When controlling for patient demographics and vaccination status, several viral clades were associated with risk for hospitalization, but this association was negated by the inclusion of population-level confounders, including case count, sampling bias, and shifting standards of care. These data highlight the importance of integrating non-virological factors into disease severity and outcome models for the accurate assessment of patient risk.
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Affiliation(s)
- Ted Ling-Hu
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Taylor J Dean
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Estefany Rios-Guzman
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Matthew T Caputo
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Arghavan Alisoltani
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Chao Qi
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Michael Malczynski
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Timothy Blanke
- Diagnostic Molecular Biology Laboratory, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Lawrence J Jennings
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Michael G Ison
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chad J Achenbach
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Paige M Larkin
- Department of Molecular Microbiology, Northshore University HealthSystem, Evanston, IL 60201, USA
| | - Karen L Kaul
- Department of Pathology, Northshore University HealthSystem, Evanston, IL 60201, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA.
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18
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Zaidi AK, Singh RB. SARS-CoV-2 variant biology and immune evasion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 202:45-66. [PMID: 38237990 DOI: 10.1016/bs.pmbts.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
This chapter discusses the SARS-CoV-2 variants and their immune evasion strategies, shedding light on the dynamic nature of the COVID-19 pandemic. The ecological dynamics and viral evolution of SARS-CoV-2 are explored, considering carriers of infection, individual immunity profiles, and human movement as key factors in the emergence and dissemination of variants. The chapter discusses SARS-CoV-2 mutation, including mutation rate, substitution rate, and recombination, influencing genetic diversity and evolution. Transmission bottlenecks are highlighted as determinants of dominant variants during viral spread. The evolution phases of the pandemic are outlined, from limited early evolution to the emergence of notable changes like the D614G substitution and variants with heavy mutations. Variants of Concern (VOCs), including Alpha, Beta, Gamma, and the recent Omicron variant, are examined, with insights into inter-lineage and intra-lineage dynamics. The origin of VOCs and the Omicron variant is explored, alongside the role of the furin cleavage site (FCS) in variant emergence. The impact of structural and non-structural proteins on viral infectivity is assessed, as well as innate immunity evasion strategies employed by SARS-CoV-2 variants. The chapter concludes by considering future possibilities, including ongoing virus evolution, the need for surveillance, vaccine development, and public health measures.
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Affiliation(s)
| | - Rohan Bir Singh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States; Department of Population, Policy and Practice, Greater Ormond Street Institute of Child Health, University College London, United Kingdom; Discipline of Ophthalmology and Visual Sciences, Adelaide Medical School, University of Adelaide, Australia.
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19
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John RS, Miller JC, Muylaert RL, Hayman DTS. High connectivity and human movement limits the impact of travel time on infectious disease transmission. J R Soc Interface 2024; 21:20230425. [PMID: 38196378 PMCID: PMC10777149 DOI: 10.1098/rsif.2023.0425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024] Open
Abstract
The speed of spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic highlights the importance of understanding how infections are transmitted in a highly connected world. Prior to vaccination, changes in human mobility patterns were used as non-pharmaceutical interventions to eliminate or suppress viral transmission. The rapid spread of respiratory viruses, various intervention approaches, and the global dissemination of SARS-CoV-2 underscore the necessity for epidemiological models that incorporate mobility to comprehend the spread of the virus. Here, we introduce a metapopulation susceptible-exposed-infectious-recovered model parametrized with human movement data from 340 cities in China. Our model replicates the early-case trajectory in the COVID-19 pandemic. We then use machine learning algorithms to determine which network properties best predict spread between cities and find travel time to be most important, followed by the human movement-weighted personalized PageRank. However, we show that travel time is most influential locally, after which the high connectivity between cities reduces the impact of travel time between individual cities on transmission speed. Additionally, we demonstrate that only significantly reduced movement substantially impacts infection spread times throughout the network.
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Affiliation(s)
- Reju Sam John
- Massey University, Palmerston North 4474, New Zealand
- University of Auckland, Auckland 1010, New Zealand
| | - Joel C. Miller
- La Trobe University, Melbourne 3086, Victoria, Australia
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20
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Ferrareze PAG, Cybis GB, de Oliveira LFV, Zimerman RA, Schiavon DEB, Peter C, Thompson CE. Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study. Microbes Infect 2024; 26:105216. [PMID: 37827275 DOI: 10.1016/j.micinf.2023.105216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/30/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023]
Abstract
The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Gabriela Betella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | - Dieine Estela Bernieri Schiavon
- Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
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21
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Wang H, Rizvi SRA, Dong D, Lou J, Wang Q, Sopipong W, Su Y, Najar F, Agarwal PK, Kozielski F, Haider S. Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16. eLife 2023; 12:RP87884. [PMID: 38127066 PMCID: PMC10735223 DOI: 10.7554/elife.87884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
The coronavirus SARS-CoV-2 protects its RNA from being recognized by host immune responses by methylation of its 5' end, also known as capping. This process is carried out by two enzymes, non-structural protein 16 (NSP16) containing 2'-O-methyltransferase and NSP14 through its N7 methyltransferase activity, which are essential for the replication of the viral genome as well as evading the host's innate immunity. NSP10 acts as a crucial cofactor and stimulator of NSP14 and NSP16. To further understand the role of NSP10, we carried out a comprehensive analysis of >13 million globally collected whole-genome sequences (WGS) of SARS-CoV-2 obtained from the Global Initiative Sharing All Influenza Data (GISAID) and compared it with the reference genome Wuhan/WIV04/2019 to identify all currently known variants in NSP10. T12I, T102I, and A104V in NSP10 have been identified as the three most frequent variants and characterized using X-ray crystallography, biophysical assays, and enhanced sampling simulations. In contrast to other proteins such as spike and NSP6, NSP10 is significantly less prone to mutation due to its crucial role in replication. The functional effects of the variants were examined for their impact on the binding affinity and stability of both NSP14-NSP10 and NSP16-NSP10 complexes. These results highlight the limited changes induced by variant evolution in NSP10 and reflect on the critical roles NSP10 plays during the SARS-CoV-2 life cycle. These results also indicate that there is limited capacity for the virus to overcome inhibitors targeting NSP10 via the generation of variants in inhibitor binding pockets.
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Affiliation(s)
- Huan Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Syed RA Rizvi
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Danni Dong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Jiaqi Lou
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Qian Wang
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Watanyoo Sopipong
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Yufeng Su
- College of Engineering, Design and Physical Sciences, Brunel University LondonUxbridgeUnited Kingdom
| | - Fares Najar
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Pratul K Agarwal
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College LondonLondonUnited Kingdom
- UCL Centre for Advanced Research Computing, University College LondonLondonUnited Kingdom
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22
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Girma A. The Many Mutations of the COVID-19 Variant: Current Perspectives on EG.5/Eris. ENVIRONMENTAL HEALTH INSIGHTS 2023; 17:11786302231217805. [PMID: 38084254 PMCID: PMC10710748 DOI: 10.1177/11786302231217805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/06/2023] [Indexed: 02/05/2024]
Abstract
Viral diseases pose a significant threat to public health around the world. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was originally identified in Wuhan, China, in 2019. Throughout the epidemic, SARS-CoV-2 has continually changed genetically, giving rise to variants that are distinct from the original virus. SARS-CoV-2 has a high-frequency mutation rate, resulting in more genetic diversity. EG.5/Eris is a subvariant and descendant of Omicron, which remains the world's most prevalent coronavirus strain of current concern. The percentage of EG.5 recorded has steadily increased across the board. Epidemiological week 29 (17-23 July 2023) saw a 17.4% global prevalence of EG.5. Mutations in the virus's genome can cause false-negative results in molecular detection and cause increased transmissibility, morbidity, and mortality due to a reduction in vaccine efficiency. Furthermore, these changes in S-protein structure alter the neutralising ability of neutralising antibodies (Nabs), resulting in a reduction in vaccine efficiency. Therefore, all countries should take efficient infection prevention and control measures as per the guidelines of the world, continental, and their country's health organisations, along with vaccine and treatment investigations.
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Affiliation(s)
- Abayeneh Girma
- Department of Biology, College of Natural and Computational Science, Mekdela Amba University, Tulu Awuliya, Ethiopia
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23
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Ramlall V, Gisladottir U, Kefeli J, Tanaka Y, May B, Tatonetti N. Using machine learning probabilities to identify effects of COVID-19. PATTERNS (NEW YORK, N.Y.) 2023; 4:100889. [PMID: 38106616 PMCID: PMC10724367 DOI: 10.1016/j.patter.2023.100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023]
Abstract
Coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has had extensive economic, social, and public health impacts in the United States and around the world. To date, there have been more than 600 million reported infections worldwide with more than 6 million reported deaths. Retrospective analysis, which identified comorbidities, risk factors, and treatments, has underpinned the response. As the situation transitions to an endemic, retrospective analyses using electronic health records will be important to identify the long-term effects of COVID-19. However, these analyses can be complicated by incomplete records, which makes it difficult to differentiate visits where the patient had COVID-19. To address this issue, we trained a random Forest classifier to assign a probability of a patient having been diagnosed with COVID-19 during each visit. Using these probabilities, we found that higher COVID-19 probabilities were associated with a future diagnosis of myocardial infarction, urinary tract infection, acute renal failure, and type 2 diabetes.
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Affiliation(s)
- Vijendra Ramlall
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Physiology and Cellular Biophysics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jenna Kefeli
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yutaro Tanaka
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Applied Physics and Applied Mathematics, Fu Foundation School of Engineering and Applied Sciences, Columbia University, New York, NY 10027, USA
| | - Benjamin May
- Herbert Irving Comprehensive Cancer Center, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nicholas Tatonetti
- Department of Biomedical Informatics, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Medicine, Columbia University, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, New York Presbyterian/Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90069, USA
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24
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Thakur S, Planeta Kepp K, Mehra R. Predicting virus Fitness: Towards a structure-based computational model. J Struct Biol 2023; 215:108042. [PMID: 37931730 DOI: 10.1016/j.jsb.2023.108042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India
| | - Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kongens Lyngby, Denmark
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India; Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India.
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25
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Murakami K, Kubota SI, Tanaka K, Tanaka H, Akabane K, Suzuki R, Shinohara Y, Takei H, Hashimoto S, Tanaka Y, Hojyo S, Sakamoto O, Naono N, Takaai T, Sato K, Kojima Y, Harada T, Hattori T, Fuke S, Yokota I, Konno S, Washio T, Fukuhara T, Teshima T, Taniguchi M, Murakami M. High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore. LAB ON A CHIP 2023; 23:4909-4918. [PMID: 37877206 DOI: 10.1039/d3lc00572k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
A digital platform that can rapidly and accurately diagnose pathogenic viral variants, including SARS-CoV-2, will minimize pandemics, public anxiety, and economic losses. We recently reported an artificial intelligence (AI)-nanopore platform that enables testing for Wuhan SARS-CoV-2 with high sensitivity and specificity within five minutes. However, which parts of the virus are recognized by the platform are unknown. Similarly, whether the platform can detect SARS-CoV-2 variants or the presence of the virus in clinical samples needs further study. Here, we demonstrated the platform can distinguish SARS-CoV-2 variants. Further, it identified mutated Wuhan SARS-CoV-2 expressing spike proteins of the delta and omicron variants, indicating it discriminates spike proteins. Finally, we used the platform to identify omicron variants with a sensitivity and specificity of 100% and 94%, respectively, in saliva specimens from COVID-19 patients. Thus, our results demonstrate the AI-nanopore platform is an effective diagnostic tool for SARS-CoV-2 variants.
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Affiliation(s)
- Kaoru Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shimpei I Kubota
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Kumiko Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroki Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Keiichiroh Akabane
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Yuta Shinohara
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Shigeru Hashimoto
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Yuki Tanaka
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shintaro Hojyo
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Takayui Takaai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Kazuki Sato
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Yuichi Kojima
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Toshiyuki Harada
- Department of Respiratory Medicine, Japan Community Healthcare Organization Hokkaido Hospital, Sapporo, 062-8618, Japan
| | - Takeshi Hattori
- Department of Respiratory Medicine, Hokkaido Medical Center, National Hospital Organization, Sapporo, 063-0005, Japan
| | - Satoshi Fuke
- Department of Respiratory Medicine, KKR Sapporo Medical Center, Sapporo, 062-0931, Japan
| | - Isao Yokota
- Department of Biostatistics, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, 060-8638, Japan
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Masaaki Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0020, Japan
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26
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Mustafa SS, Stern RA, Patel PC, Chu DK. COVID-19 Treatments: Then and Now. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:3321-3333. [PMID: 37558163 DOI: 10.1016/j.jaip.2023.07.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has evolved over the past 3+ years, and strategies to prevent illness and treat infection have changed over time. As COVID-19 transitions from a pandemic to an endemic infection, widespread nonpharmaceutical interventions such as mask mandates and governmental policies requiring social distancing have given way to more selective strategies for risk mitigation. Monoclonal antibody therapies used for disease prevention and treatment lost utility owing to the emergence of resistant viral variants. Oral antiviral medications have become the mainstay of treatment in nonhospitalized individuals, whereas systemic corticosteroids remain the cornerstone of therapy in those requiring supplemental oxygen. Emerging literature also supports the use of additional immune-modulating therapies in select admitted patients. Importantly, the COVID-19 pandemic highlighted both unprecedented research and development of medical interventions while also drawing attention to significant pitfalls in the global response. This review provides a comprehensive update in prevention and management of COVID-19.
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Affiliation(s)
- S Shahzad Mustafa
- Department of Medicine, Rochester Regional Health, Rochester, NY; Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY.
| | - Rebecca A Stern
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Pratish C Patel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Derek K Chu
- Department of Medicine, Evidence in Allergy Group, Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ont, Canada
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27
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Markin A, Wagle S, Grover S, Vincent Baker AL, Eulenstein O, Anderson TK. PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny. Syst Biol 2023; 72:1052-1063. [PMID: 37208300 PMCID: PMC10627562 DOI: 10.1093/sysbio/syad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
The use of next-generation sequencing technology has enabled phylogenetic studies with hundreds of thousands of taxa. Such large-scale phylogenies have become a critical component in genomic epidemiology in pathogens such as SARS-CoV-2 and influenza A virus. However, detailed phenotypic characterization of pathogens or generating a computationally tractable dataset for detailed phylogenetic analyses requires objective subsampling of taxa. To address this need, we propose parnas, an objective and flexible algorithm to sample and select taxa that best represent observed diversity by solving a generalized k-medoids problem on a phylogenetic tree. parnas solves this problem efficiently and exactly by novel optimizations and adapting algorithms from operations research. For more nuanced selections, taxa can be weighted with metadata or genetic sequence parameters, and the pool of potential representatives can be user-constrained. Motivated by influenza A virus genomic surveillance and vaccine design, parnas can be applied to identify representative taxa that optimally cover the diversity in a phylogeny within a specified distance radius. We demonstrated that parnas is more efficient and flexible than existing approaches. To demonstrate its utility, we applied parnas to 1) quantify SARS-CoV-2 genetic diversity over time, 2) select representative influenza A virus in swine genes derived from over 5 years of genomic surveillance data, and 3) identify gaps in H3N2 human influenza A virus vaccine coverage. We suggest that our method, through the objective selection of representatives in a phylogeny, provides criteria for quantifying genetic diversity that has application in the the rational design of multivalent vaccines and genomic epidemiology. PARNAS is available at https://github.com/flu-crew/parnas.
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Affiliation(s)
- Alexey Markin
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Sanket Wagle
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| | - Siddhant Grover
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| | - Amy L Vincent Baker
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Oliver Eulenstein
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
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28
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Xing M, Wang Y, Wang X, Liu J, Dai W, Hu G, He F, Zhao Q, Li Y, Sun L, Wang Y, Du S, Dong Z, Pang C, Hu Z, Zhang X, Xu J, Cai Q, Zhou D. Broad-spectrum vaccine via combined immunization routes triggers potent immunity to SARS-CoV-2 and its variants. J Virol 2023; 97:e0072423. [PMID: 37706688 PMCID: PMC10617383 DOI: 10.1128/jvi.00724-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/09/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE The development of broad-spectrum SARS-CoV-2 vaccines will reduce the global economic and public health stress from the COVID-19 pandemic. The use of conserved T-cell epitopes in combination with spike antigen that induce humoral and cellular immune responses simultaneously may be a promising strategy to further enhance the broad spectrum of COVID-19 vaccine candidates. Moreover, this research suggests that the combined vaccination strategies have the ability to induce both effective systemic and mucosal immunity, which may represent promising strategies for maximizing the protective efficacy of respiratory virus vaccines.
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Affiliation(s)
- Man Xing
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yihan Wang
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyu Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaojiao Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Weiqian Dai
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Gaowei Hu
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Furong He
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Zhao
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ying Li
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lingjin Sun
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuyan Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shujuan Du
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhongwei Dong
- MOE&NHC&CAMS Key Laboratory of Medical Molecular, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chongjie Pang
- Department of Infectious Diseases, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhidong Hu
- Department of Clinical Laboratory, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qiliang Cai
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dongming Zhou
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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29
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Togkousidis A, Kozlov OM, Haag J, Höhler D, Stamatakis A. Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty. Mol Biol Evol 2023; 40:msad227. [PMID: 37804116 PMCID: PMC10584362 DOI: 10.1093/molbev/msad227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023] Open
Abstract
Phylogenetic inferences under the maximum likelihood criterion deploy heuristic tree search strategies to explore the vast search space. Depending on the input dataset, searches from different starting trees might all converge to a single tree topology. Often, though, distinct searches infer multiple topologies with large log-likelihood score differences or yield topologically highly distinct, yet almost equally likely, trees. Recently, Haag et al. introduced an approach to quantify, and implemented machine learning methods to predict, the dataset difficulty with respect to phylogenetic inference. Easy multiple sequence alignments (MSAs) exhibit a single likelihood peak on their likelihood surface, associated with a single tree topology to which most, if not all, independent searches rapidly converge. As difficulty increases, multiple locally optimal likelihood peaks emerge, yet from highly distinct topologies. To make use of this information, we introduce and implement an adaptive tree search heuristic in RAxML-NG, which modifies the thoroughness of the tree search strategy as a function of the predicted difficulty. Our adaptive strategy is based upon three observations. First, on easy datasets, searches converge rapidly and can hence be terminated at an earlier stage. Second, overanalyzing difficult datasets is hopeless, and thus it suffices to quickly infer only one of the numerous almost equally likely topologies to reduce overall execution time. Third, more extensive searches are justified and required on datasets with intermediate difficulty. While the likelihood surface exhibits multiple locally optimal peaks in this case, a small proportion of them is significantly better. Our experimental results for the adaptive heuristic on 9,515 empirical and 5,000 simulated datasets with varying difficulty exhibit substantial speedups, especially on easy and difficult datasets (53% of total MSAs), where we observe average speedups of more than 10×. Further, approximately 94% of the inferred trees using the adaptive strategy are statistically indistinguishable from the trees inferred under the standard strategy (RAxML-NG).
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Affiliation(s)
- Anastasis Togkousidis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Oleksiy M Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Julia Haag
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Dimitri Höhler
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
- Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology - Hellas, GR - 711 10 Heraklion, Crete, Greece
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30
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Ma W, Shi L, Li M. A fast and accurate method for SARS-CoV-2 genomic tracing. Brief Bioinform 2023; 24:bbad339. [PMID: 37779249 DOI: 10.1093/bib/bbad339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023] Open
Abstract
To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach for investigating the source and transmission of pathogens. In this study, we first presented the rationale for genomic tracing of SARS-CoV-2 and the challenges we currently face. Identifying the most genetically similar reference sequence to the query sequence is a critical step in genome tracing, typically achieved using either a phylogenetic tree or a sequence similarity search. However, these methods become inefficient or computationally prohibitive when dealing with tens of millions of sequences in the reference database, as we encountered during the COVID-19 pandemic. To address this challenge, we developed a novel genomic tracing algorithm capable of processing 6 million SARS-CoV-2 sequences in less than a minute. Instead of constructing a giant phylogenetic tree, we devised a weighted scoring system based on mutation characteristics to quantify sequences similarity. The developed method demonstrated superior performance compared to previous methods. Additionally, an online platform was developed to facilitate genomic tracing and visualization of the spatiotemporal distribution of sequences. The method will be a valuable addition to standard epidemiological investigations, enabling more efficient genomic tracing. Furthermore, the computational framework can be easily adapted to other pathogens, paving the way for routine genomic tracing of infectious diseases.
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Affiliation(s)
- Wentai Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leisheng Shi
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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31
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DeFoor N, Paul S, Li S, Basso EKG, Stevenson V, Browning JL, Prater AK, Brindley S, Tao G, Pickrell AM. Remdesivir increases mtDNA copy number causing mild alterations to oxidative phosphorylation. Sci Rep 2023; 13:15339. [PMID: 37714940 PMCID: PMC10504289 DOI: 10.1038/s41598-023-42704-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023] Open
Abstract
SARS-CoV-2 causes the severe respiratory disease COVID-19. Remdesivir (RDV) was the first fast-tracked FDA approved treatment drug for COVID-19. RDV acts as an antiviral ribonucleoside (adenosine) analogue that becomes active once it accumulates intracellularly. It then diffuses into the host cell and terminates viral RNA transcription. Previous studies have shown that certain nucleoside analogues unintentionally inhibit mitochondrial RNA or DNA polymerases or cause mutational changes to mitochondrial DNA (mtDNA). These past findings on the mitochondrial toxicity of ribonucleoside analogues motivated us to investigate what effects RDV may have on mitochondrial function. Using in vitro and in vivo rodent models treated with RDV, we observed increases in mtDNA copy number in Mv1Lu cells (35.26% increase ± 11.33%) and liver (100.27% increase ± 32.73%) upon treatment. However, these increases only resulted in mild changes to mitochondrial function. Surprisingly, skeletal muscle and heart were extremely resistant to RDV treatment, tissues that have preferentially been affected by other nucleoside analogues. Although our data suggest that RDV does not greatly impact mitochondrial function, these data are insightful for the treatment of RDV for individuals with mitochondrial disease.
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Affiliation(s)
- Nicole DeFoor
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Swagatika Paul
- Graduate Program in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA
| | - Shuang Li
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Erwin K Gudenschwager Basso
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA
| | - Valentina Stevenson
- Virginia Tech Animal Laboratory Services, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA
| | - Jack L Browning
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Anna K Prater
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Samantha Brindley
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Ge Tao
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Alicia M Pickrell
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA.
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32
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Wu HB, Wang CH, Chung YD, Shan YS, Lin YJ, Tsai HP, Lee GB. Highly-specific aptamer targeting SARS-CoV-2 S1 protein screened on an automatic integrated microfluidic system for COVID-19 diagnosis. Anal Chim Acta 2023; 1274:341531. [PMID: 37455073 DOI: 10.1016/j.aca.2023.341531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
Variants of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) have evolved such that it may be challenging for diagnosis and clinical treatment of the pandemic coronavirus disease-19 (COVID-19). Compared with developed SARS-CoV-2 diagnostic tools recently, aptamers may exhibit some advantages, including high specificity/affinity, longer shelf life (vs. antibodies), and could be easily prepared. Herein an integrated microfluidic system was developed to automatically carry out one novel screening process based on the systematic evolution of ligands by exponential enrichment (SELEX) for screening aptamers specific with SARS-CoV-2. The new screening process started with five rounds of positive selection (with the S1 protein of SARS-CoV-2). In addition, including non-target viruses (influenza A and B), human respiratory tract-related cancer cells (adenocarcinoma human alveolar basal epithelial cells and dysplastic oral keratinocytes), and upper respiratory tract-related infectious bacteria (including methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae), and human saliva were involved to increase the specificity of the screened aptamer during the negative selection. Totally, all 10 rounds could be completed within 20 h. The dissociation constant of the selected aptamer was determined to be 63.0 nM with S1 protein. Limits of detection for Wuhan and Omicron clinical strains were found to be satisfactory for clinical applications (i.e. 4.80 × 101 and 1.95 × 102 copies/mL, respectively). Moreover, the developed aptamer was verified to be capable of capturing inactivated SARS-CoV-2 viruses, eight SARS-CoV-2 pseudo-viruses, and clinical isolates of SARS-CoV-2 viruses. For high-variable emerging viruses, this developed integrated microfluidic system can be used to rapidly select highly-specific aptamers based on the novel SELEX methods to deal with infectious diseases in the future.
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Affiliation(s)
- Hung-Bin Wu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Da Chung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan; Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Jun Lin
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan.
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33
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Maldonado-Cabrera A, Colin-Vilchis JA, Haque U, Velazquez C, Alvarez Villaseñor AS, Magdaleno-Márquez LE, Calleros-Muñoz CI, Figueroa-Enríquez KF, Angulo-Molina A, Gallego-Hernández AL. SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population. Infect Dis Rep 2023; 15:535-548. [PMID: 37737000 PMCID: PMC10514801 DOI: 10.3390/idr15050053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) presents global heterogeneity, and their relative effect on pediatric severity is still limited. In this study, we associate VOCs with pediatric clinical severity outcomes in Mexico. Bioinformatics methods were used to characterize VOCs and single amino acid (aa) mutations in 75,348 SARS-CoV-2 genetic sequences from February 2020 to October 2022. High-predominance VOCs groups were calculated and subsequently associated with 372,989 COVID-19 clinical pediatric outcomes. We identified 21 high-frequency mutations related to Omicron lineages with an increased prevalence in pediatric sequences compared to adults. Alpha and the other lineages had a significant increase in case fatality rate (CFR), intensive critical unit (ICU) admission, and automated mechanical ventilation (AMV). Furthermore, a logistic model with age-adjusted variables estimated an increased risk of hospitalization, ICU/AMV, and death in Gamma and Alpha, in contrast to the other lineages. We found that, regardless of the VOCs lineage, infant patients presented the worst severity prognoses. Our findings improve the understanding of the impact of VOCs on pediatric patients across time, regions, and clinical outcomes. Enhanced understanding of the pediatric severity for VOCs would enable the development and improvement of public health strategies worldwide.
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Affiliation(s)
- Anahí Maldonado-Cabrera
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
- Department of Epidemiology, Family Medicine Unit No. 37, Mexican Social Security Institute (IMSS), Hermosillo 83260, Mexico
| | | | - Ubydul Haque
- Rutgers Global Health Institute, New Brunswick, NJ 08901, USA;
- Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ 08854, USA
| | - Carlos Velazquez
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
| | | | | | | | | | - Aracely Angulo-Molina
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Ana Lucía Gallego-Hernández
- Department of Chemical Biological Sciences, University of Sonora, Hermosillo 83000, Mexico; (A.M.-C.); (C.V.)
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34
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Chan TF, Yu Y. Building a global community of health for all: A positive discourse analysis of COVID-19 discourse. DISCOURSE & COMMUNICATION 2023; 17:522-537. [PMCID: PMC10051005 DOI: 10.1177/17504813231163078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
‘A global community of health for all’ has become a dominant concept in China’s global health governance system. Although this concept has been investigated by several studies in different domains, little attention has been given to its discursive legitimation in China’s media communication from a linguistic perspective. To fill this gap, the present study employs positive discourse analysis to investigate how the aforementioned concept is legitimised via the predominant discourses associated with COVID-19 in state-run Chinese English-language newspapers. The findings show that the Chinese news media attempted to formulate the positive discourses, including cooperation as a win-win solution, people’s lives and well-being as the priority and science as the spirit, though the discourses may not resonate with some countries. The findings shed light on the use of language by the media in promoting official ideologies, projecting China’s national image and improving China’s international relations amid a global health crisis.
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Affiliation(s)
| | - Yating Yu
- Department of English and Communication, The Hong Kong Polytechnic University, Hong Kong SAR
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35
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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Sinha A, Sangeet S, Roy S. Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective. ACS OMEGA 2023; 8:23283-23304. [PMID: 37426203 PMCID: PMC10324094 DOI: 10.1021/acsomega.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023]
Abstract
Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure-function and passed through several variants of concern. Recent advances in high-resolution structure determination and multiscale imaging techniques, cost-effective next-generation sequencing, and development of new computational methods (including information theory, statistical methods, machine learning, and many other artificial intelligence-based techniques) have hugely contributed to the characterization of sequence, structure, function of spike proteins, and its different variants to understand viral pathogenesis, evolutions, and transmission. Laying on the foundation of the sequence-structure-function paradigm, this review summarizes not only the important findings on structure/function but also the structural dynamics of different spike components, highlighting the effects of mutations on them. As dynamic fluctuations of three-dimensional spike structure often provide important clues for functional modulation, quantifying time-dependent fluctuations of mutational events over spike structure and its genetic/amino acidic sequence helps identify alarming functional transitions having implications for enhanced fusogenicity and pathogenicity of the virus. Although these dynamic events are more difficult to capture than quantifying a static, average property, this review encompasses those challenging aspects of characterizing the evolutionary dynamics of spike sequence and structure and their implications for functions.
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Rahimian K, Arefian E, Mahdavi B, Mahmanzar M, Kuehu D, Deng Y. SARS2Mutant: SARS-CoV-2 amino-acid mutation atlas database. NAR Genom Bioinform 2023; 5:lqad037. [PMID: 37101659 PMCID: PMC10124966 DOI: 10.1093/nargab/lqad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/27/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly pathogenic viral infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in the global pandemic of 2020. A lack of therapeutic and preventive strategies has quickly posed significant threats to world health. A comprehensive understanding of SARS-CoV-2 evolution and natural selection, how it impacts host interaction, and phenotype symptoms is vital to develop effective strategies against the virus. The SARS2Mutant database (http://sars2mutant.com/) was developed to provide valuable insights based on millions of high-quality, high-coverage SARS-CoV-2 complete protein sequences. Users of this database have the ability to search for information on three amino acid substitution mutation strategies based on gene name, geographical zone, or comparative analysis. Each strategy is presented in five distinct formats which includes: (i) mutated sample frequencies, (ii) heat maps of mutated amino acid positions, (iii) mutation survivals, (iv) natural selections and (v) details of substituted amino acids, including their names, positions, and frequencies. GISAID is a primary database of genomics sequencies of influenza viruses updated daily. SARS2Mutant is a secondary database developed to discover mutation and conserved regions from the primary data to assist with design for targeted vaccine, primer, and drug discoveries.
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Affiliation(s)
- Karim Rahimian
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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38
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Kakhki RK, Neshani A, Kakhki MK, Zare H. Clinical Evaluation of Commercial HARDSON COVID-19 Antigen Rapid Test Kit for Routine COVID-19 Diagnosis. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2023; 5:113-117. [PMID: 38633014 PMCID: PMC10986721 DOI: 10.36519/idcm.2023.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/11/2023] [Indexed: 04/19/2024]
Abstract
Objective This study aimed to evaluate the sensitivity, specificity, and accuracy of the commercial HARDSON COVID-19 Antigen Rapid Test Kit for diagnosing COVID-19 among the Iranian population by compared with the results of commercial RT-PCR. Materials and Methods Two nasopharyngeal swabs were collected from each patient. One swab was tested with HARDSON COVID-19 Antigen Rapid Test Kit, and the second swab was placed in 3 mL of a virus-transmitted inactivated media for RT-PCR testing. Then, the results of both tests were compared to investigate the diagnostic accuracy of the rapid antigen test. Results A total of 275 suspected COVID-19 patients' samples were collected to investigate the diagnostic accuracy of HARDSON COVID-19 Antigen Rapid Test Kit. In this study, 162 positive and 113 negative samples were evaluated. As a result, the sensitivity, specificity, and accuracy of HARDSON COVID-19 Antigen Rapid Test Kit were 90%, 100%, and 94%, respectively. Conclusion The diagnostic kit analyzed in this study indicated excellent specificity and a relatively good overall sensitivity for the diagnosis of COVID-19 when compared with the RT-PCR detection kit. Based on the result of this study, COVID-19 Antigen Rapid Test Kit indicated a good sensitivity (96%) in low cycle threshold (Ct) value, and it would be recommended to be integrated into routine diagnostic laboratories and used as an at-home rapid antigen test.
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Affiliation(s)
| | - Alireza Neshani
- Mashhad Gene Azma Inc., Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Hosna Zare
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences
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39
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Liang F. Quantitative Mutation Analysis of Genes and Proteins of Major SARS-CoV-2 Variants of Concern and Interest. Viruses 2023; 15:v15051193. [PMID: 37243278 DOI: 10.3390/v15051193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
Of various SARS-CoV-2 variants, some have drawn special concern or interest because of their heightened disease threat. The mutability of individual SARS-CoV-2 genes/proteins presumably varies. The present study quantified gene/protein mutations in 13 major SARS-CoV-2 variants of concern/interest, and analyzed viral protein antigenicity using bioinformatics. The results from 187 carefully perused genome clones showed significantly higher mean percent mutations in the spike, ORF8, nucleocapsid, and NSP6 than in other viral proteins. The ORF8 and spike proteins also tolerated higher maximal percent mutations. The omicron variant presented more percent mutations in the NSP6 and structural proteins, whereas the delta featured more in the ORF7a. Omicron subvariant BA.2 exhibited more mutations in ORF6, and omicron BA.4 had more in NSP1, ORF6, and ORF7b, relative to omicron BA.1. Delta subvariants AY.4 and AY.5 bore more mutations in ORF7b and ORF8 than delta B.1.617.2. Predicted antigen ratios of SARS-CoV-2 proteins significantly vary (range: 38-88%). To overcome SARS-CoV-2 immune evasion, the relatively conserved, potentially immunogenic NSP4, NSP13, NSP14, membrane, and ORF3a viral proteins may serve as more suitable targets for molecular vaccines or therapeutics than the mutation-prone NSP6, spike, ORF8, or nucleocapsid protein. Further investigation into distinct mutations of the variants/subvariants may help understand SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Fengyi Liang
- Department of Anatomy, Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore 117594, Singapore
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40
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Cheng Y, Ji C, Zhou HY, Zheng H, Wu A. Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking. Viruses 2023; 15:v15051158. [PMID: 37243244 DOI: 10.3390/v15051158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.
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Affiliation(s)
- Yexiao Cheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Chengyang Ji
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
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41
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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42
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Landis JT, Moorad R, Pluta LJ, Caro-Vegas C, McNamara RP, Eason AB, Bailey A, Villamor FCS, Juarez A, Wong JP, Yang B, Broussard GS, Damania B, Dittmer DP. Intra-Host Evolution Provides for the Continuous Emergence of SARS-CoV-2 Variants. mBio 2023; 14:e0344822. [PMID: 36786605 PMCID: PMC10127995 DOI: 10.1128/mbio.03448-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/13/2023] [Indexed: 02/15/2023] Open
Abstract
Variants of concern (VOC) in SARS-CoV-2 refer to viruses whose viral genomes differ from the ancestor virus by ≥3 single-nucleotide variants (SNVs) and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Still, too little is known regarding how frequently new viral variants emerge and under what circumstances. We report a study to determine the degree of SARS-CoV-2 sequence evolution in 94 patients and to estimate the frequency at which highly diverse variants emerge. Two cases accumulated ≥9 SNVs over a 2-week period and one case accumulated 23 SNVs over 3 weeks, including three nonsynonymous mutations in the spike protein (D138H, E554D, D614G). The remainder of the infected patients did not show signs of intra-host evolution. We estimate that in as much as 2% of hospitalized COVID-19 cases, variants with multiple mutations in the spike glycoprotein emerge in as little as 1 month of persistent intra-host virus replication. This suggests the continued local emergence of variants with multiple nonsynonymous SNVs, even in patients without overt immune deficiency. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of reinfection, and (iii) patients with diminished immune function may offer broad public health benefits. IMPORTANCE New SARS-CoV-2 variants can potentially disrupt ongoing public health measures and vaccine efforts. Still, little is known regarding how frequently new viral variants emerge and under what circumstances. Based on this study, we estimate that in hospitalized COVID-19 cases, variants with multiple mutations may emerge locally in as little as 1 month, even in patients without overt immune deficiency. Surveillance by sequencing for continuously shedding patients, patients suspected of reinfection, and patients with diminished immune function may offer broad public health benefits.
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Affiliation(s)
- Justin T. Landis
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Razia Moorad
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Linda J. Pluta
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Carolina Caro-Vegas
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Ryan P. McNamara
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Anthony B. Eason
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Aubrey Bailey
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Femi Cleola S. Villamor
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Angelica Juarez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Jason P. Wong
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Brian Yang
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Grant S. Broussard
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Blossom Damania
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA
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Van Egeren D, Stoddard M, White LF, Hochberg NS, Rogers MS, Zetter B, Joseph-McCarthy D, Chakravarty A. Vaccines Alone Cannot Slow the Evolution of SARS-CoV-2. Vaccines (Basel) 2023; 11:853. [PMID: 37112765 PMCID: PMC10143044 DOI: 10.3390/vaccines11040853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
The rapid emergence of immune-evading viral variants of SARS-CoV-2 calls into question the practicality of a vaccine-only public-health strategy for managing the ongoing COVID-19 pandemic. It has been suggested that widespread vaccination is necessary to prevent the emergence of future immune-evading mutants. Here, we examined that proposition using stochastic computational models of viral transmission and mutation. Specifically, we looked at the likelihood of emergence of immune escape variants requiring multiple mutations and the impact of vaccination on this process. Our results suggest that the transmission rate of intermediate SARS-CoV-2 mutants will impact the rate at which novel immune-evading variants appear. While vaccination can lower the rate at which new variants appear, other interventions that reduce transmission can also have the same effect. Crucially, relying solely on widespread and repeated vaccination (vaccinating the entire population multiple times a year) is not sufficient to prevent the emergence of novel immune-evading strains, if transmission rates remain high within the population. Thus, vaccines alone are incapable of slowing the pace of evolution of immune evasion, and vaccinal protection against severe and fatal outcomes for COVID-19 patients is therefore not assured.
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Affiliation(s)
- Debra Van Egeren
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- New York Genome Center, New York, NY 10013, USA
| | | | - Laura F. White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Natasha S. Hochberg
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael S. Rogers
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Bruce Zetter
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
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44
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Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 234.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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45
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Hasan TN, Naqvi SS, Rehman MU, Ullah R, Ammad M, Arshad N, Ain QU, Perween S, Hussain A. Ginger ring compounds as an inhibitor of spike binding protein of alpha, beta, gamma and delta variants of SARS-CoV-2: An in-silico study. NARRA J 2023; 3:e98. [PMID: 38455706 PMCID: PMC10919719 DOI: 10.52225/narra.v3i1.98] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/01/2023] [Indexed: 03/09/2024]
Abstract
The available drugs against coronavirus disease 2019 (COVOD-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are limited. This study aimed to identify ginger-derived compounds that might neutralize SARS-CoV-2 and prevent its entry into host cells. Ring compounds of ginger were screened against spike (S) protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The S protein FASTA sequence was retrieved from Global Initiative on Sharing Avian Influenza Data (GISAID) and converted into ".pdb" format using Open Babel tool. A total of 306 compounds were identified from ginger through food and phyto-databases. Out of those, 38 ring compounds were subjected to docking analysis using CB Dock online program which implies AutoDock Vina for docking. The Vina score was recorded, which reflects the affinity between ligands and receptors. Further, the Protein Ligand Interaction Profiler (PLIP) program for detecting the type of interaction between ligand-receptor was used. SwissADME was used to compute druglikeness parameters and pharmacokinetics characteristics. Furthermore, energy minimization was performed by using Swiss PDB Viewer (SPDBV) and energy after minimization was recorded. Molecular dynamic simulation was performed to find the stability of protein-ligand complex and root-mean- square deviation (RMSD) as well as root-mean-square fluctuation (RMSF) were calculated and recorded by using myPresto v5.0. Our study suggested that 17 out of 38 ring compounds of ginger were very likely to bind the S protein of SARS-CoV-2. Seventeen out of 38 ring compounds showed high affinity of binding with S protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The RMSD showed the stability of the complex was parallel to the S protein monomer. These computer-aided predictions give an insight into the possibility of ginger ring compounds as potential anti-SARS-CoV-2 worthy of in vitro investigations.
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Affiliation(s)
- Tarique N. Hasan
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Syed S. Naqvi
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Mati Ur Rehman
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
- College de Paris, France
| | - Rooh Ullah
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Muhammad Ammad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Narmeen Arshad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Qurat Ul Ain
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Shabana Perween
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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47
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Cheng C, Zhang Z. SARS-CoV-2 shows a much earlier divergence in the world than in the Chinese mainland. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-023-2294-5. [PMID: 36897494 PMCID: PMC9999321 DOI: 10.1007/s11427-023-2294-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/12/2023] [Indexed: 03/11/2023]
Affiliation(s)
- Chaoyuan Cheng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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48
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Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time. Viruses 2023; 15:v15030684. [PMID: 36992393 PMCID: PMC10057463 DOI: 10.3390/v15030684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately captured, so that only the SARS-CoV-2 genomes obtained in 2019 and the first few months of 2020 (resulting from the first wave of the global expansion from Wuhan) are sufficient for dating the common ancestor. Empirical data contradict the first assumption. The second assumption is not warranted because mounting evidence suggests the presence of early SARS-CoV-2 lineages cocirculating with the Wuhan strains. Large trees with SARS-CoV-2 genomes beyond the first few months are needed to increase the likelihood of finding SARS-CoV-2 lineages that might have originated at the same time as (or even before) those early Wuhan strains. I extended a previously published rapid rooting method to model evolutionary rate as a linear function instead of a constant. This substantially improves the dating of the common ancestor of sampled SARS-CoV-2 genomes. Based on two large trees with 83,688 and 970,777 high-quality and full-length SARS-CoV-2 genomes that contain complete sample collection dates, the common ancestor was dated to 12 June 2019 and 7 July 2019 with the two trees, respectively. The two data sets would give dramatically different or even absurd estimates if the rate was treated as a constant. The large trees were also crucial for overcoming the high rate-heterogeneity among different viral lineages. The improved method was implemented in the software TRAD.
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Perdalkar S, Basthi Mohan P, Musunuri B, Rajpurohit S, Shetty S, Bhat K, Pai CG. Thiopurine therapy in inflammatory bowel disease in the pandemic era: Safe or unsafe? Int Immunopharmacol 2023; 116:109597. [PMID: 36702073 DOI: 10.1016/j.intimp.2022.109597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/03/2022] [Accepted: 12/11/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract. Crohn's disease (CD) and Ulcerative colitis (UC) are the two major types affecting millions across the globe. Various immunomodulatory drugs consisting of small molecules (thiopurines, methotrexate and tofacitinib) and biologics are used to treat IBD. Thiopurines (TP) are widely used in the treatment of IBD and it plays an important role both alone and in combination with anti-TNF agents as IBD maintenance therapy. Although the advent of biologics therapy has significantly advanced the management of IBD, TP remains the mainstay of treatment in resource-limited and low economic settings. However, the recently commenced pandemic has raised uncertainty over the safety of the use of immunosuppressant drugs such as TP among healthcare care providers and patients, as there is a scarcity of data on whether IBD patients are at higher risk of COVID-19 infection or more prone to its severe outcomes. AIM This review aims to encapsulate evidence on the risk of COVID-19 infection and its severe prognosis in IBD patients on TP. Additionally, it also evaluates the role of TP in inhibiting the viral protease, a potential drug target, essential for the replication and pathogenesis of the virus. CONCLUSION Emerging evidence suggests that TP therapy is safe during the current pandemic and does not carry an elevated risk when used as monotherapy or in combination with other IBD drugs. In-vitro studies demonstrate that TP is a potential therapeutic for present and future betacoronavirus pandemics.
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Affiliation(s)
- Shailesh Perdalkar
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Pooja Basthi Mohan
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Balaji Musunuri
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Siddheesh Rajpurohit
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Shiran Shetty
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Krishnamurthy Bhat
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Cannanore Ganesh Pai
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India.
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50
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Abbasian MH, Mahmanzar M, Rahimian K, Mahdavi B, Tokhanbigli S, Moradi B, Sisakht MM, Deng Y. Global landscape of SARS-CoV-2 mutations and conserved regions. J Transl Med 2023; 21:152. [PMID: 36841805 PMCID: PMC9958328 DOI: 10.1186/s12967-023-03996-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management. METHODS 10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence. RESULTS Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively. CONCLUSION Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.
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Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Karim Rahimian
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Samaneh Tokhanbigli
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, Australia
| | - Bahman Moradi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, 2040, 3000 CA, Rotterdam, The Netherlands
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
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