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El Mazouri S, Essabbar A, Aanniz T, Eljaoudi R, Belyamani L, Ibrahimi A, Ouadghiri M. Genetic diversity and evolutionary dynamics of the Omicron variant of SARS-CoV-2 in Morocco. Pathog Glob Health 2024; 118:241-252. [PMID: 37635364 PMCID: PMC11221468 DOI: 10.1080/20477724.2023.2250942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Among the numerous variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that have been reported worldwide, the emergence of the Omicron variant has drastically changed the landscape of the coronavirus disease (COVID-19) pandemic. Here, we analyzed the genetic diversity of Moroccan SARS-CoV-2 genomes with a focus on Omicron variant after one year of its detection in Morocco in order to understand its genomic dynamics, features and its potential introduction sources. From 937 Omicron genomes, we identified a total of 999 non-unique mutations distributed across 92 Omicron lineages, of which 13 were specific to the country. Our findings suggest multiple introductory sources of the Omicron variant to Morocco. In addition, we found that four Omicron clades are more infectious in comparison to other Omicron clades. Remarkably, a clade of Omicron is particularly more transmissible and has become the dominant variant worldwide. Moreover, our assessment of Receptor-Binding Domain (RBD) mutations showed that the Spike K444T and N460K mutations enabled a clade higher ability of immune vaccine escape. In conclusion, our analysis highlights the unique genetic diversity of the Omicron variant in Moroccan SARS-CoV-2 genomes, with multiple introductory sources and the emergence of highly transmissible clades. The distinctiveness of the Moroccan strains compared to global ones underscores the importance of ongoing surveillance and understanding of local genomic dynamics for effective response strategies in the evolving COVID-19 pandemic.
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Affiliation(s)
- Safae El Mazouri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Rachid Eljaoudi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Lahcen Belyamani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Mouna Ouadghiri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
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2
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Tanwar N, Ojha R, Aggarwal S, Prajapati VK, Munde M. Design of inhibitor peptide sequences based on the interfacial knowledge of the protein G-IgG crystallographic complex and their binding studies with IgG. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:159-170. [PMID: 38493432 DOI: 10.1007/s00249-024-01704-0] [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: 12/21/2023] [Revised: 02/18/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Protein-protein interactions (PPI) have emerged as valuable targets in medicinal chemistry due to their key roles in important biological processes. The modulation of PPI by small peptides offers an excellent opportunity to develop drugs against human diseases. Here, we exploited the knowledge of the binding interface of the IgG-protein G complex (PDB:1FCC) for designing peptides that can inhibit these complexes. Herein, we have designed several closely related peptides, and the comparison of results from experiments and computational studies indicated that all the peptides bind close to the expected binding site on IgG and the complexes are stable. A minimal sequence consisting of 11 amino acids (P5) with binding constants in the range of 100 nM was identified. We propose that the main affinity differences across the series of peptides arose from the presence of polar amino acid residues. Further, the molecular dynamic studies helped to understand the dynamic properties of complexes in terms of flexibility of residues and structural stability at the interface. The ability of P5 to compete with the protein G in recognizing IgG can help in the detection and purification of antibodies. Further, it can serve as a versatile tool for a better understanding of protein-protein interactions.
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Affiliation(s)
- Neetu Tanwar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rupal Ojha
- Department of Nephrology, Washington University School of Medicine, St. Louis, MO, USA
| | - Soumya Aggarwal
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | | | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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3
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Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [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: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
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Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
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Rana N, Patel D, Parmar M, Mukherjee N, Jha PC, Manhas A. Targeting allosteric binding site in methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to identify natural product inhibitors via structure-based computational approach. Sci Rep 2023; 13:18090. [PMID: 37872243 PMCID: PMC10593809 DOI: 10.1038/s41598-023-45175-3] [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: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
Cancer has been viewed as one of the deadliest diseases worldwide. Among various types of cancer, breast cancer is the most common type of cancer in women. Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is a promising druggable target and is overexpressed in cancerous cells, like, breast cancer. We conducted structure-based modeling on the allosteric site of the enzyme. Targeting the allosteric site avoids the problem of drug resistance. Pharmacophore modeling, molecular docking, HYDE assessment, drug-likeness, ADMET predictions, simulations, and free-energy calculations were performed. The RMSD, RMSF, RoG, SASA, and Hydrogen-bonding studies showed that seven candidates displayed stable behaviour. As per the literature, average superimposed simulated structures revealed a similar protein conformational change in the αE'-βf' loop, causing its displacement away from the allosteric site. The MM-PBSA showed tight binding of six compounds with the allosteric pocket. The effect of inhibitors interacting in the allosteric site causes a decrease in the binding energy of J49 (active-site inhibitor), suggesting the effect of allosteric binding. The PCA and FEL analysis revealed the significance of the docked compounds in the stable behaviour of the complexes. The outcome can contribute to the development of potential natural products with drug-like properties that can inhibit the MTHFD2 enzyme.
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Affiliation(s)
- Nisarg Rana
- Department of Chemistry, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, India
| | - Dhaval Patel
- Department of Industrial Biotechnology, Gujarat Biotechnology University, Gandhinagar, India
| | - Meet Parmar
- Department of Industrial Biotechnology, Gujarat Biotechnology University, Gandhinagar, India
| | - Nandini Mukherjee
- Department of Chemistry, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, 382030, India
| | - Anu Manhas
- Department of Chemistry, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, India.
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Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction. Mol Divers 2023; 27:45-57. [PMID: 35243596 PMCID: PMC8893242 DOI: 10.1007/s11030-022-10405-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/08/2022] [Indexed: 02/08/2023]
Abstract
In India, during the second wave of the COVID-19 pandemic, the breakthrough infections were mainly caused by the SARS-COV-2 delta variant (B.1.617.2). It was reported that, among majority of the infections due to the delta variant, only 9.8% percent cases required hospitalization, whereas only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections cases were observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Downregulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant resulted in structural instability of ORF8 dimer caused by disruption of hydrogen bonds and salt bridges as revealed by structural analysis and MD simulation studies. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild-type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 of SARS-CoV-2 delta variant may not be hindering the MHC-I expression thereby resulting in a better immune response against the SARS-CoV-2 delta variant, which partly explains the possible reason for sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India.
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Parmar M, Thumar R, Patel B, Athar M, Jha PC, Patel D. Structural differences in 3C-like protease (Mpro) from SARS-CoV and SARS-CoV-2: molecular insights revealed by Molecular Dynamics Simulations. Struct Chem 2022; 34:1-18. [PMID: 36467259 PMCID: PMC9686461 DOI: 10.1007/s11224-022-02089-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 10/29/2022] [Indexed: 11/25/2022]
Abstract
Novel coronavirus SARS-CoV-2 has infected millions of people with thousands of mortalities globally. The main protease (Mpro) is vital in processing replicase polyproteins. Both the CoV's Mpro shares 97% identity, with 12 mutations, but none are present in the active site. Although many therapeutics and vaccines are available to combat SARS-CoV-2, these treatments may not be practical due to their high mutational rate. On the other hand, Mpro has a high degree of conservation throughout variants, making Mpro a stout drug target. Here, we report a detailed comparison of both the monomeric Mpro and the biologically active dimeric Mpro using MD simulation to understand the impact of the 12 divergent residues (T35V, A46S, S65N, L86V, R88K, S94A, H134F, K180N, L202V, A267S, T285A and I286L) on the molecular microenvironment and the interaction between crucial residues. The present study concluded that the change in the microenvironment of residues at the entrance (T25, T26, M49 and Q189), near the catalytic site (F140, H163, H164, M165 and H172) and in the substrate-binding site (V35, N65, K88 and N180) is due to 12 mutations in the SARS-CoV-2 Mpro. Furthermore, the involvement of F140, E166 and H172 residues in dimerization stabilizes the Mpro dimer, which should be considered. We anticipate that networks and microenvironment changes identified here might guide repurposing attempts and optimization of new Mpro inhibitors. Supplementary Information The online version contains supplementary material available at 10.1007/s11224-022-02089-6.
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Affiliation(s)
- Meet Parmar
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, Gujarat 382426 India
| | - Ritik Thumar
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, Gujarat 382426 India
| | - Bhumi Patel
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, Gujarat 382426 India
| | - Mohd Athar
- Center for Chemical Biology and Therapeutics, InStem, Bangalore, 560065 Karnataka India
- Physics Department, University of Cagliari, Monserrato (CA), Italy
| | - Prakash C. Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, 382030 Gujarat India
| | - Dhaval Patel
- Department of Biotechnology and Bioengineering, Institute of Advanced Research, Gandhinagar, Gujarat 382426 India
- Gujarat Biotechnology University, Gujarat International Finance Tec-City, Gandhinagar, 382355 Gujarat India
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Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus. Vaccines (Basel) 2022; 10:vaccines10081352. [PMID: 36016239 PMCID: PMC9415835 DOI: 10.3390/vaccines10081352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 01/14/2023] Open
Abstract
SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. SARS-CoV-2 infections in humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies on the mutational analysis of human-derived SARS-CoV-2 have been published, but insight into the mink-derived SARS-CoV-2 genome of mutations is still required. Here, we performed a mutation analysis of the mink-derived SARS-CoV-2 genome sequences. We analyzed all available full-length mink-derived SARS-CoV-2 genome sequences on GISAID (214 genome sequences from the Netherlands and 133 genome sequences from Denmark). We found a striking resemblance between human-derived and mink-derived SARS-CoV-2. Our study showed that mutation patterns in the SARS-CoV-2 genome samples from the Netherlands and Denmark were different. Out of the 201 mutations we found, only 13 mutations were shared by the Netherlands' and Denmark's mink-derived samples. We found that six mutations were prevalent in the mink-derived SARS-CoV-2 genomes, and these six mutations are also known to be prevalent in human-derived SARS-CoV-2 variants. Our study reveals that the G27948T mutation in SARS-CoV-2 leads to truncation of ORF8, which was also reported in human-derived SARS-CoV-2, thus indicating that the virus can replicate without the full-length ORF8. These resemblances between mink-derived and human-derived SARS-CoV-2 enable the virus to cross the species barrier and suggest mink a potential reservoir for the virus.
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Chaudhari AM, Joshi M, Kumar D, Patel A, Lokhande KB, Krishnan A, Hanack K, Filipek S, Liepmann D, Renugopalakrishnan V, Paulmurugan R, Joshi C. Evaluation of immune evasion in SARS-CoV-2 Delta and Omicron variants. Comput Struct Biotechnol J 2022; 20:4501-4516. [PMID: 35965661 PMCID: PMC9359593 DOI: 10.1016/j.csbj.2022.08.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 12/18/2022] Open
Abstract
Emerging SARS-CoV-2 variants with higher transmissibility and immune escape remain a persistent threat across the globe. This is evident from the recent outbreaks of the Delta (B.1.617.2) and Omicron variants. These variants have originated from different continents and spread across the globe. In this study, we explored the genomic and structural basis of these variants for their lineage defining mutations of the spike protein through computational analysis, protein modeling, and molecular dynamic (MD) simulations. We further experimentally validated the importance of these deletion mutants for their immune escape using a pseudovirus-based neutralization assay, and an antibody (4A8) that binds directly to the spike protein's NTD. Delta variant with the deletion and mutations in the NTD revealed a better rigidity and reduced flexibility as compared to the wild-type spike protein (Wuhan isolate). Furthermore, computational studies of 4A8 monoclonal antibody (mAb) revealed a reduced binding of Delta variant compared to the wild-type strain. Similarly, the MD simulation data and virus neutralization assays revealed that the Omicron also exhibits immune escape, as antigenic beta-sheets appear to be disrupted. The results of the present study demonstrate the higher possibility of immune escape and thereby achieved better fitness advantages by the Delta and Omicron variants, which warrants further demonstrations through experimental evidences. Our study, based on in-silico computational modelling, simulations, and pseudovirus-based neutralization assay, highlighted and identified the probable mechanism through which the Delta and Omicron variants are more pathogenically evolved with higher transmissibility as compared to the wild-type strain.
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Affiliation(s)
- Armi M Chaudhari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Amrutlal Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Kiran Bharat Lokhande
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
| | - Anandi Krishnan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
| | - Katja Hanack
- Immunotechnology Group, Department of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Slawomir Filipek
- Faculty of Chemistry & Biological and Chemical Research, Centre, University of Warsaw, ul, Pasteura 1, 02-093 Warsaw, Poland
| | - Dorian Liepmann
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Venkatesan Renugopalakrishnan
- Department of Chemistry, Northeastern University, Boston Children's Hospital, Harvard Medical School, Boston, MGB Center for COVID Innovation, MA 02115, United States
| | - Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, United States
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar 382011, India
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Pandit R, Singh I, Ansari A, Raval J, Patel Z, Dixit R, Shah P, Upadhyay K, Chauhan N, Desai K, Shah M, Modi B, Joshi M, Joshi C. First report on genome wide association study in western Indian population reveals host genetic factors for COVID-19 severity and outcome. Genomics 2022; 114:110399. [PMID: 35680011 PMCID: PMC9169419 DOI: 10.1016/j.ygeno.2022.110399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023]
Abstract
Different human races across the globe responded in a different way to the SARS-CoV-2 infection leading to different disease severity. Therefore, it is anticipated that host genetic factors have a straight association with the COVID-19. We identified a total 6, 7, and 6 genomic loci for deceased-recovered, asymptomatic-recovered, and deceased-asymptomatic group comparison, respectively. Unfavourable alleles of the markers nearby the genes which are associated with lung and heart diseases such as Tumor necrosis factor superfamily (TNFSF4&18), showed noteworthy association with the disease severity and outcome for the COVID-19 patients in the western Indian population. The markers found with significant association with disease prognosis or recovery are of value in determining the individual's response to SARS-CoV-2 infection and can be used for the risk prediction in COVID-19. Besides, GWAS study in other populations from India may help to strengthen the outcome of this study.
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Affiliation(s)
- Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Indra Singh
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India
| | - Raghav Dixit
- Commissionerate of Health Medical Services and Medical Education Gandhinagar, Gujarat 382010, India
| | - Pranay Shah
- Department of Microbiology, B.J. Medical College and Civil hospital, Institute of Medical Post-Graduate Studies and Research, Ahmedabad, Gujarat 380016, India
| | - Kamlesh Upadhyay
- Department of Medicine, B.J. Medical College and Civil hospital, Institute of Medical Post-Graduate Studies and Research, Ahmedabad, Gujarat 380016, India
| | - Naresh Chauhan
- Department of Community Medicine, Government Medical College, Surat, Gujarat 395001, India
| | - Kairavi Desai
- Department of Microbiology, Government Medical College, Bhavnagar, Gujarat 364001, India
| | - Meenakshi Shah
- Department of General Medicine, GMERS Medical College & Hospital, Gotri, Vadodara, Gujarat 390021, India
| | - Bhavesh Modi
- Department of Community Medicine, GMERS Medical College, Gandhinagar, Gujarat 382012, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (Government of Gujarat), Gandhinagar, Gujarat 382011, India.
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Huang F, Chen L, Guo W, Zhou X, Feng K, Huang T, Cai Y. Identifying COVID-19 Severity-Related SARS-CoV-2 Mutation Using a Machine Learning Method. Life (Basel) 2022; 12:life12060806. [PMID: 35743837 PMCID: PMC9225528 DOI: 10.3390/life12060806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 shows great evolutionary capacity through a high frequency of genomic variation during transmission. Evolved SARS-CoV-2 often demonstrates resistance to previous vaccines and can cause poor clinical status in patients. Mutations in the SARS-CoV-2 genome involve mutations in structural and nonstructural proteins, and some of these proteins such as spike proteins have been shown to be directly associated with the clinical status of patients with severe COVID-19 pneumonia. In this study, we collected genome-wide mutation information of virulent strains and the severity of COVID-19 pneumonia in patients varying depending on their clinical status. Important protein mutations and untranslated region mutations were extracted using machine learning methods. First, through Boruta and four ranking algorithms (least absolute shrinkage and selection operator, light gradient boosting machine, max-relevance and min-redundancy, and Monte Carlo feature selection), mutations that were highly correlated with the clinical status of the patients were screened out and sorted in four feature lists. Some mutations such as D614G and V1176F were shown to be associated with viral infectivity. Moreover, previously unreported mutations such as A320V of nsp14 and I164ILV of nsp14 were also identified, which suggests their potential roles. We then applied the incremental feature selection method to each feature list to construct efficient classifiers, which can be directly used to distinguish the clinical status of COVID-19 patients. Meanwhile, four sets of quantitative rules were set up, which can help us to more intuitively understand the role of each mutation in differentiating the clinical status of COVID-19 patients. Identified key mutations linked to virologic properties will help better understand the mechanisms of infection and will aid in the development of antiviral treatments.
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Affiliation(s)
- Feiming Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200025, China;
| | - Xianchao Zhou
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai 200025, China;
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510060, China;
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (T.H.); (Y.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.C.)
| | - Yudong Cai
- School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.H.); (Y.C.); Tel.: +86-21-54923269 (T.H.); +86-21-66136132 (Y.C.)
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Esposito S, D’Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G. Host and Viral Zinc-Finger Proteins in COVID-19. Int J Mol Sci 2022; 23:ijms23073711. [PMID: 35409070 PMCID: PMC8998646 DOI: 10.3390/ijms23073711] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
An unprecedented effort to tackle the ongoing COVID-19 pandemic has characterized the activity of the global scientific community over the last two years. Hundreds of published studies have focused on the comprehension of the immune response to the virus and on the definition of the functional role of SARS-CoV-2 proteins. Proteins containing zinc fingers, both belonging to SARS-CoV-2 or to the host, play critical roles in COVID-19 participating in antiviral defenses and regulation of viral life cycle. Differentially expressed zinc finger proteins and their distinct activities could thus be important in determining the severity of the disease and represent important targets for drug development. Therefore, we here review the mechanisms of action of host and viral zinc finger proteins in COVID-19 as a contribution to the comprehension of the disease and also highlight strategies for therapeutic developments.
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12
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Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China. Virol Sin 2022; 37:187-197. [PMID: 35279413 PMCID: PMC8786408 DOI: 10.1016/j.virs.2022.01.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/21/2022] [Indexed: 01/10/2023] Open
Abstract
The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of 2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-CoV-2 epidemics in several large cities or provinces of China. However, information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-CoV-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-CoV-2 transmission profiles. Genomic epidemiology revealed multiple SARS-CoV-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size. Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-CoV-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-CoV-2 strains during the early COVID-19 epidemic in China. The SARS-CoV-2 strains from multiple regions and multiple lineages together caused the outbreak of COVID-19 in Anyang. The traditional family/community facilitates the widespread of SARS-CoV-2 in small and medium-sized Chinese cities. The iSNV analysis is an effective approach to studying cluster infections and reconstructing the transmission chain.
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