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Sarvmeili J, Baghban Kohnehrouz B, Gholizadeh A, Shanehbandi D, Ofoghi H. Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer. Sci Rep 2024; 14:10297. [PMID: 38704475 PMCID: PMC11069592 DOI: 10.1038/s41598-024-61025-2] [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: 11/13/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.
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Affiliation(s)
- Javad Sarvmeili
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 51666, Iran
| | | | - Ashraf Gholizadeh
- Department of Animal Biology, University of Tabriz, Tabriz, 51666, Iran
| | - Dariush Shanehbandi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 51666, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, 33131, Iran
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2
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Ray P, Ledgerwood-Lee M, Brickner H, Clark AE, Garretson A, Graham R, Van Zant W, Carlin AF, Aronoff-Spencer ES. Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels. Viruses 2024; 16:662. [PMID: 38793544 PMCID: PMC11125937 DOI: 10.3390/v16050662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 05/26/2024] Open
Abstract
The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.
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Affiliation(s)
- Partha Ray
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Melissa Ledgerwood-Lee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Howard Brickner
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Alex E. Clark
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron Garretson
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Rishi Graham
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Westley Van Zant
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Eliah S. Aronoff-Spencer
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
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3
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Hakim MS, Gunadi, Rahayu A, Wibawa H, Eryvinka LS, Supriyati E, Vujira KA, Iskandar K, Afiahayati, Daniwijaya EW, Oktoviani FN, Annisa L, Utami FDT, Amadeus VC, Nurhidayah SS, Leksono TP, Halim FV, Arguni E, Nuryastuti T, Wibawa T. Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia. Virus Genes 2024:10.1007/s11262-023-02048-1. [PMID: 38244104 DOI: 10.1007/s11262-023-02048-1] [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: 06/25/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
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Affiliation(s)
- Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendra Wibawa
- Disease Investigation Center Wates, Directorate General of Livestok Services, Ministry of Agriculture, Yogyakarta, Indonesia
| | - Laudria Stella Eryvinka
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Khanza Adzkia Vujira
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kristy Iskandar
- Department of Child Health and Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Farida Nur Oktoviani
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Luthvia Annisa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Setiani Silvy Nurhidayah
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tiara Putri Leksono
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery and Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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4
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Yadav V, Ravichandran S. Significance of understanding the genomics of host-pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic. Brief Funct Genomics 2024; 23:69-74. [PMID: 36722037 DOI: 10.1093/bfgp/elad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The entire world is facing the stiff challenge of COVID-19 pandemic. To overcome the spread of this highly infectious disease, several short-sighted strategies were adopted such as the use of broad-spectrum antibiotics and antifungals. However, the misuse and/or overuse of antibiotics have accentuated the emergence of the next pandemic: antimicrobial resistance (AMR). It is believed that pathogens while transferring between humans and the environment carry virulence and antibiotic-resistant factors from varied species. It is presumed that all such genetic factors are quantifiable and predictable, a better understanding of which could be a limiting step for the progression of AMR. Herein, we have reviewed how genomics-based understanding of host-pathogen interactions during COVID-19 could reduce the non-judicial use of antibiotics and prevent the eruption of an AMR-based pandemic in future.
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Affiliation(s)
- Vikas Yadav
- Department of Translational Medicine, Clinical Research Centre, Skaone University Hospital, Lund University, Malmo SE-20213, Sweden
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5
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Islam MA, Marzan AA, Arman MS, Shahi S, Sakif TI, Hossain M, Islam T, Hoque MN. Some common deleterious mutations are shared in SARS-CoV-2 genomes from deceased COVID-19 patients across continents. Sci Rep 2023; 13:18644. [PMID: 37903828 PMCID: PMC10616235 DOI: 10.1038/s41598-023-45517-1] [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: 06/19/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
The identification of deleterious mutations in different variants of SARS-CoV-2 and their roles in the morbidity of COVID-19 patients has yet to be thoroughly investigated. To unravel the spectrum of mutations and their effects within SARS-CoV-2 genomes, we analyzed 5,724 complete genomes from deceased COVID-19 patients sourced from the GISAID database. This analysis was conducted using the Nextstrain platform, applying a generalized time-reversible model for evolutionary phylogeny. These genomes were compared to the reference strain (hCoV-19/Wuhan/WIV04/2019) using MAFFT v7.470. Our findings revealed that SARS-CoV-2 genomes from deceased individuals belonged to 21 Nextstrain clades, with clade 20I (Alpha variant) being the most predominant, followed by clade 20H (Beta variant) and clade 20J (Gamma variant). The majority of SARS-CoV-2 genomes from deceased patients (33.4%) were sequenced in North America, while the lowest percentage (0.98%) came from Africa. The 'G' clade was dominant in the SARS-CoV-2 genomes of Asian, African, and North American regions, while the 'GRY' clade prevailed in Europe. In our analysis, we identified 35,799 nucleotide (NT) mutations throughout the genome, with the highest frequency (11,402 occurrences) found in the spike protein. Notably, we observed 4150 point-specific amino acid (AA) mutations in SARS-CoV-2 genomes, with D614G (20%) and N501Y (14%) identified as the top two deleterious mutations in the spike protein on a global scale. Furthermore, we detected five common deleterious AA mutations, including G18V, W45S, I33T, P30L, and Q418H, which play a key role in defining each clade of SARS-CoV-2. Our novel findings hold potential value for genomic surveillance, enabling the monitoring of the evolving pattern of SARS-CoV-2 infection, its emerging variants, and their impact on the development of effective vaccination and control strategies.
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Affiliation(s)
- Md Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, 2310, Bangladesh.
- COVID-19 Diagnostic Lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Abdullah Al Marzan
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj, Kishoreganj, 2310, Bangladesh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Sakil Arman
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shatila Shahi
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, 26506-6109, USA
| | - Maqsud Hossain
- University of Nottingham, Sutton Bonington Campus, LE12 5RD, Loughborough, NG7 2RD, Leicestershire, UK
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - M Nazmul Hoque
- Molecular Biology and Bioinformatics Laboratory, Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
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6
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Cecchetto R, Tonon E, Medaina N, Turri G, Diani E, Piccaluga PP, Salomoni A, Conti M, Tacconelli E, Lagni A, Lotti V, Favarato M, Gibellini D. Detection of SARS-CoV-2 Δ426 ORF8 Deletion Mutant Cluster in NGS Screening. Microorganisms 2023; 11:2378. [PMID: 37894036 PMCID: PMC10609088 DOI: 10.3390/microorganisms11102378] [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: 08/02/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Next-generation sequencing (NGS) from SARS-CoV-2-positive swabs collected during the last months of 2022 revealed a large deletion spanning ORF7b and ORF8 (426 nt) in six patients infected with the BA.5.1 Omicron variant. This extensive genome loss removed a large part of these two genes, maintaining in frame the first 22 aminoacids of ORF7b and the last three aminoacids of ORF8. Interestingly, the deleted region was flanked by two small repeats, which were likely involved in the formation of a hairpin structure. Similar rearrangements, comparable in size and location to the deletion, were also identified in 15 sequences in the NCBI database. In this group, seven out of 15 cases from the USA and Switzerland presented both the BA.5.1 variant and the same 426 nucleotides deletion. It is noteworthy that three out of six cases were detected in patients with immunodeficiency, and it is conceivable that this clinical condition could promote the replication and selection of these mutations.
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Affiliation(s)
- Riccardo Cecchetto
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Emil Tonon
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Nicoletta Medaina
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Giona Turri
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
| | - Erica Diani
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
| | - Pier Paolo Piccaluga
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, Bologna University, 40126 Bologna, Italy;
| | - Angela Salomoni
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, 35020 Padua, Italy;
| | - Michela Conti
- Infectious Diseases Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (M.C.); (E.T.)
| | - Evelina Tacconelli
- Infectious Diseases Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (M.C.); (E.T.)
| | - Anna Lagni
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
| | - Virginia Lotti
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
| | - Mosé Favarato
- Molecular Diagnostics and Genetics, AULSS 3 Serenissima, 30174 Venice, Italy;
| | - Davide Gibellini
- Microbiology Section, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy; (R.C.); (E.T.); (A.L.); (V.L.); (D.G.)
- UOC Microbiology Unit, AOUI Verona, 37134 Verona, Italy; (N.M.); (G.T.)
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7
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Yang S, Multani A, Garrigues JM, Oh MS, Hemarajata P, Burleson T, Green NM, Oliai C, Gaynor PT, Beaird OE, Winston DJ, Seet CS, Schaenman JM. Transient SARS-CoV-2 RNA-Dependent RNA Polymerase Mutations after Remdesivir Treatment for Chronic COVID-19 in Two Transplant Recipients: Case Report and Intra-Host Viral Genomic Investigation. Microorganisms 2023; 11:2096. [PMID: 37630656 PMCID: PMC10460003 DOI: 10.3390/microorganisms11082096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Remdesivir is the first FDA-approved drug for treating severe SARS-CoV-2 infection and targets RNA-dependent RNA polymerase (RdRp) that is required for viral replication. To monitor for the development of mutations that may result in remdesivir resistance during prolonged treatment, we sequenced SARS-CoV-2 specimens collected at different treatment time points in two transplant patients with severe COVID-19. In the first patient, an allogeneic hematopoietic stem cell transplant recipient, a transient RdRp catalytic subunit mutation (nsp12:A449V) was observed that has not previously been associated with remdesivir resistance. As no in vitro study had been conducted to elucidate the phenotypic effect of nsp12:A449V, its clinical significance is unclear. In the second patient, two other transient RdRp mutations were detected: one in the catalytic subunit (nsp12:V166A) and the other in an accessory subunit important for processivity (nsp7:D67N). This is the first case report for a potential link between the nsp12:V166A mutation and remdesivir resistance in vivo, which had only been previously described by in vitro studies. The nsp7:D67N mutation has not previously been associated with remdesivir resistance, and whether it has a phenotypic effect is unknown. Our study revealed SARS-CoV-2 genetic dynamics during remdesivir treatment in transplant recipients that involved mutations in the RdRp complex (nsp7 and nsp12), which may be the result of selective pressure. These results suggest that close monitoring for potential resistance during the course of remdesivir treatment in highly vulnerable patient populations may be beneficial. Development and utilization of diagnostic RdRp genotyping tests may be a future direction for improving the management of chronic COVID-19.
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Affiliation(s)
- Shangxin Yang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Ashrit Multani
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
| | - Jacob M. Garrigues
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Michael S. Oh
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Peera Hemarajata
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Taylor Burleson
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Nicole M. Green
- Public Health Laboratories, Los Angeles County Department of Public Health, Downey, CA 90242, USA (P.H.); (T.B.); (N.M.G.)
| | - Caspian Oliai
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Pryce T. Gaynor
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
| | - Omer E. Beaird
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
| | - Drew J. Winston
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Christopher S. Seet
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (M.S.O.); (C.O.); (D.J.W.)
| | - Joanna M. Schaenman
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; (A.M.); (P.T.G.); (O.E.B.)
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8
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Ndiaye AJS, Beye M, Lo G, Kacel I, Sow A, Leye N, Padane A, Mboup A, Diop-Ndiaye H, Sokhna C, Kane CT, Colson P, Fenollar F, Mboup S, Fournier PE. Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal. Viruses 2023; 15:1233. [PMID: 37376533 DOI: 10.3390/v15061233] [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: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.
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Affiliation(s)
- Anna Julienne Selbé Ndiaye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Mamadou Beye
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Gora Lo
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Idir Kacel
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
| | - Aissatou Sow
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Nafissatou Leye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Abdou Padane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Aminata Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Halimatou Diop-Ndiaye
- Laboratoire Bactériologie-Virologie, Hôpital Aristide Le Dantec, Dakar 3001, Senegal
| | - Cheikh Sokhna
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar 1386, Senegal
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
| | - Coumba Touré Kane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Philippe Colson
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France
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9
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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10
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Nyagupe C, de Oliveira Martins L, Gumbo H, Mashe T, Takawira T, Maeka KK, Juru A, Chikanda LK, Tauya AR, Page AJ, Kingsley RA, Simbi R, Chirenda J, Manasa J, Ruhanya V, Mavenyengwa RT. SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis. S Afr Med J 2023; 113:141-147. [PMID: 36876349 DOI: 10.7196/samj.2023.v113i3.16762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND SARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccinescaused by inequitable distribution. OBJECTIVE To monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health. METHODS Here we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples weresequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed. RESULTS The Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acidsubstitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previousinfection or vaccination. CONCLUSION There were nine lineages circulating in Zimbabwe during the second wave. The B.1.351 was dominant, accounting for >75%.There were over 3 000 mutations on the diagnostic genes and lineage B.1.351, contributing almost two-thirds of the mutations. The S-genehad the most mutations and the E-gene was the least mutated.
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Affiliation(s)
- C Nyagupe
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | | | - H Gumbo
- National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | - T Mashe
- National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | - T Takawira
- National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | - K K Maeka
- National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | - A Juru
- National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | - L K Chikanda
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.
| | - A R Tauya
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.
| | - A J Page
- Quadram Institute Bioscience, Norwich, UK.
| | | | - R Simbi
- Directorate of Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe.
| | - J Chirenda
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.
| | - J Manasa
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.
| | - V Ruhanya
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.
| | - R T Mavenyengwa
- Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe.
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11
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Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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12
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Abdelmalick A, Sehli S, Idrissi Azami A, Habib N, Al Idrissi N, Belyamani L, Houmeida A, Ghazal H. Genomic Evidence of Multiple Introductions of SARS-CoV-2 in Mauritania. Bioinform Biol Insights 2023; 17:11779322231167927. [PMID: 37124130 PMCID: PMC10130938 DOI: 10.1177/11779322231167927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/05/2023] [Indexed: 05/02/2023] Open
Abstract
The rapid and global spread of the novel coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has raised serious public health concerns, including in Mauritania. We sequenced and analyzed the entire genome of 13 SARS-CoV-2 virus strains isolated from polymerase chain reaction (PCR)-positive symptomatic patients sampled from March 3 to May 31, 2021 to better understand SARS-CoV-2 introduction, propagation, and evolution in Mauritania. A phylogenetic tree using available data from the EpiCoV GISAID database and a variant network with non-Mauritanian sequences were constructed. Variant analysis of the 13 Mauritanian SARS-CoV-2 genome sequences indicated an average mutational percentage of 0.39, which is similar to that in other countries. Phylogenetic analysis revealed multiple spatiotemporal introductions, mainly from Europe (France, Belgium) and Africa (Senegal, Côte d'Ivoire), which also provided evidence of early community transmission. A total of 2 unique mutations, namely, NSP6_Q208K and NSP15_S273T, were detected in the NSP6 and NSP15 genes, respectively, confirming the aforementioned introduction of SARS-CoV-2 in Mauritania. These findings highlight the relevance of continuous genomic monitoring strategies for understanding virus transmission dynamics and acquiring knowledge to address forthcoming sources of infection in Africa.
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Affiliation(s)
| | - Sofia Sehli
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Abdellah Idrissi Azami
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Nihal Habib
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
| | - Najib Al Idrissi
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Cheikh Khalifa International University Hospital, Casablanca, Morocco
| | - Lahcen Belyamani
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Ahmed Houmeida
- Faculty of Science and Technology, University of Nouakchott, Nouakchott, Mauritania
| | - Hassan Ghazal
- Laboratory of Genomics, Bioinformatics and Digital Health, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Mohammed VI Center for Research and Innovation, Rabat, Morocco
- National Center for Scientific and Technical Research (CNRST), Scientific Departement, Rabat, Morocco
- Hassan Ghazal, National Center for Scientific and Technical Research (CNRST), Angle avenues des FAR et Allal El Fassi, Hay Ryad, B.P. 8027 N.U, Rabat 10102, Morocco.
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13
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Ghosh N, Saha I, Sharma N, Nandi S. Bioinformatics pipeline unveils genetic variability to synthetic vaccine design for Indian SARS-CoV-2 genomes. Int Immunopharmacol 2022; 112:109224. [PMID: 36116149 PMCID: PMC9444899 DOI: 10.1016/j.intimp.2022.109224] [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: 06/24/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022]
Abstract
In the worrisome scenarios of various waves of SARS-CoV-2 pandemic, a comprehensive bioinformatics pipeline is essential to analyse the virus genomes in order to understand its evolution, thereby identifying mutations as signature SNPs, conserved regions and subsequently to design epitope based synthetic vaccine. We have thus performed multiple sequence alignment of 4996 Indian SARS-CoV-2 genomes as a case study using MAFFT followed by phylogenetic analysis using Nextstrain to identify virus clades. Furthermore, based on the entropy of each genomic coordinate of the aligned sequences, conserved regions are identified. After refinement of the conserved regions, based on its length, one conserved region is identified for which the primers and probes are reported for virus detection. The refined conserved regions are also used to identify T-cell and B-cell epitopes along with their immunogenic and antigenic scores. Such scores are used for selecting the most immunogenic and antigenic epitopes. By executing this pipeline, 40 unique signature SNPs are identified resulting in 23 non-synonymous signature SNPs which provide 28 amino acid changes in protein. On the other hand, 12 conserved regions are selected based on refinement criteria out of which one is selected as the potential target for virus detection. Additionally, 22 MHC-I and 21 MHC-II restricted T-cell epitopes with 10 unique HLA alleles each and 17 B-cell epitopes are obtained for 12 conserved regions. All the results are validated both quantitatively and qualitatively which show that from genetic variability to synthetic vaccine design, the proposed pipeline can be used effectively to combat SARS-CoV-2.
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Affiliation(s)
- Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Suman Nandi
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India
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14
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Brault A, Néré R, Prados J, Boudreault S, Bisaillon M, Marchand P, Couture P, Labbé S. Cellulosic copper nanoparticles and a hydrogen peroxide-based disinfectant trigger rapid inactivation of pseudoviral particles expressing the Spike protein of SARS-CoV-2, SARS-CoV, and MERS-CoV. Metallomics 2022; 14:mfac044. [PMID: 35731587 DOI: 10.1093/mtomcs/mfac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a viral respiratory infection caused by human coronaviruses that include SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV). Although their primary mode of transmission is through contaminated respiratory droplets from infected carriers, the deposition of expelled virus particles onto surfaces and fomites could contribute to viral transmission. Here, we use replication-deficient murine leukemia virus (MLV) pseudoviral particles expressing SARS-CoV-2, SARS-CoV, or MERS-CoV Spike (S) protein on their surface. These surrogates of native coronavirus counterparts serve as a model to analyze the S-mediated entry into target cells. Carboxymethyl cellulose (CMC) nanofibers that are combined with copper (Cu) exhibit strong antimicrobial properties. S-pseudovirions that are exposed to CMC-Cu nanoparticles (30 s) display a dramatic reduction in their ability to infect target Vero E6 cells, with ∼97% less infectivity as compared to untreated pseudovirions. In contrast, addition of the Cu chelator tetrathiomolybdate protects S-pseudovirions from CMC-Cu-mediated inactivation. When S-pseudovirions were treated with a hydrogen peroxide-based disinfectant (denoted SaberTM) used at 1:250 dilution, their infectivity was dramatically reduced by ∼98%. However, the combined use of SaberTM and CMC-Cu is the most effective approach to restrict infectivity of SARS-CoV-2-S, SARS-CoV-S, and MERS-CoV-S pseudovirions in Vero E6 cell assays. Together, these results show that cellulosic Cu nanoparticles enhance the effectiveness of diluted SaberTM sanitizer, setting up an improved strategy to lower the risk of surface- and fomite-mediated transmission of enveloped respiratory viruses.
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Affiliation(s)
- Ariane Brault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Raphael Néré
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Jérôme Prados
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Simon Boudreault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Martin Bisaillon
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | | | | | - Simon Labbé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
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15
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Cooksey R, Underwood J, Brophy S, Atkinson M, Kennedy J, Choy E. Shielding reduced incidence of COVID-19 in patients with inflammatory arthritis but vulnerability is associated with increased mortality. Rheumatology (Oxford) 2022; 61:SI120-SI128. [PMID: 35567479 PMCID: PMC9248059 DOI: 10.1093/rheumatology/keac283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Investigate whether individuals with inflammatory arthritis (IA), their treatments and shielding status affect the risk of adverse outcomes from COVID-19 for the entire population of Wales, UK. METHODS Retrospective, population-based cohort study using linked, anonymized electronic health data from SAIL Databank, including primary/secondary care, rheumatology, Office for National Statistics Mortality and COVID-19 laboratory data. Individuals aged 18 years and over testing positive for COVID-19 between March 2020 and May 2021 with READ Codes present for rheumatoid arthritis, psoriatic arthritis and ankylosing spondylitis formed the study cases. RESULTS A total of 1966 people with IA and 166 602 without tested positive for COVID-19. The incidence rate was 3.5% (1966/56 914) in IA, vs 6% in the general population (166 602/2 760 442), (difference: 2.5%, 95% CI: 2.4%, 2.7%, P ≤0.001). In an adjusted Cox proportional hazard model, IA was not associated with higher mortality (HR: 0.56, 95% CI: 0.18, 1.64, P=0.286). Significant risk factors included shielding (HR: 1.52, 95% CI: 1.40, 1.64, P ≤0.001), hospitalization for previous infections (HR: 1.20, 95% CI: 1.12, 1.28, P ≤0.001), hospitalizations one year pre-pandemic (HR: 1.34, 95% CI: 1.25, 1.44, P ≤0.001) and glucocorticoid use (HR: 1.17, 95% CI: 1.09, 1.25, P ≤0.001). CONCLUSIONS Individuals with IA had a lower incidence of COVID-19, probably due to shielding. IA was not associated with increased mortality following COVID-19 infection; being vulnerable (shielded), comorbidities and other factors were associated with increased risk. These key risk factors can identify individuals with IA at greater risk from COVID-19 and advised to shield during high community prevalence.
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Affiliation(s)
- Roxanne Cooksey
- CREATE Centre, Section of Rheumatology, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff
- National Centre for Population Health and Wellbeing Research
| | - Jonathan Underwood
- CREATE Centre, Section of Rheumatology, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff
- School of Medicine, Heath Park Campus, Cardiff
| | - Sinead Brophy
- School of Medicine, Heath Park Campus, Cardiff
- Health Data Research UK, Data Science Building, Swansea University Medical School, Swansea, UK
| | - Mark Atkinson
- School of Medicine, Heath Park Campus, Cardiff
- Health Data Research UK, Data Science Building, Swansea University Medical School, Swansea, UK
| | - Jonathan Kennedy
- School of Medicine, Heath Park Campus, Cardiff
- Health Data Research UK, Data Science Building, Swansea University Medical School, Swansea, UK
| | - Ernest Choy
- CREATE Centre, Section of Rheumatology, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff
- National Centre for Population Health and Wellbeing Research
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16
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Sia BZ, Boon WX, Yap YY, Kumar S, Ng CH. Prediction of the effects of the top 10 nonsynonymous variants from 30229 SARS-CoV-2 strains on their proteins. F1000Res 2022; 11:9. [PMID: 35707000 PMCID: PMC9184924 DOI: 10.12688/f1000research.72904.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2022] [Indexed: 12/23/2022] Open
Abstract
Background: SARS-CoV-2 virus is a highly transmissible pathogen that causes COVID-19. The outbreak originated in Wuhan, China in December 2019. A number of nonsynonymous mutations located at different SARS-CoV-2 proteins have been reported by multiple studies. However, there are limited computational studies on the biological impacts of these mutations on the structure and function of the proteins. Methods: In our study nonsynonymous mutations of the SARS-CoV-2 genome and their frequencies were identified from 30,229 sequences. Subsequently, the effects of the top 10 highest frequency nonsynonymous mutations of different SARS-CoV-2 proteins were analyzed using bioinformatics tools including co-mutation analysis, prediction of the protein structure stability and flexibility analysis, and prediction of the protein functions. Results: A total of 231 nonsynonymous mutations were identified from 30,229 SARS-CoV-2 genome sequences. The top 10 nonsynonymous mutations affecting nine amino acid residues were ORF1a nsp5 P108S, ORF1b nsp12 P323L and A423V, S protein N501Y and D614G, ORF3a Q57H, N protein P151L, R203K and G204R. Many nonsynonymous mutations showed a high concurrence ratio, suggesting these mutations may evolve together and interact functionally. Our result showed that ORF1a nsp5 P108S, ORF3a Q57H and N protein P151L mutations may be deleterious to the function of SARS-CoV-2 proteins. In addition, ORF1a nsp5 P108S and S protein D614G may destabilize the protein structures while S protein D614G may have a more open conformation compared to the wild type. Conclusion: The biological consequences of these nonsynonymous mutations of SARS-CoV-2 proteins should be further validated by in vivo and in vitro experimental studies in the future.
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Affiliation(s)
- Boon Zhan Sia
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Wan Xin Boon
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Yoke Yee Yap
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Shalini Kumar
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
| | - Chong Han Ng
- Faculty of Information Science and Technology, Multimedia University, Bukit Beruang, Melaka, 75450, Malaysia
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17
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Yavarian J, Nejati A, Salimi V, Shafiei Jandaghi NZ, Sadeghi K, Abedi A, Sharifi Zarchi A, Gouya MM, Mokhtari-Azad T. Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic. PLoS One 2022; 17:e0267847. [PMID: 35499994 PMCID: PMC9060343 DOI: 10.1371/journal.pone.0267847] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/14/2022] [Indexed: 12/23/2022] Open
Abstract
Purpose Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. Results During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd wave were GH and GR. In the fourth wave GRY (alpha variant), GK (delta variant) and one GH clade (beta variant) were detected. All viruses in the fifth wave were in clade GK (delta variant). There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. Conclusions These findings display the significance of SARS-CoV2 monitoring to help on time detection of possible variants for pandemic control and vaccination plans.
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Affiliation(s)
- Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Adel Abedi
- Mathematics Department, Shahid Beheshti University, Tehran, Iran
| | - Ali Sharifi Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | | | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- * E-mail:
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Okeke ES, Olovo CV, Nkwoemeka NE, Okoye CO, Nwankwo CEI, Onu CJ. Microbial ecology and evolution is key to pandemics: using the coronavirus model to mitigate future public health challenges. Heliyon 2022; 8:e09449. [PMID: 35601228 PMCID: PMC9113781 DOI: 10.1016/j.heliyon.2022.e09449] [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: 09/23/2021] [Revised: 01/03/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. The recent coronavirus model was used to study issues leading to microbial evolution, towards preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious diseases.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences and Environmental Biology, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, 212013, PR China
| | - Chinasa Valerie Olovo
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University Zhenjiang, 212013, Jiangsu, PR China
| | - Ndidi Ethel Nkwoemeka
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
| | - Charles Obinwanne Okoye
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Biofuels Institute, School of Environment and Safety Engineering Jiangsu University, Zhenjiang, 212013, China
| | - Chidiebele Emmanuel Ikechukwu Nwankwo
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 400001, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
| | - Chisom Joshua Onu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, 400001, Enugu State, Nigeria
- Department of Biological Sciences, College of Liberal Arts and Sciences, Detroit, Michigan, 48202, USA
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19
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De Marco C, Marascio N, Veneziano C, Biamonte F, Trecarichi EM, Santamaria G, Leviyang S, Liberto MC, Mazzitelli M, Quirino A, Longhini F, Torella D, Quattrone A, Matera G, Torti C, Costanzo FS, Viglietto G. Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. INFECTION, GENETICS AND EVOLUTION 2022; 99:105253. [PMID: 35189404 PMCID: PMC8855624 DOI: 10.1016/j.meegid.2022.105253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/16/2022] [Indexed: 12/23/2022]
Abstract
Background Nursing homes have represented important hotspots of viral spread during the initial wave of COVID-19 pandemics. The proximity of patients inside nursing homes allows investigate the dynamics of viral transmission, which may help understand SARS-Cov2 biology and spread. Methods SARS-CoV-2 viral genomes obtained from 46 patients infected in an outbreak inside a nursing home in Calabria region (South Italy) were analyzed by Next Generation Sequencing. We also investigated the evolution of viral genomes in 8 patients for which multiple swabs were available. Phylogenetic analysis and haplotype reconstruction were carried out with IQ-TREE software and RegressHaplo tool, respectively. Results All viral strains isolated from patients infected in the nursing home were classified as B.1 lineage, clade G. Overall, 14 major single nucleotide variations (SNVs) (frequency > 80%) and 12 minor SNVs (frequency comprised between 20% and 80%) were identified with reference to the Wuhan-H-1 sequence (NC_045512.2). All patients presented the same 6 major SNVs: D614G in the S gene; P4715L, ntC3037T (F924F) and S5398P in Orf1ab gene; ntC26681T (F53F) in the M gene; and ntC241T in the non-coding UTR region. However, haplotype reconstruction identified a founder haplotype (Hap A) in 36 patients carrying only the 6 common SNVs indicated above, and 10 other haplotypes (Hap B—K) derived from Hap A in the remaining 10 patients. Notably, no significant association between a specific viral haplotype and clinical parameters was found. Conclusion The predominant viral strain responsible for the infection in a nursing home in Calabria was the B.1 lineage (clade G). Viral genomes were classified into 11 haplotypes (Hap A in 36 patients, Hap B—K in the remaining patients).
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Affiliation(s)
- Carmela De Marco
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Italy; Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Italy
| | - Nadia Marascio
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Italy
| | - Claudia Veneziano
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Italy; Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Italy
| | - Flavia Biamonte
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Italy; Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Italy
| | | | - Gianluca Santamaria
- Department of Medicine I Molecular Cardiology, Technical University of Munich, Munich, Germany
| | - Sivan Leviyang
- Department of Mathematics, Georgetown University, Washington, DC, USA
| | - Maria Carla Liberto
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Italy
| | | | - Angela Quirino
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Italy
| | - Federico Longhini
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Italy
| | - Daniele Torella
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Italy
| | - Aldo Quattrone
- Neuroscience Research Center, "Magna Graecia" University of Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Italy
| | - Francesco Saverio Costanzo
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Italy; Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Italy; "Mater Domini" University Hospital of Catanzaro, Italy.
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20
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Agwa SHA, Elghazaly H, El Meteini MS, Yahia YA, Khaled R, Abd Elsamee AM, Darwish RM, Elsayed SM, Hafez H, Mahmoud BS, EM F, Matboli M. Identifying SARS-CoV-2 Lineage Mutation Hallmarks and Correlating Them With Clinical Outcomes in Egypt: A Pilot Study. Front Mol Biosci 2022; 9:817735. [PMID: 35350713 PMCID: PMC8958014 DOI: 10.3389/fmolb.2022.817735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic has led to over 4.9 million deaths as of October 2021. One of the main challenges of creating vaccines, treatment, or diagnostic tools for the virus is its mutations and emerging variants. A couple of variants were declared as more virulent and infectious than others. Some approaches were used as nomenclature for SARS-CoV-2 variants and lineages. One of the most used is the Pangolin nomenclature. In our study, we enrolled 35 confirmed SARS-CoV-2 patients and sequenced the viral RNA in their samples. We also aimed to highlight the hallmark mutations in the most frequent lineage. We identified a seven-mutation signature for the SARS-CoV-2 C36 lineage, detected in 56 countries and an emerging lineage in Egypt. In addition, we identified one mutation which was highly negatively correlated with the lineage. On the other hand, we found no significant correlation between our clinical outcomes and the C36 lineage. In conclusion, the C36 lineage is an emerging SARS-CoV-2 variant that needs more investigation regarding its clinical outcomes compared to other strains. Our study paves the way for easier diagnosis of variants of concern using mutation signatures.
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Affiliation(s)
- Sara H. A. Agwa
- Clinical Pathology and Molecular Genomics Unit of Medical Ain Shams Research Institute (MASRI), Faculty of Medicine, Ain Shams University, Cairo, Egypt
- *Correspondence: Sara H. A. Agwa, ; Marwa Matboli,
| | - Hesham Elghazaly
- Oncology Department, Medical Ain Shams Research Institute (MASRI), Cairo, Egypt
| | - Mahmoud Shawky El Meteini
- Department of General Surgery, The School of Medicine, University of Ain Shams, Abbassia, Cairo, Egypt
| | - Yahia A. Yahia
- Biochemistry Department, Faculty of Pharmacy, Misr University for Science and Technology, Giza, Egypt
| | - Radwa Khaled
- Biotechnology/Biomolecular Chemistry Program, Faculty of Science, Cairo University, Cairo, Egypt
- Biochemistry Department, Faculty of Medicine, Modern University for Technology and Information, Cairo, Egypt
| | - Aya M. Abd Elsamee
- Biochemistry and Molecular Genomics Unit of Medical Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Reham M. Darwish
- Biochemistry and Molecular Genomics Unit of Medical Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Shaimaa M. Elsayed
- Biochemistry and Molecular Genomics Unit of Medical Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hala Hafez
- Clinical Pathology Department, Infection Control Unit, University of Ain Shams, Cairo, Egypt
| | - Basma S. Mahmoud
- Clinical Pathology Department, Infection Control Unit, University of Ain Shams, Cairo, Egypt
| | - Fouda EM
- Pediatric Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marwa Matboli
- Medicinal Biochemistry and Molecular Biology Department, Faculty of Medicine, University of Ain Shams, Cairo, Egypt
- *Correspondence: Sara H. A. Agwa, ; Marwa Matboli,
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Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Microbiol Spectr 2022; 10:e0151121. [PMID: 35171035 PMCID: PMC8849062 DOI: 10.1128/spectrum.01511-21] [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] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM.
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22
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Ghorbani A, Samarfard S, Jajarmi M, Bagheri M, Karbanowicz TP, Afsharifar A, Eskandari MH, Niazi A, Izadpanah K. Highlight of potential impact of new viral genotypes of SARS-CoV-2 on vaccines and anti-viral therapeutics. GENE REPORTS 2022; 26:101537. [PMID: 35128175 PMCID: PMC8808475 DOI: 10.1016/j.genrep.2022.101537] [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: 07/27/2021] [Revised: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease (COVID-19) pandemic, has infected millions of people globally. Genetic variation and selective pressures lead to the accumulation of single nucleotide polymorphism (SNP) within the viral genome that may affect virulence, transmission rate, viral recognition and the efficacy of prophylactic and interventional measures. To address these concerns at the genomic level, we assessed the phylogeny and SNPs of the SARS-CoV-2 mutant population collected to date in Iran in relation to globally reported variants. Phylogenetic analysis of mutant strains revealed the occurrence of the variants known as B.1.1.7 (Alpha), B.1.525 (Eta), and B.1.617 (Delta) that appear to have delineated independently in Iran. SNP analysis of the Iranian sequences revealed that the mutations were predominantly positioned within the S protein-coding region, with most SNPs localizing to the S1 subunit. Seventeen S1-localizing SNPs occurred in the RNA binding domain that interacts with ACE2 of the host cell. Importantly, many of these SNPs are predicted to influence the binding of antibodies and anti-viral therapeutics, indicating that the adaptive host response appears to be imposing a selective pressure that is driving the evolution of the virus in this closed population through enhancing virulence. The SNPs detected within these mutant cohorts are addressed with respect to current prophylactic measures and therapeutic interventions.
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Key Words
- ACE2, Angiotensin-converting enzyme 2
- Antiviral drugs
- Bioinformatics
- CSSE, Center for Systems Science and Engineering
- E, Envelope
- FP, Fusion peptide
- HR1, Heptad repeat 1
- HR2, Heptad repeat 2
- IC, Intracellular domain
- JHU, Johns Hopkins University
- M, Membrane
- Mutation detection
- N, Nucleocapsid
- NAG, N-acetylglucosamine
- NSP, Non-structural proteins
- NTD, N-terminal domain
- Phylogenetic analysis
- RBD, Receptor-binding domain
- S, Spike glycoprotein
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2;
- SD1, Subdomain 1
- SD2, Subdomain 2
- SNP, Single nucleotide polymorphism
- SP, Structural proteins
- TM, Transmembrane region
- UTRs, Untranslated regions
- Viral vaccines
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT 0828 Australia
| | - Maziar Jajarmi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahboube Bagheri
- Department of Food Science and Technology, Bardsir Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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Escobedo RA, Kaushal D, Singh DK. Insights Into the Changing Landscape of Coronavirus Disease 2019. Front Cell Infect Microbiol 2022; 11:761521. [PMID: 35083164 PMCID: PMC8784834 DOI: 10.3389/fcimb.2021.761521] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious, infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in late 2019 in Wuhan China. A year after the World Health Organization declared COVID-19 a global pandemic, over 215 million confirmed cases and approximately 5 million deaths have been reported worldwide. In this multidisciplinary review, we summarize important insights for COVID-19, ranging from its origin, pathology, epidemiology, to clinical manifestations and treatment. More importantly, we also highlight the foundational connection between genetics and the development of personalized medicine and how these aspects have an impact on disease treatment and management in the dynamic landscape of this pandemic.
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Affiliation(s)
- Ruby A. Escobedo
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
- The Integrated Biomedical Sciences (IBMS) Graduate Program, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Dhiraj K. Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
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24
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Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. EPMA J 2022; 13:149-175. [PMID: 35013687 PMCID: PMC8732965 DOI: 10.1007/s13167-021-00267-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022]
Abstract
Aims The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein–protein interface. Results Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike “boat-shaped” receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the “stern” or “bow” regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the “hull” region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00267-w.
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25
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Durand M, Thibault P, Lévesque S, Brault A, Carignan A, Valiquette L, Martin P, Labbé S. Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its first variants in fourplex real-time quantitative reverse transcription-PCR assays. MICROBIAL CELL (GRAZ, AUSTRIA) 2022; 9:1-20. [PMID: 35083313 PMCID: PMC8717086 DOI: 10.15698/mic2022.01.767] [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: 09/20/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 11/23/2022]
Abstract
The early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is required to identify and isolate contagious patients to prevent further transmission of SARS-CoV-2. In this study, we present a multitarget real-time TaqMan reverse transcription PCR (rRT-PCR) assay for the quantitative detection of SARS-CoV-2 and some of its circulating variants harboring mutations that give the virus a selective advantage. Seven different primer-probe sets that included probes containing locked nucleic acid (LNA) nucleotides were designed to amplify specific wild-type and mutant sequences in Orf1ab, Envelope (E), Spike (S), and Nucleocapsid (N) genes. Furthermore, a newly developed primer-probe set targeted human β2-microglobulin (B2M) as a highly sensitive internal control for RT efficacy. All singleplex and fourplex assays detected ≤ 14 copies/reaction of quantified synthetic RNA transcripts, with a linear amplification range of nine logarithmic orders. Primer-probe sets for detection of SARS-CoV-2 exhibited no false-positive amplifications with other common respiratory pathogens, including human coronaviruses NL63, 229E, OC43, and HKU-1. Fourplex assays were evaluated using 160 clinical samples positive for SARS-CoV-2. Results showed that SARS-CoV-2 viral RNA was detected in all samples, including viral strains harboring mutations in the Spike coding sequence that became dominant in the pandemic. Given the emergence of SARS-CoV-2 variants and their rapid spread in some populations, fourplex rRT-PCR assay containing four primer-probe sets represents a reliable approach to allow quicker detection of circulating relevant variants in a single reaction.
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Affiliation(s)
- Mathieu Durand
- Plateforme RNomique et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe Thibault
- Plateforme RNomique et de Génomique Fonctionnelle, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon Lévesque
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada.,Laboratoire de Microbiologie, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) de l'Estrie, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Ariane Brault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alex Carignan
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Louis Valiquette
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Philippe Martin
- Département de Microbiologie et d'Infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon Labbé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
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26
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Saha I, Ghosh N, Sharma N, Nandi S. Hotspot Mutations in SARS-CoV-2. Front Genet 2021; 12:753440. [PMID: 34912372 PMCID: PMC8667557 DOI: 10.3389/fgene.2021.753440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/07/2021] [Indexed: 12/23/2022] Open
Abstract
Since its emergence in Wuhan, China, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread very rapidly around the world, resulting in a global pandemic. Though the vaccination process has started, the number of COVID-affected patients is still quite large. Hence, an analysis of hotspot mutations of the different evolving virus strains needs to be carried out. In this regard, multiple sequence alignment of 71,038 SARS-CoV-2 genomes of 98 countries over the period from January 2020 to June 2021 is performed using MAFFT followed by phylogenetic analysis in order to visualize the virus evolution. These steps resulted in the identification of hotspot mutations as deletions and substitutions in the coding regions based on entropy greater than or equal to 0.3, leading to a total of 45 unique hotspot mutations. Moreover, 10,286 Indian sequences are considered from 71,038 global SARS-CoV-2 sequences as a demonstrative example that gives 52 unique hotspot mutations. Furthermore, the evolution of the hotspot mutations along with the mutations in variants of concern is visualized, and their characteristics are discussed as well. Also, for all the non-synonymous substitutions (missense mutations), the functional consequences of amino acid changes in the respective protein structures are calculated using PolyPhen-2 and I-Mutant 2.0. In addition to this, SSIPe is used to report the binding affinity between the receptor-binding domain of Spike protein and human ACE2 protein by considering L452R, T478K, E484Q, and N501Y hotspot mutations in that region.
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Affiliation(s)
- Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, India
| | - Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, India
| | - Suman Nandi
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, India
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27
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A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients. Life (Basel) 2021; 11:life11111224. [PMID: 34833100 PMCID: PMC8620851 DOI: 10.3390/life11111224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Since its first detection in December 2019, more than 232 million cases of COVID-19, including 4.7 million deaths, have been reported by the WHO. The SARS-CoV-2 viral genomes have evolved rapidly worldwide, causing the emergence of new variants. This systematic review and meta-analysis was conducted to provide a global mutational profile of SARS-CoV-2 from December 2019 to October 2020. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA), and a study protocol was lodged with PROSPERO. Data from 62 eligible studies involving 368,316 SARS-CoV-2 genomes were analyzed. The mutational data analyzed showed most studies detected mutations in the Spike protein (n = 50), Nucleocapsid phosphoprotein (n = 34), ORF1ab gene (n = 29), 5′-UTR (n = 28) and ORF3a (n = 25). Under the random-effects model, pooled prevalence of SARS-CoV-2 variants was estimated at 95.1% (95% CI; 93.3–96.4%; I2 = 98.952%; p = 0.000) while subgroup meta-analysis by country showed majority of the studies were conducted ‘Worldwide’ (n = 10), followed by ‘Multiple countries’ (n = 6) and the USA (n = 5). The estimated prevalence indicated a need to continuously monitor the prevalence of new mutations due to their potential influence on disease severity, transmissibility and vaccine effectiveness.
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28
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Characterisation of SARS-CoV-2 clades based on signature SNPs unveils continuous evolution. Methods 2021; 203:282-296. [PMID: 34547443 PMCID: PMC8450220 DOI: 10.1016/j.ymeth.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022] Open
Abstract
Since the emergence of SARS-CoV-2 in Wuhan, China more than a year ago, it has spread across the world in a very short span of time. Although, different forms of vaccines are being rolled out for vaccination programs around the globe, the mutation of the virus is still a cause of concern among the research communities. Hence, it is important to study the constantly evolving virus and its strains in order to provide a much more stable form of cure. This fact motivated us to conduct this research where we have initially carried out multiple sequence alignment of 15359 and 3033 global dataset without Indian and the dataset of exclusive Indian SARS-CoV-2 genomes respectively, using MAFFT. Subsequently, phylogenetic analyses are performed using Nextstrain to identify virus clades. Consequently, the virus strains are found to be distributed among 5 major clades or clusters viz. 19A, 19B, 20A, 20B and 20C. Thereafter, mutation points as SNPs are identified in each clade. Henceforth, from each clade top 10 signature SNPs are identified based on their frequency i.e. number of occurrences in the virus genome. As a result, 50 such signature SNPs are individually identified for global dataset without Indian and dataset of exclusive Indian SARS-CoV-2 genomes respectively. Out of each 50 signature SNPs, 39 and 41 unique SNPs are identified among which 25 non-synonymous signature SNPs (out of 39) resulted in 30 amino acid changes in protein while 27 changes in amino acid are identified from 22 non-synonymous signature SNPs (out of 41). These 30 and 27 amino acid changes for the non-synonymous signature SNPs are visualised in their respective protein structure as well. Finally, in order to judge the characteristics of the identified clades, the non-synonymous signature SNPs are considered to evaluate the changes in proteins as biological functions with the sequences using PROVEAN and PolyPhen-2 while I-Mutant 2.0 is used to evaluate their structural stability. As a consequence, for global dataset without Indian sequences, G251V in ORF3a in clade 19A, F308Y and G196V in NSP4 and ORF3a in 19B are the unique amino acid changes which are responsible for defining each clade as they are all deleterious and unstable. Such changes which are common for both global dataset without Indian and dataset of exclusive Indian sequences are R203M in Nucleocapsid for 20B, T85I and Q57H in NSP2 and ORF3a respectively for 20C while for exclusive Indian sequences such unique changes are A97V in RdRp, G339S and G339C in NSP2 in 19A and Q57H in ORF3a in 20A.
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29
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Matyášek R, Řehůřková K, Berta Marošiová K, Kovařík A. Mutational Asymmetries in the SARS-CoV-2 Genome May Lead to Increased Hydrophobicity of Virus Proteins. Genes (Basel) 2021; 12:826. [PMID: 34072181 PMCID: PMC8227412 DOI: 10.3390/genes12060826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.
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Affiliation(s)
| | | | | | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic; (R.M.); (K.Ř.); (K.B.M.)
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30
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Zhussupov B, Saliev T, Sarybayeva G, Altynbekov K, Tanabayeva S, Altynbekov S, Tuleshova G, Pavalkis D, Fakhradiyev I. Analysis of COVID-19 pandemics in Kazakhstan. J Res Health Sci 2021; 21:e00512. [PMID: 34465636 PMCID: PMC8957677 DOI: 10.34172/jrhs.2021.52] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 12/17/2022] Open
Abstract
Background: This study aimed to analyze the demographic and epidemiological features of identified COVID-19 cases in Kazakhstan.
Study design: A cross-sectional study.
Methods: This cross-sectional study aimed to analyze COVID-19 cases (n=5116) collected from March 13 to June 6, 2020, in Kazakhstan. The data were obtained from a state official medical electronic database. The study investigated the geographic and demographic data of patients as well as the association of COVID-19 cases with gender and age. The prevalence of symptoms, the presence of comorbidities, complications, and COVID-19 mortality were determined for all patients.
Results: The mean ±SD age of the patients in this study was 34.8 ±17.6 years, and the majority (55.7%) of COVID-19 cases were male and residents of cities (79.6%). In total, 80% of the cases had the asymptomatic/mild form of the disease. Cough (20.8 %) and sore throat (17.1%) were the most common symptoms among patients, and pneumonia was diagnosed in 1 out of 5 cases. Acute respiratory distress syndrome (ARDS) was recorded in 1.2% of the patients. The fatality rate was 1% in the study population and lethality was 2.6 times higher in males compared to females. Each additional year in age increased the probability of COVID-19 infection by 1.06 times. The presence of cardiovascular, diabetes, respiratory, and kidney diseases affected the rate of mortality (P<0.05).
Conclusions: The results demonstrated a high proportion (40%) of the asymptomatic type of coronavirus infection in the Kazakhstan population. The severity of COVID-19 symptoms and lethality were directly related to the age of patients and the presence of comorbidities.
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Affiliation(s)
- Baurzhan Zhussupov
- National Center for Public Health, Nur-Sultan, Kazakhstan.,S. D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Timur Saliev
- S.D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | | | - Kuanysh Altynbekov
- Republican Scientific and Practical Centre of Mental Health of the Ministry of Health of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Shynar Tanabayeva
- S. D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Sagat Altynbekov
- S. D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | | | | | - Ildar Fakhradiyev
- S. D. Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan.
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31
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Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Int J Biol Sci 2021; 17:1547-1554. [PMID: 33907518 PMCID: PMC8071772 DOI: 10.7150/ijbs.59943] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Suppression of type I interferon (IFN) response is one pathological outcome of the infection of highly pathogenic human coronaviruses. To effect this, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 encode multiple IFN antagonists. In this study, we reported on the IFN antagonism of SARS-CoV-2 main protease NSP5. NSP5 proteins of both SARS-CoV and SARS-CoV-2 counteracted Sendai virus-induced IFN production. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. The suppressive effect of NSP5 on IFN-β gene transcription induced by RIG-I, MAVS, TBK1 and IKKϵ suggested that NSP5 likely acts at a step downstream of IRF3 phosphorylation in the cytoplasm. NSP5 did not influence steady-state expression or phosphorylation of IRF3, suggesting that IRF3, regardless of its phosphorylation state, might not be the substrate of NSP5 protease. However, nuclear translocation of phosphorylated IRF3 was severely compromised in NSP5-expressing cells. Taken together, our work revealed a new mechanism by which NSP5 proteins encoded by SARS-CoV and SARS-CoV-2 antagonize IFN production by retaining phosphorylated IRF3 in the cytoplasm. Our findings have implications in rational design and development of antiviral agents against SARS-CoV-2.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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32
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Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res 2021; 31:635-644. [PMID: 33602693 PMCID: PMC8015855 DOI: 10.1101/gr.268961.120] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/12/2021] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we investigated 129 RNA-seq data sets and 6928 consensus genomes to contrast the intra-host and inter-host diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights intra-host single nucleotide variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.
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Affiliation(s)
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael D Jochum
- Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA
| | - Yunxi Liu
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - R A Leo Elworth
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Qi Wang
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University, Houston, Texas 77005, USA
| | - Dreycey Albin
- Systems, Synthetic, and Physical Biology (SSPB) Graduate Program, Rice University, Houston, Texas 77005, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Michael D Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, California 94043, USA
- Blue Marble Space Institute of Science, Seattle, Washington 98104, USA
| | - Sonia Villapol
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Kyle M Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA
- Center for Translational Data Science, University of Chicago, Chicago, Illinois 60637, USA
| | | | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, California 94035, USA
| | | | - Kjersti M Aagaard
- Department of Obstetrics and Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas 77030, USA
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10021, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
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33
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Wang Y, Wang D, Zhang L, Sun W, Zhang Z, Chen W, Zhu A, Huang Y, Xiao F, Yao J, Gan M, Li F, Luo L, Huang X, Zhang Y, Wong SS, Cheng X, Ji J, Ou Z, Xiao M, Li M, Li J, Ren P, Deng Z, Zhong H, Xu X, Song T, Mok CKP, Peiris M, Zhong N, Zhao J, Li Y, Li J, Zhao J. Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients. Genome Med 2021; 13:30. [PMID: 33618765 PMCID: PMC7898256 DOI: 10.1186/s13073-021-00847-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/05/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. METHODS Using high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT). RESULTS The 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks. CONCLUSIONS Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses.
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Affiliation(s)
- Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Daxi Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lu Zhang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Wanying Sun
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Weijun Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen, Shenzhen, 518083, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fei Xiao
- Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China
| | - Jinxiu Yao
- Yangjiang People's Hospital, Yangjiang, Guangdong, China
| | - Mian Gan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Ling Luo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Xiaofang Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Sook-San Wong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Xinyi Cheng
- BGI-Shenzhen, Shenzhen, 518083, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jingkai Ji
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhihua Ou
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Min Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Jiandong Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Peidi Ren
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tie Song
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China
| | - Chris Ka Pun Mok
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, 19406, China
| | - Malik Peiris
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
- The HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, 19406, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Yimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, 518083, China.
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
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