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Oróstica KY, Mohr SB, Dehning J, Bauer S, Medina-Ortiz D, Iftekhar EN, Mujica K, Covarrubias PC, Ulloa S, Castillo AE, Daza-Sánchez A, Verdugo RA, Fernández J, Olivera-Nappa Á, Priesemann V, Contreras S. Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile. Sci Rep 2024; 14:16000. [PMID: 38987406 PMCID: PMC11237036 DOI: 10.1038/s41598-024-66885-2] [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: 10/24/2023] [Accepted: 07/05/2024] [Indexed: 07/12/2024] Open
Abstract
Genomic surveillance (GS) programmes were crucial in identifying and quantifying the mutating patterns of SARS-CoV-2 during the COVID-19 pandemic. In this work, we develop a Bayesian framework to quantify the relative transmissibility of different variants tailored for regions with limited GS. We use it to study the relative transmissibility of SARS-CoV-2 variants in Chile. Among the 3443 SARS-CoV-2 genomes collected between January and June 2021, where sampling was designed to be representative, the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. We found that Lambda and Gamma variants' reproduction numbers were 5% (95% CI: [1%, 14%]) and 16% (95% CI: [11%, 21%]) larger than Alpha's, respectively. Besides, we observed a systematic mutation enrichment in the Spike gene for all circulating variants, which strongly correlated with variants' transmissibility during the studied period (r = 0.93, p-value = 0.025). We also characterised the mutational signatures of local samples and their evolution over time and with the progress of vaccination, comparing them with those of samples collected in other regions worldwide. Altogether, our work provides a reliable method for quantifying variant transmissibility under subsampling and emphasises the importance of continuous genomic surveillance.
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Affiliation(s)
| | - Sebastian B Mohr
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Jonas Dehning
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Simon Bauer
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - David Medina-Ortiz
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Emil N Iftekhar
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Karen Mujica
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Paulo C Covarrubias
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Soledad Ulloa
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Andrés E Castillo
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | | | - Ricardo A Verdugo
- Facultad de Medicina, Universidad de Talca, Talca, Chile
- Departamento de Oncología Básico-Clínica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jorge Fernández
- Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Santiago, Chile
| | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Seba Contreras
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany.
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Zhou B, Chen D, Zhang T, Song C, Zhang X, Lin L, Huang J, Peng X, Liu Y, Wu G, Li J, Chen W. Recent advancements in the discovery of small-molecule non-nucleoside inhibitors targeting SARS-CoV-2 RdRp. Biomed Pharmacother 2024; 171:116180. [PMID: 38266622 DOI: 10.1016/j.biopha.2024.116180] [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] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 plays a pivotal role in the life cycle of the novel coronavirus and stands as a significant and promising target for anti-SARS-CoV-2 drugs. Non-nucleoside inhibitors (NNIs), as a category of compounds directed against SARS-CoV-2 RdRp, exhibit a unique and highly effective mechanism, effectively overcoming various factors contributing to drug resistance against nucleoside inhibitors (NIs). This review investigates various NNIs, including both natural and synthetic inhibitors, that closely interacting with the SARS-CoV-2 RdRp with valid evidences from in vitro and in silico studies.
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Affiliation(s)
- Bangdi Zhou
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Dianming Chen
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Tingyan Zhang
- School of Nusing, Gannan Medical University, Ganzhou 341000, PR China
| | - Chenggui Song
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Xianwu Zhang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Leying Lin
- School of Basic Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Jiuzhong Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Xiaopeng Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Yuanchang Liu
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Gaorong Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Jingyuan Li
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Weiming Chen
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China.
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3
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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Makowski JA, Kensinger AH, Cunningham CL, Frye CJ, Shine M, Lackey PE, Mihailescu MR, Evanseck JD. Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation. ACS PHYSICAL CHEMISTRY AU 2023; 3:434-443. [PMID: 37780540 PMCID: PMC10540284 DOI: 10.1021/acsphyschemau.3c00008] [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: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 10/03/2023]
Abstract
Bioinformatic analysis of the Delta SARS-CoV-2 genome reveals a single nucleotide mutation (G15U) in the stem-loop II motif (s2m) relative to ancestral SARS-CoV-2. Despite sequence similarity, unexpected differences between SARS-CoV-2 and Delta SARS-CoV-2 s2m homodimerization experiments require the discovery of unknown structural and thermodynamic changes necessary to rationalize the data. Using our reported SARS-CoV-2 s2m model, we induced the G15U substitution and performed 3.5 microseconds of unbiased molecular dynamics simulation at 283 and 310 K. The resultant Delta s2m adopted a secondary structure consistent with our reported NMR data, resulting in significant deviations in the tertiary structure and dynamics from our SARS-CoV-2 s2m model. First, we find differences in the overall three-dimensional structure, where the characteristic 90° L-shaped kink of the SARS-CoV-2 s2m did not form in the Delta s2m resulting in a "linear" hairpin with limited bending dynamics. Delta s2m helical parameters are calculated to align closely with A-form RNA, effectively eliminating a hinge point to form the L-shape kink by correcting an upper stem defect in SARS-CoV-2 induced by a noncanonical and dynamic G:A base pair. Ultimately, the shape difference rationalizes the migration differences in reported electrophoresis experiments. Second, increased fluctuation of the Delta s2m palindromic sequence, within the terminal loop, compared to SARS-CoV-2 s2m results in an estimated increase of entropy of 6.8 kcal/mol at 310 K relative to the SARS-CoV-2 s2m. The entropic difference offers a unique perspective on why the Delta s2m homodimerizes less spontaneously, forming fewer kissing dimers and extended duplexes compared to SARS-CoV-2. In this work, both the L-shape reduction and palindromic entropic penalty provides an explanation of our reported in vitro electrophoresis homodimerization results. Ultimately, the structural, dynamical, and entropic differences between the SARS-CoV-2 s2m and Delta s2m serve to establish a foundation for future studies of the s2m function in the viral lifecycle.
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Affiliation(s)
- Joseph A. Makowski
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Adam H. Kensinger
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caylee L. Cunningham
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Caleb J. Frye
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Morgan Shine
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Patrick E. Lackey
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania 16172, United States
| | - Mihaela Rita Mihailescu
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Jeffrey D. Evanseck
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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Bestari R, Nainggolan IRA, Hasibuan M, Ratnanggana R, Rahardjo K, Nastri AM, Dewantari JR, Soetjipto S, Lusida MI, Mori Y, Shimizu K, Kusumawati RL, Ichwan M, Lubis IND. SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia. IJID REGIONS 2023; 8:S1-S7. [PMID: 37799539 PMCID: PMC10548867 DOI: 10.1016/j.ijregi.2023.07.006] [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: 01/02/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023]
Abstract
Objectives To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia. Methods A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument. Results Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%). Conclusion The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.
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Affiliation(s)
- Ramadhan Bestari
- Faculty of Medicine, Universitas Islam Sumatera Utara, Medan, Indonesia
| | | | - Mirzan Hasibuan
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Rima Ratnanggana
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Krisnoadi Rahardjo
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | | | | | - Maria Inge Lusida
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Yasuko Mori
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Chuo-ku, Japan
| | - Kazufumi Shimizu
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Chuo-ku, Japan
| | - R Lia Kusumawati
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Muhammad Ichwan
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
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Yaghoobizadeh F, Roayaei Ardakani M, Ranjbar MM, Khosravi M, Galehdari H. Preparation, Purification and Performance Evaluation of Polyclonal Antibody Against SARS-CoV-2 Produced in Rat. Adv Pharm Bull 2023; 13:563-572. [PMID: 37646054 PMCID: PMC10460799 DOI: 10.34172/apb.2023.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/21/2022] [Accepted: 11/02/2022] [Indexed: 09/01/2023] Open
Abstract
Purpose Among all known human coronaviruses, some viruses (e.g., SARS-CoV-2) cause severe pneumonia or even death. With the regard to its spread and the importance of its rapid identification/treatment, and because pAbs are relatively cheap, able to bind to more sites on antigens and even neutralize them, this study was done for the production and purification of anti-SARS-CoV-2 polyclonal antibodies (pAb) in rats. Methods Viral antigen purification was performed by PEG/NaCl precipitation. The efficiency of the sucrose cushion method was also investigated to produce a purer antigen. Immunization was done and antibody purification was performed by ammonium sulfate precipitation (33%), dialysis, and ion-exchange chromatography. Western blotting and enzyme-linked immunosorbent assay (ELISA) were performed to verify the antibody specificity. All data were analyzed by SPSS software. Results The results showed that the amount of concentrated virus increased with the increase of PEG concentration. Moreover, the sucrose cushion method increased its purity. Besides, induction of immune response in rats for pAb production with high titers was reached via these antigens and ELISA/western blot results indicated a suitable antibody-antigen interaction. Additionally, it was shown that ion-exchange chromatography could be a suitable technique for IgG purification. Conclusion Herein, we presented a simple and cheap method for the purification of whole viral particles with relatively high quality. The results verified that these antigens could elicit a good immune response in the rat. The obtained pAbs showed a good specificity toward SARS-CoV-2 antigens. Accordingly, this study proposes a promising method for viral vaccine development.
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Affiliation(s)
- Fatemeh Yaghoobizadeh
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Mohammad Roayaei Ardakani
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | | | - Mohammad Khosravi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Khouzestan, Iran
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7
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Shoaei P, Ranjbar MM, Tokhanbigli S, Ataei B, Alibakhshi A, Haghjooy Javanmard S, Ahangarzadeh S. Comparative Analysis and Identification of Spike Mutations in Iranian COVID-19 Samples from the First Three Waves of Disease. Adv Biomed Res 2023; 12:153. [PMID: 37564431 PMCID: PMC10410413 DOI: 10.4103/abr.abr_171_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/16/2022] [Accepted: 12/04/2022] [Indexed: 08/12/2023] Open
Abstract
Background The spike surface glycoprotein of SARS-CoV-2 is the essential protein in virus attachment to the target cell and cell entrance. As this protein contains immunodominant epitopes and is the main target for immune recognition, it is the critical target for vaccine and therapeutics development. In the current research, we analyzed the variability and mutations of the spike glycoprotein isolated from 72 COVID-19-positive patients from Iran's first three waves of disease. Materials and Methods The RNA was extracted from nasopharyngeal samples of confirmed COVID-19 cases and served as a template for cDNA synthesis and reverse transcriptase polymerase chain reaction. The reverse transcriptase polymerase chain reaction products of each sample were assembled and sequenced. Results After analysis of 72 sequences, we obtained 46 single nucleotide polymorphisms, including 23 that produce amino acid changes. Our analysis showed that the most frequent mutation was the D614G (in the samples of the second and third waves). Conclusions Our findings suggest that developing effective vaccines requires identifying the predominant variants of SARS-CoV-2 in each community.
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Affiliation(s)
- Parisa Shoaei
- Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad M. Ranjbar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Samaneh Tokhanbigli
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behrouz Ataei
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Alibakhshi
- Molecular Medicine Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shaghayegh Haghjooy Javanmard
- Department of Physiology, Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shahrzad Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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Messali S, Rondina A, Giovanetti M, Bonfanti C, Ciccozzi M, Caruso A, Caccuri F. Traceability of SARS-CoV-2 transmission through quasispecies analysis. J Med Virol 2023; 95:e28848. [PMID: 37294038 DOI: 10.1002/jmv.28848] [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: 04/26/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023]
Abstract
During COVID-19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS-CoV-2 consists in an ensemble of replicating and closely related viral variants so-called quasispecies. Here we show that intrahost single nucleotide variants (iSNVs) represent a target for contact tracing analysis. Our data indicate that in the acute phase of infection, in highly likely transmission links, the number of viral particles transmitted from one host to another (bottleneck size) is large enough to propagate iSNVs among individuals. Furthermore, we demonstrate that, during SARS-CoV-2 outbreaks when the consensus sequences are identical, it is possible to reconstruct the transmission chains by genomic investigations of iSNVs. Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well-conserved genes, namely nsp2, ORF3, and ORF7.
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Affiliation(s)
- Serena Messali
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Alessandro Rondina
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Rome, Italy
| | - Carlo Bonfanti
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Massimo Ciccozzi
- Clinical Pathology and Microbiology Laboratory, Unit of Medical Statistics and Molecular Epidemiology, University Hospital Campus Biomedico, Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
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Paulino-Ramírez R, López P, Mueses S, Cuevas P, Jabier M, Rivera-Amill V. Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085503. [PMID: 37107785 PMCID: PMC10138544 DOI: 10.3390/ijerph20085503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10-3 (95% HPD: 1.2358 × 10-3, 1.8635 × 10-3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
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Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Correspondence:
| | - Pablo López
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
| | - Sayira Mueses
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Paula Cuevas
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic
| | - Vanessa Rivera-Amill
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
- Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA
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Quispe-Ricalde MA, Castelán-Sánchez HG, Meza-Rodríguez PM, Dávila-Ramos S, Sierra JL, Batista-Garcia R, Concha-Velasco F, Lucana SF, De Santa Cruz J, Zea V, Galarza M, Caceres-Rey O, Tsukayama P, Foronda P, Soto-Chambi BJ, Abreu N. Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru. Arch Virol 2023; 168:88. [PMID: 36786950 PMCID: PMC9926449 DOI: 10.1007/s00705-022-05645-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 02/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage C.37 (Lambda) has spread rapidly in Peru and other Latin American countries. However, most studies in Peru have focused on Lima, the capital city, without knowing the dynamics of the spread of the variant in other departments. Cusco, Peru, is one of the most popular departments in the country for tourists, so the introduction of new variants of SARS-CoV-2 might occur despite closure of the borders. Therefore, in this work, we analyzed the variants circulating in Cusco. The aim of this work was to better understand the distribution of SARS-CoV-2 lineages circulating in Cusco and to characterize the genomes of these strains. To this end, 46 SARS-CoV-2 genomes from vaccinated and unvaccinated patients were sequenced in the first half of 2021. The genomes were analyzed using phylogenetic and natural selection methods. Phylogenetic trees from Cusco showed dominance of the Lambda lineage over the variants of concern (VOCs), and there was no clustering of variants by district. Natural selection analysis revealed mutations, mainly in the spike protein, at positions 75, 246, 247, 707, 769, and 1020. In addition, we found that unvaccinated patients accumulated more new mutations than did vaccinated patients, and these included the F101Y mutation in ORF7a, E419A in NSP3, a deletion in S (21,618-22,501), and a deletion in ORF3a (25,437-26,122).
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Affiliation(s)
- Maria Antonieta Quispe-Ricalde
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, C.P. 0800, Cusco, Perú.
| | - Hugo G Castelán-Sánchez
- Programa de Investigadoras e Investigadores por México. Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Crédito Constructo, Benito Juárez, Ciudad de México, C.P. 03940, México.
| | - Pablo M Meza-Rodríguez
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - José Luis Sierra
- Escuela de Postgrado, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, Cusco, C.P. 0800, Perú
| | - Ramón Batista-Garcia
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - Fátima Concha-Velasco
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
- Dirección de epidemiología e investigación. Gerencia regional de salud, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Sonia Flores Lucana
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - José De Santa Cruz
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Víctor Zea
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Marco Galarza
- Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Omar Caceres-Rey
- Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porres 15102, Lima, C.P. 15102, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Av. Honorio Delgado 430, San Martín de Porres, Lima, Peru
- Wellcome Sanger Institute, Saffron Walden, Cambridge, Reino Unido. Z.P. CB10 1SA, Hinxton, UK
| | - Pilar Foronda
- University Institute of Tropical Diseases and Public Health of the Canary Islands, Av. Astrofísico FranciscoSánchez, s/n, San Cristóbal de La Laguna, Tenerife, C.P.38200, Spain
| | - Brandon Jason Soto-Chambi
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, C.P. 0800, Cusco, Perú
| | - Nestor Abreu
- University Institute of Tropical Diseases and Public Health of the Canary Islands, Av. Astrofísico FranciscoSánchez, s/n, San Cristóbal de La Laguna, Tenerife, C.P.38200, Spain.
- NERTALAB, SL., C, /José Rodríguez Mouré, 4, Santa Cruz de Tenerife, Tenerife, C.P. 38008, España.
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11
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Khamis F, Al Awaidy S, Ba’Omar M, Osman W, Chhetri S, Ambusaid Z, Al Fahdi Z, Al Lawati J, Al Sulaimi K, Al Bulushi SA, Al Bahrani M, Al-Zakwani I. The Impact of Demographic, Clinical Characteristics and the Various COVID-19 Variant Types on All-Cause Mortality: A Case-Series Retrospective Study. Diseases 2022; 10:100. [PMID: 36412594 PMCID: PMC9680441 DOI: 10.3390/diseases10040100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
(1) Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into a pandemic affecting virtually every country in the world. We evaluated the demographic, clinical, laboratory, and all-cause mortality of moderate and severe COVID-19 patients admitted to a tertiary care hospital in Oman during the different COVID-19 waves and variant types. (2) Methods: A case-series retrospective study was carried out between 12 March 2020 and 30 June 2022. All adults over the age of 18 with laboratory-confirmed COVID-19 were enrolled. Analyses were performed using univariate and multivariate statistics. (3) Results: A total of 1462 confirmed cases enrolled with the mean age of the cohort was 55 ± 17 years with significant differences among the groups (p = 0.006). A total of 63% and 80% of the patients were males and citizens of Oman, respectively. Patients infected with the Alpha COVID-19 variant type were more likely to have acute respiratory distress syndrome (ARDS) (p < 0.001), stay longer in the hospital (p < 0.001), and get admitted to the intensive care unit (ICU) (p < 0.001). At the same time, those who had the Omicron COVID-19 type were more likely to have renal impairment (p < 0.001) and less likely to be associated with non-invasive ventilation (NIV) (p = 0.001) compared with other COVID-19 variant types. The Delta (adjusted odds ratio (aOR), 1.8; 95% confidence interval (CI): 1.22−2.66; p = 0.003) and Omicron (aOR, 1.88; 95% CI: 1.09−3.22; p = 0.022) COVID-19 variant types were associated with higher all-cause mortality when compared to the initial COVID-19 variant. Old age (aOR, 1.05; 95% CI: 1.04−1.06; p < 0.001), the presence of respiratory disease (aOR, 1.58; 95% CI: 1.02−2.44; p = 0.04), ICU admission (aOR, 3.41; 95% CI: 2.16−5.39; p < 0.001), lower eGFR (aOR, 1.61; 95% CI: 1.17−2.23; p = 0.004), and ARDS (aOR, 5.75; 95% CI: 3.69−8.98; p < 0.001) were also associated with higher mortality while NIV requirements were associated with lower odds of dying (aOR, 0.65; 95% CI: 0.46−0.91; p = 0.012). (4) Conclusions: Alpha and Delta variants were associated with a longer hospital stay, need for intensive care, mechanical ventilation, and increased mortality. Old age, cardiac renal dysfunction were commonly associated with Omicron variants. Large-scale national studies to further assess the risk factors for mortality related to COVID-19 waves are warranted.
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Affiliation(s)
- Faryal Khamis
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | | | - Muna Ba’Omar
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | - Wessam Osman
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Shabnam Chhetri
- Department of Infectious Disease, The Royal Hospital, Muscat, PC 111, Oman
| | - Zaiyana Ambusaid
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Zakariya Al Fahdi
- Department of Medicine, Nizwa Hospital, Ministry of Health, Nizwa, PC 611, Oman
| | - Jaber Al Lawati
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Khalsa Al Sulaimi
- Department of Medicine, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | | | - Maher Al Bahrani
- Department of Anaesthesia, Royal Hospital, Ministry of Health, Muscat, PC 111, Oman
| | - Ibrahim Al-Zakwani
- Department of Pharmacology & Clinical Pharmacy, College of Medicine & Health Sciences, Sultan Qaboos University, Al Khoudh, PC 123, Oman
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12
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SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods. Pathogens 2022; 11:pathogens11091058. [PMID: 36145490 PMCID: PMC9504725 DOI: 10.3390/pathogens11091058] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.
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Considering epitopes conservity in targeting SARS-CoV-2 mutations in variants: a novel immunoinformatics approach to vaccine design. Sci Rep 2022; 12:14017. [PMID: 35982065 PMCID: PMC9386201 DOI: 10.1038/s41598-022-18152-5] [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: 04/10/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing mutations can increase the virus's pathogenicity and virulence; reduce the efficacy of vaccines, antibodies neutralization, and even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) in different variants with appropriate antigenicity to target the variants by an appropriate vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, mutations in the immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, and also predicted epitopes were calculated. In the following, epitopes conservity score against the total number of events (mutations) and the number of mutated sites in each epitope was weighted by Shannon entropy and then calculated by the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). Based on the TOPSIS conservity score and antigenicity score, the epitopes were plotted. The result demonstrates that almost all epitopes and IDRs with various lengths have gained different numbers of mutations in dissimilar sites. Herein, our two-step calculation for conservity recommends only 8 IDRs, 14 IEDB epitopes, and 10 predicted epitopes among all epitopes. The selected ones have higher conservity and higher immunogenicity. This method is an open-source multi-criteria decision-making platform, which provides a scientific approach to selecting epitopes with appropriate conservity and immunogenicity; against ever-changing viruses.
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14
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Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview. J Diabetes Metab Disord 2022; 21:1763-1783. [PMID: 35891981 PMCID: PMC9305048 DOI: 10.1007/s40200-022-01002-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022]
Abstract
With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.
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15
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Mayes CM, Santarpia J. Evaluating the Impact of gRNA SNPs in CasRx Activity for Reducing Viral RNA in HCoV-OC43. Cells 2022; 11:1859. [PMID: 35740988 PMCID: PMC9220780 DOI: 10.3390/cells11121859] [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: 05/07/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 12/10/2022] Open
Abstract
Viruses within a given family often share common essential genes that are highly conserved due to their critical role for the virus's replication and survival. In this work, we developed a proof-of-concept for a pan-coronavirus CRISPR effector system by designing CRISPR targets that are cross-reactive among essential genes of different human coronaviruses (HCoV). We designed CRISPR targets for both the RNA-dependent RNA polymerase (RdRp) gene as well as the nucleocapsid (N) gene in coronaviruses. Using sequencing alignment, we determined the most highly conserved regions of these genes to design guide RNA (gRNA) sequences. In regions that were not completely homologous among HCoV species, we introduced mismatches into the gRNA sequence and tested the efficacy of CasRx, a Cas13d type CRISPR effector, using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in HCoV-OC43. We evaluated the effect that mismatches in gRNA sequences has on the cleavage activity of CasRx and found that this CRISPR effector can tolerate up to three mismatches while still maintaining its nuclease activity in HCoV-OC43 viral RNA. This work highlights the need to evaluate off-target effects of CasRx with gRNAs containing up to three mismatches in order to design safe and effective CRISPR experiments.
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Affiliation(s)
- Cathryn Michelle Mayes
- Sandia National Laboratories, Albuquerque, NM 87123, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Joshua Santarpia
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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16
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Xiao J, Wu Y, Wang M, Ma Z. Scope Issue in Contingent Valuation Studies of the COVID-19 Vaccine: The Case of China. APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2022; 20:417-429. [PMID: 35001293 PMCID: PMC8743235 DOI: 10.1007/s40258-021-00706-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Assessing the public's willingness to pay (WTP) for the coronavirus disease 2019 (COVID-19) vaccine by the contingent valuation (CV) method can provide a relevant basis for government pricing. However, the scope issue of the CV method can seriously affect the validity and reliability of the estimation results. AIM To examine whether there are scope issues in respondents' WTP for the COVID-19 vaccine and to further verify the validity and reliability of the CV estimate results. METHOD In this study, nine different CV double-bounded dichotomous choices (DBDC) hypothetical COVID-19 vaccine scenarios were designed using an orthogonal experimental design based on the vaccine's attributes. A total of 2450 samples from 31 provinces in Mainland China were collected to independently estimate the public's WTP in these nine scenarios with logistic, normal, log-logistic and log-normal parameter models. Based on this estimation, several external scope tests were designed to verify the validity and reliability of the CV estimate results. RESULTS In the 20 pairs of COVID-19 vaccine scenarios, 6 pairs of scenarios were classified as negative scope issues, therefore not passing the external scope test. Of the remaining 14 pairs of scenarios, only four pairs of scenarios completely passed the external scope test, and one pair of scenarios partially passed the external scope test. Significant negative scope and scope insensitivity issues were revealed. CONCLUSION In the context of a dynamic pandemic environment, the findings of this study reveal that the CV method may face difficulty in effectively estimating respondents' WTP for the COVID-19 vaccine. We suggest that future studies be cautious in applying the CV method to estimate the public's WTP for the COVID-19 vaccine.
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Affiliation(s)
- Jianhong Xiao
- School of Tourism and Geography Science, Qingdao University, Qingdao, China
| | - Yihui Wu
- School of Tourism and Geography Science, Qingdao University, Qingdao, China
| | - Min Wang
- Business College, Qingdao University, Qingdao, China
| | - Zegang Ma
- Department of Physiology, School of Basic Medicine, Qingdao University, Qingdao, China
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17
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Naigaonkar A, Patil K, Joseph S, Hinduja I, Mukherjee S. Ovarian granulosa cells from women with PCOS express low levels of SARS-CoV-2 receptors and co-factors. Arch Gynecol Obstet 2022; 306:547-555. [PMID: 35477803 PMCID: PMC9045021 DOI: 10.1007/s00404-022-06567-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
Purpose Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is global pandemic with more than 5 million deaths so far. Female reproductive tract organs express coronavirus-associated receptors and factors (SCARFs), suggesting they may be susceptible to SARS-CoV-2 infection; however, the susceptibility of ovary/follicle/oocyte to the same is still elusive. Co-morbidities like obesity, type-2 diabetes mellitus, cardiovascular disease, etc. increase the risk of SARS-CoV-2 infection. These features are common in women with polycystic ovary syndrome (PCOS), warranting further scope to study SCARFs expression in ovary of these women. Materials and methods SCARFs expression in ovary and ovarian tissues of women with PCOS and healthy women was explored by analyzing publically available microarray datasets. Transcript expressions of SCARFs were investigated in mural and cumulus granulosa cells (MGCs and CGCs) from control and PCOS women undergoing in vitro fertilization (IVF). Results Microarray data revealed that ovary expresses all genes necessary for SARS-CoV-2 infection. PCOS women mostly showed down-regulated/unchanged levels of SCARFs. MGCs and CGCs from PCOS women showed lower expression of receptors ACE2, BSG and DPP4 and protease CTSB than in controls. MGCs showed lower expression of protease CTSL in PCOS than in controls. Expression of TMPRSS2 was not detected in both cell types. Conclusion Human ovarian follicle may be susceptible to SARS-CoV-2 infection. Lower expression of SCARFs in PCOS indicates that the risk of SARS-CoV-2 infection to the ovary may be lesser in these women than controls. This knowledge may help in safe practices at IVF settings in the current pandemic. Supplementary Information The online version contains supplementary material available at 10.1007/s00404-022-06567-4.
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Affiliation(s)
- Aalaap Naigaonkar
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Indian Council of Medical Research, J.M. Street, Parel, Mumbai, 400012, India
| | - Krutika Patil
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Indian Council of Medical Research, J.M. Street, Parel, Mumbai, 400012, India
| | - Shaini Joseph
- Genetic Research Centre, National Institute for Research in Reproductive Health, Indian Council of Medical Research, J.M. Street, Parel, Mumbai, 400012, India
| | - Indira Hinduja
- P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, 400016, India
| | - Srabani Mukherjee
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Indian Council of Medical Research, J.M. Street, Parel, Mumbai, 400012, India.
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Sokhansanj BA, Rosen GL. Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences. mSystems 2022; 7:e0003522. [PMID: 35311562 PMCID: PMC9040592 DOI: 10.1128/msystems.00035-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2022] [Indexed: 12/22/2022] Open
Abstract
Next-generation sequencing has been essential to the global response to the COVID-19 pandemic. As of January 2022, nearly 7 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences are available to researchers in public databases. Sequence databases are an abundant resource from which to extract biologically relevant and clinically actionable information. As the pandemic has gone on, SARS-CoV-2 has rapidly evolved, involving complex genomic changes that challenge current approaches to classifying SARS-CoV-2 variants. Deep sequence learning could be a potentially powerful way to build complex sequence-to-phenotype models. Unfortunately, while they can be predictive, deep learning typically produces "black box" models that cannot directly provide biological and clinical insight. Researchers should therefore consider implementing emerging methods for visualizing and interpreting deep sequence models. Finally, researchers should address important data limitations, including (i) global sequencing disparities, (ii) insufficient sequence metadata, and (iii) screening artifacts due to poor sequence quality control.
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Affiliation(s)
- Bahrad A. Sokhansanj
- Drexel University, Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical & Computer Engineering, College of Engineering, Philadelphia, Pennsylvania, USA
| | - Gail L. Rosen
- Drexel University, Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical & Computer Engineering, College of Engineering, Philadelphia, Pennsylvania, USA
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19
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Biswas B, Chattopadhyay S, Hazra S, Hansda AK, Goswami R. COVID-19 pandemic: the delta variant, T-cell responses, and the efficacy of developing vaccines. Inflamm Res 2022; 71:377-396. [PMID: 35292834 PMCID: PMC8923340 DOI: 10.1007/s00011-022-01555-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/07/2022] [Accepted: 02/16/2022] [Indexed: 12/15/2022] Open
Abstract
Background The mayhem COVID-19 that was ushered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) was declared pandemic by the World Health Organization in March 2020. Since its initial outbreak in late 2019, the virus has affected hundreds of million adults in the world and killing millions in the process. After the approval of newly developed vaccines, severe challenges remain to manufacture and administer them to the adult population globally in quick time. However, we have witnessed several mutations of the virus leading to ‘waves’ of viral spread and mortality. WHO has categorized these mutations as variants of concern (VOCs) and variants of interest (VOIs). The mortality due to COVID-19 has also been associated with various comorbidities and improper immune response. This has created further complications in understanding the nature of the SARS-CoV2–host interaction that has fuelled doubts in the efficacy of the approved vaccines. Whether there is requirement of booster dose and whether the impending wave could affect the children are some of the hotly debated topics. Materials and Methods A systematic literature review of PubMed, Medline, Scopus, Google Scholar was utilized to understand the nature of Delta variant and how it alters our T-cell responses and cytokine production and neutralizes vaccine-generated antibodies.
Conclusion In this review, we discuss the variants of SARS-CoV2 with specific focus on the Delta variant. We also specifically review the T-cell response against the virus and bring a narrative of various factors that may hold the key to fight against this marauding virus.
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Affiliation(s)
- Biswajit Biswas
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Sayantee Hazra
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India
| | | | - Ritobrata Goswami
- School of Bioscience, IIT Kharagpur, Kharagpur, 721302, West Bengal, India.
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20
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Naresh GKRS, Guruprasad L. Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor. J Biomol Struct Dyn 2022; 41:2368-2381. [PMID: 35109768 DOI: 10.1080/07391102.2022.2032354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The severe acute respiratory syndrome virus-2 (SARS CoV-2) infection has resulted in the current global pandemic. The binding of SARS CoV-2 spike protein receptor-binding domain (RBD) to the human angiotensin converting enzyme-2 (ACE-2) receptor causes the host infection. The spike protein has undergone several mutations with reference to the initial strain isolated during December 2019 from Wuhan, China. A number of these mutant strains have been reported as variants of concern and as variants being monitored. Some of these mutants are known to be responsible for increased transmissibility of the virus. The reason for the increased transmissibility caused by the point mutations can be understood by studying the structural implications and inter-molecular interactions in the binding of viral spike protein RBD and human ACE-2. Here, we use the crystal structure of the RBD in complex with ACE-2 available in the public domain and analyse the 250 ns molecular dynamics (MD) simulations of wild-type and mutants; K417N, K417T, N440K, N501Y, L452R, T478K, E484K and S494P. The ionic, hydrophobic and hydrogen bond interactions, amino acid residue flexibility, binding energies and structural variations are characterized. The MD simulations provide clues to the molecular mechanisms of ACE-2 receptor binding in wild-type and mutant complexes. The mutant spike proteins RBD were associated with greater binding affinity with ACE-2 receptor. Communicated by Ramaswamy H. Sarma.
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Xiao J, Wang F, Wang M, Ma Z. Attribute nonattendance in COVID-19 vaccine choice: A discrete choice experiment based on Chinese public preference. Health Expect 2022; 25:959-970. [PMID: 35049117 PMCID: PMC9122444 DOI: 10.1111/hex.13439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/04/2021] [Accepted: 01/09/2022] [Indexed: 01/25/2023] Open
Abstract
Objectives The global coronavirus disease 2019 (COVID‐19) pandemic has not been well controlled, and vaccination could be an effective way to prevent this pandemic. By accommodating attribute nonattendance (ANA) in a discrete choice experiment (DCE), this paper aimed to examine Chinese public preferences and willingness to pay (WTP) for COVID‐19 vaccine attributes, especially the influence of ANA on the estimated results. Methods A DCE was designed with four attributes: effectiveness, protection period, adverse reactions and price. A random parameter logit model with an error component (RPL‐EC) was used to analyse the heterogeneity of respondents' preferences for COVID‐19 vaccine attributes. Two equality constraint latent class (ECLC) models were used to consider the influence of ANA on the estimated results in which the ECLC‐homogeneity model considered only ANA and the ECLC‐heterogeneity model considered both ANA and preference heterogeneity. Results Data from 1,576 samples were included in the analyses. Effectiveness had the highest relative importance, followed by adverse reactions and protection period, which were determined by the attributes and levels presented in this study. The ECLC‐heterogeneity model improved the goodness of fit of the model and obtained a lower probability of ANA. In the ECLC‐heterogeneity model, only a small number of respondents (29.09%) considered all attributes, and price was the most easily ignored attribute (64.23%). Compared with the RPL‐EC model, the ECLC‐homogeneity model obtained lower WTPs for COVID‐19 vaccine attributes, and the ECLC‐heterogeneity model obtained mixed WTP results. In the ECLC‐heterogeneity model, preference group 1 obtained higher WTPs, and preference groups 2 and 3 obtained lower WTPs. Conclusions The RPL‐EC, ECLC‐homogeneity and ECLC‐heterogeneity models obtained inconsistent WTPs for COVID‐19 vaccine attributes. The study found that the results of the ECLC‐heterogeneity model considering both ANA and preference heterogeneity may be more plausible because ANA and low preference may be confused in the ECLC‐homogeneity model and the RPL‐EC model. The results showed that the probability of ANA was still high in the ECLC‐heterogeneity model, although it was lower than that in the ECLC‐homogeneity model. Therefore, in future research on DCE (such as the field of vaccines), ANA should be considered as an essential issue. Public Contribution Chinese adults from 31 provinces in mainland China participated in the study. All participants completed the COVID‐19 vaccine choice questions generated through the DCE design.
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Affiliation(s)
- Jianhong Xiao
- School of Tourism and Geography Science, Qingdao University, Qingdao, Shandong, China
| | - Fei Wang
- Business College, Qingdao University, Qingdao, Shandong, China
| | - Min Wang
- Business College, Qingdao University, Qingdao, Shandong, China
| | - Zegang Ma
- School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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22
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The role of microRNAs in solving COVID-19 puzzle from infection to therapeutics: A mini-review. Virus Res 2022; 308:198631. [PMID: 34788642 PMCID: PMC8590742 DOI: 10.1016/j.virusres.2021.198631] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 02/08/2023]
Abstract
Nowadays, one of the major global health concerns is coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Even though numerous treatments and vaccines to combat this virus are currently under development, the detailed molecular mechanisms underlying the pathogenesis of this disease are yet to be elucidated to design future therapeutic tools against SARS-CoV-2 variants. MicroRNAs (miRNAs) are small (20-24 nucleotides), non-coding RNA molecules that regulate post-transcriptional gene expression. Recently, it has been demonstrated that both host and viral-encoded miRNAs are crucial for the successful infection of SARS-CoV-2. For instance, dysregulation of miRNAs that modulate multiple genes expressed in COVID-19 patients with comorbidities (e.g., type 2 diabetes, lung adenocarcinoma, and cerebrovascular disorders) could affect the severity of the disease. Thus, altered expression levels of circulating miRNAs might be helpful to diagnose this illness and forecast whether a COVID-19 patient could develop a severe state of the disease. Besides, researchers have found a number of miRNAs could inhibit the expression of proteins, such as ACE2, TMPRSS2, spike, and Nsp12, involved in the life cycle of SARS-CoV-2. Accordingly, miRNAs represent potential biomarkers and therapeutic targets for this devastating viral disease. Therefore, in this current review, we present the recent discoveries regarding the clinical relevance and biological roles of miRNAs in COVID-19.
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Fresco-Taboada A, García-Durán M, Aira C, López L, Sastre P, van der Hoek L, van Gils MJ, Brouwer PJ, Sanders RW, Holzer B, Zimpernikc I, López-Collazo E, Muñoz P, Rueda P, Vela C. Diagnostic performance of two serological assays for the detection of SARS-CoV-2 specific antibodies: surveillance after vaccination. Diagn Microbiol Infect Dis 2022; 102:115650. [PMID: 35218991 PMCID: PMC8789399 DOI: 10.1016/j.diagmicrobio.2022.115650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023]
Abstract
Massive vaccination programs are being carried out to limit the SARS-CoV-2 pandemic that started in December 2019. Serological tests are of major importance as an indicator of circulation of the virus and to assess how vaccine-induced immunity progresses. An Enzyme-Linked Immunosorbent Assay (ELISA) and a Lateral Flow Assay (LFA) have been developed based on the SARS-CoV-2 recombinant Receptor Binding Domain (RBD) and the combination of Spike and Nucleoprotein, respectively. The validation with 1272 serum samples by comparison with INgezim COVID 19 DR showed good diagnostic performance (sensitivity: 93.2%-97.2%; specificity: 98.3%-99.3%) for detection of previous contact with SARS-CoV-2. Moreover, according to our results, these assays can help in the serosurveillance during and after vaccination, by detecting the humoral immune response as soon as 15 days postvaccination and identifying low-respondents. Hence, these tests could play a key role in the progression to a COVID-19 free world, helping to adjust future vaccination protocols.
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Shahzamani K, Mahmoudian F, Ahangarzadeh S, Ranjbar MM, Beikmohammadi L, Bahrami S, Mohammadi E, Esfandyari S, Alibakhshi A, Javanmard SH. Vaccine design and delivery approaches for COVID-19. Int Immunopharmacol 2021; 100:108086. [PMID: 34454291 PMCID: PMC8380485 DOI: 10.1016/j.intimp.2021.108086] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/23/2022]
Abstract
COVID-19 is still a deadly disease that remains yet a major challenge for humans. In recent times, many large pharmaceutical and non-pharmaceutical companies have invested a lot of time and cost in fighting this disease. In this regard, today's scientific knowledge shows that designing and producing an effective vaccine is the best possible way to diminish the disease burden and dissemination or even eradicate the disease. Due to the urgent need, many vaccines are now available earlier than scheduled. New technologies have also helped to produce much more effective vaccines, although the potential side effects must be taken into account. Thus, in this review, the types of vaccines and vaccine designs made against COVID-19, the vaccination programs, as well as the delivery methods and molecules that have been used to deliver some vaccines that need a carrier will be described.
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Affiliation(s)
- Kiana Shahzamani
- Isfahan Gastroenterology and Hepatology Research Center (lGHRC), Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahrzad Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Mehdi Ranjbar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Leila Beikmohammadi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, the Netherlands; Stem Cell and Regenerative Medicine Center of Excellence, Tehran University of Medical Sciences, 14155-6559 Tehran, Iran
| | - Samira Bahrami
- Biotechnology Department, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Elmira Mohammadi
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, Isfahan University of Medical Sciences, Isfahan, Iran; Core Research Facilities, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sahar Esfandyari
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Alibakhshi
- Molecular Medicine Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Shaghayegh Haghjooy Javanmard
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, Isfahan University of Medical Sciences, Isfahan, Iran.
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