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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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2
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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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3
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Nguyen HT, Falzarano D, Gerdts V, Liu Q. Construction and immunogenicity of SARS-CoV-2 virus-like particle expressed by recombinant baculovirus BacMam. Microbiol Spectr 2024; 12:e0095924. [PMID: 38916311 PMCID: PMC11302303 DOI: 10.1128/spectrum.00959-24] [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: 04/15/2024] [Accepted: 05/13/2024] [Indexed: 06/26/2024] Open
Abstract
The pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve to give rise to variants of concern that can escape vaccine-induced immunity. As such, more effective vaccines are urgently needed. In this study, we evaluated virus-like particle (VLP) as a vaccine platform for SARS-CoV-2. The spike, envelope, and membrane proteins of the SARS-CoV-2 Wuhan strain were expressed by a single recombinant baculovirus BacMam and assembled into VLPs in cell culture. The morphology and size of the SARS-CoV-2 VLP as shown by transmission electron microscopy were similar to the authentic SARS-CoV-2 virus particle. In a mouse trial, two intramuscular immunizations of the VLP BacMam with no adjuvant elicited spike-specific binding antibodies in both sera and bronchoalveolar lavage fluids. Importantly, BacMam VLP-vaccinated mouse sera showed neutralization activity against SARS-CoV-2 spike pseudotyped lentivirus. Our results indicated that the SARS-CoV-2 VLP BacMam stimulated spike-specific immune responses with neutralization activity. IMPORTANCE Although existing vaccines have significantly mitigated the impact of the COVID-19 pandemic, none of the vaccines can induce sterilizing immunity. The spike protein is the main component of all approved vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due primarily to its ability to induce neutralizing antibodies. The conformation of the spike protein in the vaccine formulation should be critical for the efficacy of a vaccine. By way of closely resembling the authentic virions, virus-like particles (VLPs) should render the spike protein in its natural conformation. To this end, we utilized the baculovirus vector, BacMam, to express virus-like particles consisting of the spike, membrane, and envelope proteins of SARS-CoV-2. We demonstrated the immunogenicity of our VLP vaccine with neutralizing activity. Our data warrant further evaluation of the virus-like particles as a vaccine candidate in protecting against virus challenges.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- SARS-CoV-2/genetics
- Vaccines, Virus-Like Particle/immunology
- Vaccines, Virus-Like Particle/genetics
- Vaccines, Virus-Like Particle/administration & dosage
- Baculoviridae/genetics
- Baculoviridae/immunology
- Mice
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- COVID-19/prevention & control
- COVID-19/immunology
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Humans
- Mice, Inbred BALB C
- Female
- Immunogenicity, Vaccine
- Coronavirus Envelope Proteins/immunology
- Coronavirus Envelope Proteins/genetics
- Coronavirus M Proteins
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Affiliation(s)
- Hai Trong Nguyen
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Qiang Liu
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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4
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Focosi D, Spezia PG, Maggi F. Subsequent Waves of Convergent Evolution in SARS-CoV-2 Genes and Proteins. Vaccines (Basel) 2024; 12:887. [PMID: 39204013 PMCID: PMC11358953 DOI: 10.3390/vaccines12080887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 09/03/2024] Open
Abstract
Beginning in 2022, following widespread infection and vaccination among the global population, the SARS-CoV-2 virus mainly evolved to evade immunity derived from vaccines and past infections. This review covers the convergent evolution of structural, nonstructural, and accessory proteins in SARS-CoV-2, with a specific look at common mutations found in long-lasting infections that hint at the virus potentially reverting to an enteric sarbecovirus type.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Pietro Giorgio Spezia
- Laboratory of Virology and Laboratory of Biosecurity, National Institute of Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
| | - Fabrizio Maggi
- Laboratory of Virology and Laboratory of Biosecurity, National Institute of Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
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5
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Rasmussen TB, Qvesel AG, Pedersen AG, Olesen AS, Fonager J, Rasmussen M, Sieber RN, Stegger M, Calvo-Artavia FF, Goedknegt MJF, Thuesen ER, Lohse L, Mortensen S, Fomsgaard A, Boklund A, Bøtner A, Belsham GJ. Emergence and spread of SARS-CoV-2 variants from farmed mink to humans and back during the epidemic in Denmark, June-November 2020. PLoS Pathog 2024; 20:e1012039. [PMID: 38950065 PMCID: PMC11244769 DOI: 10.1371/journal.ppat.1012039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/12/2024] [Accepted: 06/07/2024] [Indexed: 07/03/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. However, the routes of transmission of the virus to, and from, the mink have been unclear. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. Detailed analysis of changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants with the Y453F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early in the outbreak. However, further introductions of the virus, by variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of viral genome data, we estimate, using a conservative approach, that about 17 separate examples of mink to human transmission occurred in Denmark but up to 59 such events (90% credible interval: (39-77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using Bayesian methods. Using the latter approach, 136 jumps (90% credible interval: (117-164)) from humans to mink were found, which may underlie the farm-to-farm spread. Thus, transmission of SARS-CoV-2 from humans to mink, mink to mink, from mink to humans and between humans were all observed.
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Affiliation(s)
- Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- PandemiX Center, Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- PandemiX Center, Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Ann Sofie Olesen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marc Stegger
- Department of Bioinformatics, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Esben Rahbek Thuesen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kgs. Lyngby, Denmark
- PandemiX Center, Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Louise Lohse
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Sten Mortensen
- Danish Veterinary and Food Administration, Ministry of Environment and Food, Glostrup, Denmark
| | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anette Boklund
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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6
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Thomas A, Battenfeld T, Kraiselburd I, Anastasiou O, Dittmer U, Dörr AK, Dörr A, Elsner C, Gosch J, Le-Trilling VTK, Magin S, Scholtysik R, Yilmaz P, Trilling M, Schöler L, Köster J, Meyer F. UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example. BMC Genomics 2024; 25:647. [PMID: 38943066 PMCID: PMC11214259 DOI: 10.1186/s12864-024-10539-0] [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: 04/04/2024] [Accepted: 06/18/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of variants of concern (VOCs) in late 2020. Subsequently, genome sequencing has become an indispensable tool for characterizing the ongoing pandemic, particularly for typing SARS-CoV-2 samples obtained from patients or environmental surveillance. For such SARS-CoV-2 typing, various in vitro and in silico workflows exist, yet to date, no systematic cross-platform validation has been reported. RESULTS In this work, we present the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms. Moreover, we present UnCoVar, a robust, production-grade reproducible SARS-CoV-2 typing workflow that outperforms all other tested approaches in terms of precision and recall. CONCLUSIONS In many ways, the SARS-CoV-2 pandemic has accelerated the development of techniques and analytical approaches. We believe that this can serve as a blueprint for dealing with future pandemics. Accordingly, UnCoVar is easily generalizable towards other viral pathogens and future pandemics. The fully automated workflow assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations. UnCoVar includes extensive quality control and automatically generates interactive visual reports. UnCoVar is implemented as a Snakemake workflow. The open-source code is available under a BSD 2-clause license at github.com/IKIM-Essen/uncovar.
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Affiliation(s)
- Alexander Thomas
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Thomas Battenfeld
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ivana Kraiselburd
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Olympia Anastasiou
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Ann-Kathrin Dörr
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Adrian Dörr
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Jule Gosch
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Vu Thuy Khanh Le-Trilling
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Simon Magin
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - René Scholtysik
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Pelin Yilmaz
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Mirko Trilling
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Lara Schöler
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute for the Research on HIV & AIDS-associated Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Cell Biology (Cancer Research), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Köster
- Bioinformatics and Computational Oncology, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Harvard Medical School, Boston, MA, USA
| | - Folker Meyer
- Data Science Research Group, Institute for Artificial Intelligence in Medicine (IKIM), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany.
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7
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Maiti AK. Progressive Evolutionary Dynamics of Gene-Specific ω Led to the Emergence of Novel SARS-CoV-2 Strains Having Super-Infectivity and Virulence with Vaccine Neutralization. Int J Mol Sci 2024; 25:6306. [PMID: 38928018 PMCID: PMC11204377 DOI: 10.3390/ijms25126306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
An estimation of the proportion of nonsynonymous to synonymous mutation (dn/ds, ω) of the SARS-CoV-2 genome would indicate the evolutionary dynamics necessary to evolve into novel strains with increased infection, virulence, and vaccine neutralization. A temporal estimation of ω of the whole genome, and all twenty-nine SARS-CoV-2 genes of major virulent strains of alpha, delta and omicron demonstrates that the SARS-CoV-2 genome originally emerged (ω ~ 0.04) with a strong purifying selection (ω < 1) and reached (ω ~ 0.85) in omicron towards diversifying selection (ω > 1). A marked increase in the ω occurred in the spike gene from alpha (ω = 0.2) to omicron (ω = 1.97). The ω of the replication machinery genes including RDRP, NSP3, NSP4, NSP7, NSP8, NSP10, NSP13, NSP14, and ORF9 are markedly increased, indicating that these genes/proteins are yet to be evolutionary stabilized and are contributing to the evolution of novel virulent strains. The delta-specific maximum increase in ω in the immunomodulatory genes of NSP8, NSP10, NSP16, ORF4, ORF5, ORF6, ORF7A, and ORF8 compared to alpha or omicron indicates delta-specific vulnerabilities for severe COVID-19 related hospitalization and death. The maximum values of ω are observed for spike (S), NSP4, ORF8 and NSP15, which indicates that the gene-specific temporal estimation of ω identifies specific genes for its super-infectivity and virulency that could be targeted for drug development.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield, MI 48076, USA
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8
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Wu Y, Wu Z, Jin Q, Liu J, Xu P. Identification and Analysis of Biomarkers Associated with Lipophagy and Therapeutic Agents for COVID-19. Viruses 2024; 16:923. [PMID: 38932215 PMCID: PMC11209609 DOI: 10.3390/v16060923] [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: 04/16/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Lipids, as a fundamental cell component, play an regulating role in controlling the different cellular biological processes involved in viral infections. A notable feature of coronavirus disease 2019 (COVID-19) is impaired lipid metabolism. The function of lipophagy-related genes in COVID-19 is unknown. The present study aimed to investigate biomarkers and drug targets associated with lipophagy and lipophagy-based therapeutic agents for COVID-19 through bioinformatics analysis. METHODS Lipophagy-related biomarkers for COVID-19 were identified using machine learning algorithms such as random forest, Support Vector Machine-Recursive Feature Elimination, Generalized Linear Model, and Extreme Gradient Boosting in three COVID-19-associated GEO datasets: scRNA-seq (GSE145926) and bulk RNA-seq (GSE183533 and GSE190496). The cMAP database was searched for potential COVID-19 medications. RESULTS The lipophagy pathway was downregulated, and the lipid droplet formation pathway was upregulated, resulting in impaired lipid metabolism. Seven lipophagy-related genes, including ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2, were used as biomarkers and drug targets for COVID-19. Moreover, lipophagy may play a role in COVID-19 pathogenesis. As prospective drugs for treating COVID-19, seven potential downregulators (phenoxybenzamine, helveticoside, lanatoside C, geldanamycin, loperamide, pioglitazone, and trichostatin A) were discovered. These medication candidates showed remarkable binding energies against the seven biomarkers. CONCLUSIONS The lipophagy-related genes ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2 can be used as biomarkers and drug targets for COVID-19. Seven potential downregulators of these seven biomarkers may have therapeutic effects for treating COVID-19.
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Affiliation(s)
- Yujia Wu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; (Y.W.); (Z.W.); (Q.J.)
| | - Zhenlin Wu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; (Y.W.); (Z.W.); (Q.J.)
| | - Qiying Jin
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; (Y.W.); (Z.W.); (Q.J.)
| | - Jinyuan Liu
- Basic Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, China;
| | - Peiping Xu
- Institute of Tropical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; (Y.W.); (Z.W.); (Q.J.)
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9
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Cui L, Li T, Xue W, Zhang S, Wang H, Liu H, Gu Y, Xia N, Li S. Comprehensive Overview of Broadly Neutralizing Antibodies against SARS-CoV-2 Variants. Viruses 2024; 16:900. [PMID: 38932192 PMCID: PMC11209230 DOI: 10.3390/v16060900] [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: 04/08/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, SARS-CoV-2 has evolved into various variants, including the numerous highly mutated Omicron sub-lineages, significantly increasing immune evasion ability. The development raises concerns about the possibly diminished effectiveness of available vaccines and antibody-based therapeutics. Here, we describe those representative categories of broadly neutralizing antibodies (bnAbs) that retain prominent effectiveness against emerging variants including Omicron sub-lineages. The molecular characteristics, epitope conservation, and resistance mechanisms of these antibodies are further detailed, aiming to offer suggestion or direction for the development of therapeutic antibodies, and facilitate the design of vaccines with broad-spectrum potential.
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Affiliation(s)
- Lingyan Cui
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Tingting Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Wenhui Xue
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Sibo Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hong Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Hongjing Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China (N.X.)
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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10
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Singh UB, Deb S, Rani L, Gupta R, Verma S, Kumari L, Bhardwaj D, Bala K, Ahmed J, Gaurav S, Perumalla S, Nizam M, Mishra A, Stephenraj J, Shukla J, Nayer J, Aggarwal P, Kabra M, Ahuja V, Chaudhry R, Sinha S, Guleria R. Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India. J Biomol Struct Dyn 2024; 42:4769-4781. [PMID: 37318006 DOI: 10.1080/07391102.2023.2222832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/02/2023] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sushanta Deb
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Rani
- Central Core Research Facility, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Sunita Verma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Lata Kumari
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Bhardwaj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jawed Ahmed
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sudesh Gaurav
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sowjanya Perumalla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Md Nizam
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anwita Mishra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - J Stephenraj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Shukla
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jamshed Nayer
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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11
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Rojas Chávez RA, Fili M, Han C, Rahman SA, Bicar IGL, Gregory S, Helverson A, Hu G, Darbro BW, Das J, Brown GD, Haim H. Mapping the Evolutionary Space of SARS-CoV-2 Variants to Anticipate Emergence of Subvariants Resistant to COVID-19 Therapeutics. PLoS Comput Biol 2024; 20:e1012215. [PMID: 38857308 PMCID: PMC11192331 DOI: 10.1371/journal.pcbi.1012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 06/21/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with mutations in the spike glycoprotein. In most cases, the sublineage-defining mutations vary between the VOCs. It is unclear whether these differences reflect lineage-specific likelihoods for mutations at each spike position or the stochastic nature of their appearance. Here we show that SARS-CoV-2 lineages have distinct evolutionary spaces (a probabilistic definition of the sequence states that can be occupied by expanding virus subpopulations). This space can be accurately inferred from the patterns of amino acid variability at the whole-protein level. Robust networks of co-variable sites identify the highest-likelihood mutations in new VOC sublineages and predict remarkably well the emergence of subvariants with resistance mutations to COVID-19 therapeutics. Our studies reveal the contribution of low frequency variant patterns at heterologous sites across the protein to accurate prediction of the changes at each position of interest.
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Affiliation(s)
| | - Mohammad Fili
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Changze Han
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Syed A. Rahman
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Isaiah G. L. Bicar
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Sullivan Gregory
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Guiping Hu
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Benjamin W. Darbro
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States of America
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Grant D. Brown
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, United States of America
| | - Hillel Haim
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, United States of America
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12
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Hattab D, Amer MFA, Al-Alami ZM, Bakhtiar A. SARS-CoV-2 journey: from alpha variant to omicron and its sub-variants. Infection 2024; 52:767-786. [PMID: 38554253 PMCID: PMC11143066 DOI: 10.1007/s15010-024-02223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/22/2024] [Indexed: 04/01/2024]
Abstract
The COVID-19 pandemic has affected hundreds of millions of individuals and caused more than six million deaths. The prolonged pandemic duration and the continual inter-individual transmissibility have contributed to the emergence of a wide variety of SARS-CoV-2 variants. Genomic surveillance and phylogenetic studies have shown that substantial mutations in crucial supersites of spike glycoprotein modulate the binding affinity of the evolved SARS-COV-2 lineages to ACE2 receptors and modify the binding of spike protein with neutralizing antibodies. The immunological spike mutations have been associated with differential transmissibility, infectivity, and therapeutic efficacy of the vaccines and the immunological therapies among the new variants. This review highlights the diverse genetic mutations assimilated in various SARS-CoV-2 variants. The implications of the acquired mutations related to viral transmission, infectivity, and COVID-19 severity are discussed. This review also addresses the effectiveness of human neutralizing antibodies induced by SARS-CoV-2 infection or immunization and the therapeutic antibodies against the ascended variants.
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Affiliation(s)
- Dima Hattab
- School of Pharmacy, The University of Jordan, Queen Rania Street, Amman, Jordan
| | - Mumen F A Amer
- Faculty of Pharmacy, Applied Science Private University, Amman, Jordan
| | - Zina M Al-Alami
- Department of Basic Medical Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Athirah Bakhtiar
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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13
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da Silva SM, Amaral C, Malta-Luís C, Grilo D, Duarte AG, Morais I, Afonso G, Faria N, Antunes W, Gomes I, Sá-Leão R, Miragaia M, Serrano M, Pimentel C. A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva. Biol Methods Protoc 2024; 9:bpae035. [PMID: 38835855 PMCID: PMC11147803 DOI: 10.1093/biomethods/bpae035] [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: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024] Open
Abstract
The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.
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Affiliation(s)
- Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Cláudia Malta-Luís
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Diana Grilo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Inês Morais
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Gonçalo Afonso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Nuno Faria
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Wilson Antunes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr Alfredo Bensaúde, Lisboa, 1849-012, Portugal
| | - Inês Gomes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr Alfredo Bensaúde, Lisboa, 1849-012, Portugal
| | - Raquel Sá-Leão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Maria Miragaia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
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14
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Feng S, Reid GE, Clark NM, Harrington A, Uprichard SL, Baker SC. Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies. Virol J 2024; 21:105. [PMID: 38715113 PMCID: PMC11075269 DOI: 10.1186/s12985-024-02378-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. METHODS We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status. Serial sampling of 14 patients was evaluated for viral evolution in response to antiviral treatments. RESULTS We identified hospitalized and immunosuppressed patients with significantly higher levels of viral genetic diversity and variability. Further evaluation of serial samples revealed accumulated mutations associated with escape from neutralizing antibodies in a subset of the immunosuppressed patients treated with antiviral therapies. Interestingly, the accumulated viral mutations that arose in this early Omicron wave, which were not common in the patient viral lineages, represent convergent mutations that are prevalent in the later Omicron sublineages, including the XBB, BA.2.86.1 and its descendent JN sublineages. CONCLUSIONS Our results illustrate the importance of identifying convergent mutations generated during antiviral therapy in immunosuppressed patients, as they may contribute to the future evolutionary landscape of SARS-CoV-2. Our study also provides evidence of a correlation between SARS-CoV-2 convergent mutations and specific antiviral treatments. Evaluating high-confidence genomes from distinct waves in the pandemic with detailed patient metadata allows for discerning of convergent mutations that contribute to the ongoing evolution of SARS-CoV-2.
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Affiliation(s)
- Shuchen Feng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Gail E Reid
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Nina M Clark
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Amanda Harrington
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Pathology and Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan L Uprichard
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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15
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Minami S, Kotaki T, Sakai Y, Okamura S, Torii S, Ono C, Motooka D, Hamajima R, Nouda R, Nurdin JA, Yamasaki M, Kanai Y, Ebina H, Maeda Y, Okamoto T, Tachibana T, Matsuura Y, Kobayashi T. Vero cell-adapted SARS-CoV-2 strain shows increased viral growth through furin-mediated efficient spike cleavage. Microbiol Spectr 2024; 12:e0285923. [PMID: 38415690 PMCID: PMC10986611 DOI: 10.1128/spectrum.02859-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/29/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes several host proteases to cleave the spike (S) protein to enter host cells. SARS-CoV-2 S protein is cleaved into S1 and S2 subunits by furin, which is closely involved in the pathogenicity of SARS-CoV-2. However, the effects of the modulated protease cleavage activity due to S protein mutations on viral replication and pathogenesis remain unclear. Herein, we serially passaged two SARS-CoV-2 strains in Vero cells and characterized the cell-adapted SARS-CoV-2 strains in vitro and in vivo. The adapted strains showed high viral growth, effective S1/S2 cleavage of the S protein, and low pathogenicity compared with the wild-type strain. Furthermore, the viral growth and S1/S2 cleavage were enhanced by the combination of the Δ68-76 and H655Y mutations using recombinant SARS-CoV-2 strains generated by the circular polymerase extension reaction. The recombinant SARS-CoV-2 strain, which contained the mutation of the adapted strain, showed increased susceptibility to the furin inhibitor, suggesting that the adapted SARS-CoV-2 strain utilized furin more effectively than the wild-type strain. Pathogenicity was attenuated by infection with effectively cleaved recombinant SARS-CoV-2 strains, suggesting that the excessive cleavage of the S proteins decreases virulence. Finally, the high-growth-adapted SARS-CoV-2 strain could be used as the seed for a low-cost inactivated vaccine; immunization with this vaccine can effectively protect the host from SARS-CoV-2 variants. Our findings provide novel insights into the growth and pathogenicity of SARS-CoV-2 in the evolution of cell-cell transmission. IMPORTANCE The efficacy of the S protein cleavage generally differs among the SARS-CoV-2 variants, resulting in distinct viral characteristics. The relationship between a mutation and the entry of SARS-CoV-2 into host cells remains unclear. In this study, we analyzed the sequence of high-growth Vero cell-adapted SARS-CoV-2 and factors determining the enhancement of the growth of the adapted virus and confirmed the characteristics of the adapted strain by analyzing the recombinant SARS-CoV-2 strain. We successfully identified mutations Δ68-76 and H655Y, which enhance viral growth and the S protein cleavage by furin. Using recombinant viruses enabled us to conduct a virus challenge experiment in vivo. The pathogenicity of SARS-CoV-2 introduced with the mutations Δ68-76, H655Y, P812L, and Q853L was attenuated in hamsters, indicating the possibility of the attenuation of excessive cleaved SARS-CoV-2. These findings provide novel insights into the infectivity and pathogenesis of SARS-CoV-2 strains, thereby significantly contributing to the field of virology.
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Affiliation(s)
- Shohei Minami
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yusuke Sakai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shinya Okamura
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Rina Hamajima
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryotaro Nouda
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Jeffery A. Nurdin
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Moeko Yamasaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hirotaka Ebina
- Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
| | - Yusuke Maeda
- Laboratory of Viral Dynamism Research, Research Institute for Microbial Diseases Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-creation Studies, Research Institute for Microbial Diseases Osaka University, Osaka, Japan
| | - Taro Tachibana
- Cell Engineering Corporation, Osaka, Japan
- Department of Bioengineering, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
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16
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [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: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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17
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Senevirathne TH, Wekking D, Swain JWR, Solinas C, De Silva P. COVID-19: From emerging variants to vaccination. Cytokine Growth Factor Rev 2024; 76:127-141. [PMID: 38135574 DOI: 10.1016/j.cytogfr.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
The vigorous spread of SARS-CoV-2 resulted in the rapid infection of millions of people worldwide and devastation of not only public healthcare, but also social, educational, and economic infrastructures. The evolution of SARS-CoV-2 over time is due to the mutations that occurred in the genome during each replication. These mutated forms of SARS-CoV-2, otherwise known as variants, were categorized as variants of interest (VOI) or variants of concern (VOC) based on the increased risk of transmissibility, disease severity, immune escape, decreased effectiveness of current social measures, and available vaccines and therapeutics. The swift development of COVID-19 vaccines has been a great success for biomedical research, and billions of vaccine doses, including boosters, have been administered worldwide. BNT162b2 vaccine (Pfizer-BioNTech), mRNA-1273 (Moderna), ChAdOx1 nCoV-19 (AstraZeneca), and Janssen (Johnson & Johnson) are the four major COVID-19 vaccines that received early regulatory authorization based on their efficacy. However, some SARS-CoV-2 variants resulted in higher resistance to available vaccines or treatments. It has been four years since the first reported infection of SARS-CoV-2, yet the Omicron variant and its subvariants are still infecting people worldwide. Despite this, COVID-19 vaccines are still expected to be effective at preventing severe disease, hospitalization, and death from COVID. In this review, we provide a comprehensive overview of the COVID-19 pandemic focused on evolution of VOC and vaccination strategies against them.
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Affiliation(s)
- Thilini H Senevirathne
- Faculty of Science, Katholieke Universiteit Leuven, Kasteelpark Arenberg, Leuven, Belgium
| | - Demi Wekking
- Amsterdam UMC, Location Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Cinzia Solinas
- Medical Oncology, AOU Cagliari, P.O. Duilio Casula, Monserrato (CA), Italy.
| | - Pushpamali De Silva
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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18
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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [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: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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19
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Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic surveillance of SARS-CoV-2 using long-range PCR primers. Front Microbiol 2024; 15:1272972. [PMID: 38440140 PMCID: PMC10910555 DOI: 10.3389/fmicb.2024.1272972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/03/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence nearly all of the ~30,000 nucleotide SARS-CoV-2 genome, using a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with 'Ns' inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). Methods In this study we used a set of seven long-range PCR primer pairs to sequence clinical isolates of SARS-CoV-2 on Oxford Nanopore sequencer. These long-range primers generate seven amplicons approximately 4500 bp that covered whole genome of SARS-CoV-2. One of these regions includes the full-length S-gene by using a set of flanking primers. We also evaluated the performance of these long-range primers with Midnight primers by sequencing 94 clinical isolates in a Nanopore flow cell. Results and discussion Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias. The key finding of this study is that long range primers can be used in single-molecule sequencing of RNA viruses in surveillance of emerging variants. We also show that by designing primers flanking the S-gene, we can obtain reliable identification of SARS-CoV-2 variants.
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Affiliation(s)
- Sangam Kandel
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Ashton K. Ingold
- Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Grace A. Turner
- Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Joshua L. Kennedy
- Arkansas Children's Research Institute, Little Rock, AR, United States
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - David W. Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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20
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Hilti D, Wehrli F, Berchtold S, Bigler S, Bodmer T, Seth-Smith HMB, Roloff T, Kohler P, Kahlert CR, Kaiser L, Egli A, Risch L, Risch M, Wohlwend N. S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5. Microorganisms 2024; 12:321. [PMID: 38399725 PMCID: PMC10892681 DOI: 10.3390/microorganisms12020321] [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: 12/31/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPathTM COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting three genes (i.e., ORF1AB, N, S). With emergence of the B.1.1.7 (Alpha) variant, a diagnostic flaw became apparent as the amplification of the S-gene target was absent in these samples due to a deletion (ΔH69/V70) in the Alpha variant genome. This S-gene target failure (SGTF) was the earliest indication of a new variant emerging and was also observed in subsequent variants such as Omicron BA.1 and BA4/BA.5. The Delta variant and Omicron BA.2 did not present with SGTF. From September 2020 to November 2022, we investigated the applicability of the SGTF as a surrogate marker for emerging variants such as B.1.1.7, B.1.617.2 (Delta), and Omicron BA.1, BA.2, and BA.4/BA.5 in samples with cycle threshold (Ct) values < 30. Next to true SGTF-positive and SGTF-negative samples, there were also samples presenting with delayed-type S-gene amplification (higher Ct value for S-gene than ORF1ab gene). Among these, a difference of 3.8 Ct values between the S- and ORF1ab genes was found to best distinguish between "true" SGTF and the cycle threshold variability of the assay. Samples above the cutoff were subsequently termed partial SGTF (pSGTF). Variant confirmation was performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) samples among 240,896 positives were variant-confirmed, resulting in an overall sensitivity and specificity of 93.2% [92.7%, 93.7%] and 99.3% [99.2%, 99.5%], respectively. Sensitivity was increased to 98.2% [97.9% to 98.4%] and specificity lowered to 98.9% [98.6% to 99.1%] when samples with pSGTF were included. Furthermore, weekly logistic growth rates (α) and sigmoid's midpoint (t0) were calculated based on SGTF data and did not significantly differ from calculations based on comprehensive data from GISAID. The SGTF therefore allowed for a valid real-time estimate for the introduction of all dominant variants in Switzerland and Liechtenstein.
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Affiliation(s)
- Dominique Hilti
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
- Institute of Laboratory Medicine, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein
| | - Faina Wehrli
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
| | | | - Susanna Bigler
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
| | - Thomas Bodmer
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
| | | | - Tim Roloff
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Philipp Kohler
- Zentrallabor, Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Christian R. Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Lorenz Risch
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
- Institute of Laboratory Medicine, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein
| | - Martin Risch
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland
| | - Nadia Wohlwend
- Laboratory Dr. Risch, 9470 Buchs, Switzerland (L.R.); (N.W.)
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21
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [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: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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22
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Lapuente D, Winkler TH, Tenbusch M. B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity. Cell Mol Immunol 2024; 21:144-158. [PMID: 37945737 PMCID: PMC10805925 DOI: 10.1038/s41423-023-01095-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.
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Affiliation(s)
- Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Thomas H Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany.
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
- Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054, Erlangen, Germany
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23
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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [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] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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24
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Xie M. Virus-Induced Cell Fusion and Syncytia Formation. Results Probl Cell Differ 2024; 71:283-318. [PMID: 37996683 DOI: 10.1007/978-3-031-37936-9_14] [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] [Indexed: 11/25/2023]
Abstract
Most enveloped viruses encode viral fusion proteins to penetrate host cell by membrane fusion. Interestingly, many enveloped viruses can also use viral fusion proteins to induce cell-cell fusion, both in vitro and in vivo, leading to the formation of syncytia or multinucleated giant cells (MGCs). In addition, some non-enveloped viruses encode specialized viral proteins that induce cell-cell fusion to facilitate viral spread. Overall, viruses that can induce cell-cell fusion are nearly ubiquitous in mammals. Virus cell-to-cell spread by inducing cell-cell fusion may overcome entry and post-entry blocks in target cells and allow evasion of neutralizing antibodies. However, molecular mechanisms of virus-induced cell-cell fusion remain largely unknown. Here, I summarize the current understanding of virus-induced cell fusion and syncytia formation.
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Affiliation(s)
- Maorong Xie
- Division of Infection and Immunity, UCL, London, UK.
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25
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Li J, Zhang K, Lin G, Li J. CRISPR-Cas system: A promising tool for rapid detection of SARS-CoV-2 variants. J Med Virol 2024; 96:e29356. [PMID: 38180237 DOI: 10.1002/jmv.29356] [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: 06/04/2023] [Revised: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
COVID-19, caused by SARS-CoV-2, remains a global health crisis. The emergence of multiple variants with enhanced characteristics necessitates their detection and monitoring. Genome sequencing, the gold standard, faces implementation challenges due to complexity, cost, and limited throughput. The CRISPR-Cas system offers promising potential for rapid variant detection, with advantages such as speed, sensitivity, specificity, and programmability. This review provides an in-depth examination of the applications of CRISPR-Cas in mutation detection specifically for SARS-CoV-2. It begins by introducing SARS-CoV-2 and existing variant detection platforms. The principles of the CRISPR-Cas system are then clarified, followed by an exploration of three CRISPR-Cas-based mutation detection platforms, which are evaluated from different perspectives. The review discusses strategies for mutation site selection and the utilization of CRISPR-Cas, offering valuable insights for the development of mutation detection methods. Furthermore, a critical analysis of the clinical applications, advantages, disadvantages, challenges, and prospects of the CRISPR-Cas system is provided.
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Affiliation(s)
- Jing Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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26
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Tambe LAM, Mathobo P, Matume ND, Munzhedzi M, Edokpayi JN, Viraragavan A, Glanzmann B, Tebit DM, Mavhandu-Ramarumo LG, Street R, Johnson R, Kinnear C, Bessong PO. Molecular epidemiology of SARS-CoV-2 in Northern South Africa: wastewater surveillance from January 2021 to May 2022. Front Public Health 2023; 11:1309869. [PMID: 38174083 PMCID: PMC10764116 DOI: 10.3389/fpubh.2023.1309869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction Wastewater-based genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provides a comprehensive approach to characterize evolutionary patterns and distribution of viral types in a population. This study documents the molecular epidemiology of SARS-CoV-2, in Northern South Africa, from January 2021 to May 2022. Methodology A total of 487 wastewater samples were collected from the influent of eight wastewater treatment facilities and tested for SARS-CoV-2 RNA using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). SARS-CoV-2 positive samples with genome copies/mL ≥1,500 were subjected to allele-specific genotyping (ASG) targeting the Spike protein; 75 SARS-CoV-2 positive samples were subjected to whole genome sequencing (WGS) on the ATOPlex platform. Variants of concern (VoC) and lineages were assigned using the Nextclade and PangoLIN Software. Concordance for VoC between ASG and WGS analyses was determined. Sequence relationship was determined by phylogenetic analysis. Results Seventy-five percent (365/487) of the influent samples were positive for SARS-CoV-2 RNA. Delta and Omicron VoC were more predominant at a prevalence of 45 and 32%, respectively, and they were detected as early as January and February 2021, while Beta VoC was least detected at a prevalence of 5%. A total of 11/60 (18%) sequences were assigned lineages and clades only, but not a specific VoC name. Phylogenetic analysis was used to investigate the relationship of these sequences to other study sequences, and further characterize them. Concordance in variant assignment between ASG and WGS was seen in 51.2% of the study sequences. There was more intra-variant diversity among Beta VoC sequences; mutation E484K was absent. Three previously undescribed mutations (A361S, V327I, D427Y) were seen in Delta VoC. Discussion and Conclusion The detection of Delta and Omicron VoCs in study sites earlier in the outbreak than has been reported in other regions of South Africa highlights the importance of population-based approaches over individual sample-based approaches in genomic surveillance. Inclusion of non-Spike protein targets could improve the specificity of ASG, since all VoCs share similar Spike protein mutations. Finally, continuous molecular epidemiology with the application of sensitive technologies such as next generation sequencing (NGS) is necessary for the documentation of mutations whose implications when further investigated could enhance diagnostics, and vaccine development efforts.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Nontokozo D. Matume
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Joshua Nosa Edokpayi
- Water and Environmental Management Research Group, University of Venda, Thohoyandou, South Africa
| | - Amsha Viraragavan
- South African Medical Research Council Genomics Platform, Tygerberg, South Africa
| | - Brigitte Glanzmann
- South African Medical Research Council Genomics Platform, Tygerberg, South Africa
| | - Denis M. Tebit
- Global Biomed Laboratories Inc., Lynchburg, VA, United States
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa
| | - Renee Street
- Environment and Health Research Unit, South African Medical Research Council, Johannesburg, South Africa
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Cape Town, South Africa
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Centre for Cardiometabolic Research in Africa, Stellenbosch University, Stellenbosch, South Africa
| | - Craig Kinnear
- South African Medical Research Council Genomics Platform, Tygerberg, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, South Africa
- Center for Global Health Equity, School of Medicine, University of Virginia, Charlottesville, VA, United States
- School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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27
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Salazar-Ardiles C, Asserella-Rebollo L, Cornejo C, Arias D, Vasquez-Muñoz M, Toledo C, Andrade DC. Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences. Mol Biol Rep 2023; 50:10367-10382. [PMID: 37817022 DOI: 10.1007/s11033-023-08844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.
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Affiliation(s)
- Camila Salazar-Ardiles
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | | | - Carlos Cornejo
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Dayana Arias
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Manuel Vasquez-Muñoz
- Dirección de Docencia de Especialidades Médicas, Dirección de Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Camilo Toledo
- Laboratory of Cardiorespiratory and Sleep Physiology, Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - David C Andrade
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile.
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28
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Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Cell 2023; 186:5151-5164.e13. [PMID: 37875109 PMCID: PMC10964984 DOI: 10.1016/j.cell.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, and antigenic changes that reduce cross-immunity induced by previous infections or vaccinations. How this functional variation shapes global evolution has remained unclear. Here, we establish a predictive fitness model for SARS-CoV-2 that integrates antigenic and intrinsic selection. The model is informed by tracking of time-resolved sequence data, epidemiological records, and cross-neutralization data of viral variants. Our inference shows that immune pressure, including contributions of vaccinations and previous infections, has become the dominant force driving the recent evolution of SARS-CoV-2. The fitness model can serve continued surveillance in two ways. First, it successfully predicts the short-term evolution of circulating strains and flags emerging variants likely to displace the previously predominant variant. Second, it predicts likely antigenic profiles of successful escape variants prior to their emergence.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany.
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29
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Tulsian NK, Palur RV, Qian X, Gu Y, D/O Shunmuganathan B, Samsudin F, Wong YH, Lin J, Purushotorman K, Kozma MM, Wang B, Lescar J, Wang CI, Gupta RK, Bond PJ, MacAry PA. Defining neutralization and allostery by antibodies against COVID-19 variants. Nat Commun 2023; 14:6967. [PMID: 37907459 PMCID: PMC10618280 DOI: 10.1038/s41467-023-42408-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
The changing landscape of SARS-CoV-2 Spike protein is linked to the emergence of variants, immune-escape and reduced efficacy of the existing repertoire of anti-viral antibodies. The functional activity of neutralizing antibodies is linked to their quaternary changes occurring as a result of antibody-Spike trimer interactions. Here, we reveal the conformational dynamics and allosteric perturbations linked to binding of novel human antibodies and the viral Spike protein. We identified epitope hotspots, and associated changes in Spike dynamics that distinguish weak, moderate and strong neutralizing antibodies. We show the impact of mutations in Wuhan-Hu-1, Delta, and Omicron variants on differences in the antibody-induced conformational changes in Spike and illustrate how these render certain antibodies ineffective. Antibodies with similar binding affinities may induce destabilizing or stabilizing allosteric effects on Spike, with implications for neutralization efficacy. Our results provide mechanistic insights into the functional modes and synergistic behavior of human antibodies against COVID-19 and may assist in designing effective antiviral strategies.
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Affiliation(s)
- Nikhil Kumar Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Department of Biochemistry, National University of Singapore, Singapore, 117546, Singapore.
| | - Raghuvamsi Venkata Palur
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Bhuvaneshwari D/O Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Firdaus Samsudin
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
| | - Mary McQueen Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore
| | - Bei Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore
| | - Ravindra Kumar Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Peter John Bond
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138761, Singapore.
| | - Paul Anthony MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117546, Singapore.
- Life Sciences Institute, National University of Singapore, Singapore, 117546, Singapore.
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30
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Lagare A, Faye M, Issa M, Hamidou O, Bienvenu B, Mohamed A, Aoula B, Moumouni K, Hassane F, Otto YA, Tambwe DD, Tassiou EI, Seini H, Faye O, Jambou R. First identification of the SARS-COV-2/XBB.1.5 sublineage among indigenous COVID-19 cases through the influenza sentinel surveillance system in Niger. Heliyon 2023; 9:e20916. [PMID: 37954288 PMCID: PMC10637901 DOI: 10.1016/j.heliyon.2023.e20916] [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: 04/15/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
The emergence of the Omicron variant in November 2021, has caused panic worldwide due to the rapid evolution and the ability of the virus to escape the immune system. Since, several Omicron sublineages (BA.1 to BA.5) and their descendent recombinant lineages have been circulating worldwide. Furthermore, in December 2022, a new Omicron subvariant XBB.1.5 characterized by an unusual mutation in the spike protein evolved in the United States and rapidly spread to the other continents. Our study reports on the first cases of XBB.1.5 sublineage among indigenous Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) positive cases detected through the influenza sentinel surveillance system in Niger. All influenza suspected cases were tested for both influenza and SARS-COV-2 using the Centre for Disease Control and prevention (CDC) Influenza SARS-COV-2 Multiplex quantitative Reverse-Transcription Polymerase Chain Reaction (qRT-PCR) Assay. SARS-COV-2 positive samples with cycle threshold ≤28 were selected for whole genome sequencing subsequently using the Oxford Nanopore Midnight protocol with rapid barcoding on a MinIon MK1B device. A total of 51 SARS-COV-2 positive samples were confirmed between December 2022 and March 2023. We successfully obtained 19 sequences with a predominance of the XBB.1/XBB.1.5 sublineages (73.7 %). In addition, a recombinant XBD sequence was also first-ever identified in early March 2023. Our findings support the need to strengthen the influenza sentinel surveillance for routine Coronavirus Disease 2019 (COVID-19) surveillance and SARS-COV-2 variants monitoring in Niger.
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Affiliation(s)
- Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur Dakar, 220, Dakar, Senegal
| | - Moussa Issa
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Oumou Hamidou
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Baruani Bienvenu
- World Health Organization-Country Office, Boulevard Du Roi Mohamed 6, BP 10739, Niamey, Niger
| | | | - Balki Aoula
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | | | - Fatima Hassane
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Younoussa Adamou Otto
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Didier D.K. Tambwe
- World Health Organization-Country Office, Boulevard Du Roi Mohamed 6, BP 10739, Niamey, Niger
| | | | - Haoua Seini
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur Dakar, 220, Dakar, Senegal
| | - Ronan Jambou
- Centre de Recherche Médicale et Sanitaire (CERMES), 634 Bd de la Nation, Niamey, YN034, Niger
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31
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Dabrell SN, Li YC, Yamaguchi H, Chen HF, Hung MC. Herbal Compounds Dauricine and Isoliensinine Impede SARS-CoV-2 Viral Entry. Biomedicines 2023; 11:2914. [PMID: 38001915 PMCID: PMC10669532 DOI: 10.3390/biomedicines11112914] [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: 09/24/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Targeting viral entry has been the focal point for the last 3 years due to the continued threat posed by SARS-CoV-2. SARS-CoV-2's entry is highly dependent on the interaction between the virus's Spike protein and host receptors. The virus's Spike protein is a key modulator of viral entry, allowing sequential cleavage of ACE2 at the S1/S2 and S2 sites, resulting in the amalgamation of membranes and subsequent entry of the virus. A Polybasic insertion (PRRAR) conveniently located at the S1/S2 site can also be cleaved by furin or by serine protease, TMPRSS2, at the cell surface. Since ACE2 and TMPRSS2 are conveniently located on the surface of host cells, targeting one or both receptors may inhibit receptor-ligand interaction. Here, we show that Dauricine and Isoliensinine, two commonly used herbal compounds, were capable of inhibiting SARS-CoV-2 viral entry by reducing Spike-ACE2 interaction but not suppressing TMPRSS2 protease activity. Further, our biological assays using pseudoviruses engineered to express Spike proteins of different variants revealed a reduction in infection rates following treatment with these compounds. The molecular modeling revealed an interconnection between R403 of Spike protein and both two compounds. Spike mutations at residue R403 are critical, and often utilized by ACE2 to gain cell access. Overall, our findings strongly suggest that Dauricine and Isoliensinine are effective in blocking Spike-ACE2 interaction and may serve as effective therapeutic agents for targeting SARS-CoV-2's viral entry.
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Affiliation(s)
- Shaneek Natoya Dabrell
- International Master's Program of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
| | - Yi-Chuan Li
- Department of Biological Science and Technology, China Medical University, Taichung 406040, Taiwan
| | - Hirohito Yamaguchi
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 406040, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 406040, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 406040, Taiwan
- Department of Biotechnology, Asia University, Taichung 413305, Taiwan
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32
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Lythgoe KA, Golubchik T, Hall M, House T, Cahuantzi R, MacIntyre-Cockett G, Fryer H, Thomson L, Nurtay A, Ghafani M, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith D, Bashton M, Nelson A, Crown M, McCann C, Young GR, Andre Nunes dos Santos R, Richards Z, Tariq A, Fraser C, Diamond I, Barrett J, Walker AS, Bonsall D. Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey. Proc Biol Sci 2023; 290:20231284. [PMID: 37848057 PMCID: PMC10581763 DOI: 10.1098/rspb.2023.1284] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023] Open
Abstract
The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.
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Affiliation(s)
- Katrina A. Lythgoe
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Sydney Infectious Diseases Institute (Sydney ID), School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Matthew Hall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester M13 9PL, UK
| | - Roberto Cahuantzi
- Department of Mathematics, University of Manchester, Manchester M13 9PL, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Helen Fryer
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Laura Thomson
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anel Nurtay
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Mahan Ghafani
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - David Buck
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Angie Green
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Amy Trebes
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Paolo Piazza
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Lorne J. Lonie
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | | | | | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Andrew Nelson
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Matthew Crown
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Clare McCann
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gregory R. Young
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Nothumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Rui Andre Nunes dos Santos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Zack Richards
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Adnan Tariq
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | | | | | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | | | - Jeff Barrett
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
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33
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Abdullahi A, Frimpong J, Cheng MTK, Aliyu SH, Smith C, Abimiku A, Phillips RO, Owusu M, Gupta RK. Performance of SARS COV-2 IgG Anti-N as an Independent Marker of Exposure to SARS COV-2 in an Unvaccinated West African Population. Am J Trop Med Hyg 2023; 109:890-894. [PMID: 37580023 PMCID: PMC10551093 DOI: 10.4269/ajtmh.23-0179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/22/2023] [Indexed: 08/16/2023] Open
Abstract
Determination of previous SARS-COV-2 infection is hampered by the absence of a standardized test. The marker used to assess previous exposure is IgG antibody to the nucleocapsid (IgG anti-N), although it is known to wane quickly from peripheral blood. The accuracies of seven antibody tests (virus neutralization test, IgG anti-N, IgG anti-spike [anti-S], IgG anti-receptor binding domain [anti-RBD], IgG anti-N + anti-RBD, IgG anti-N + anti-S, and IgG anti-S + anti-RBD), either singly or in combination, were evaluated on 502 cryopreserved serum samples collected before the COVID-19 vaccination rollout in Kumasi, Ghana. The accuracy of each index test was measured using a composite reference standard based on a combination of neutralization test and IgG anti-N antibody tests. According to the composite reference, 262 participants were previously exposed; the most sensitive test was the virus neutralization test, with 95.4% sensitivity (95% CI: 93.6-97.3), followed by 79.0% for IgG anti-N + anti-S (95% CI: 76.3-83.3). The most specific tests were virus neutralization and IgG anti-N, both with 100% specificity. Viral neutralization and IgG anti-N + anti-S were the overall most accurate tests, with specificity/sensitivity of 100/95.2% and 79.0/92.1%, respectively. Our findings indicate that IgG anti-N alone is an inadequate marker of prior exposure to SARS COV-2 in this population. Virus neutralization assay appears to be the most accurate assay in discerning prior infection. A combination of IgG anti-N and IgG anti-S is also accurate and suited for assessment of SARS COV-2 exposure in low-resource settings.
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Affiliation(s)
- Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Institute of Human Virology, Abuja, Nigeria
| | - James Frimpong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Mark T. K. Cheng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sani H. Aliyu
- Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | | | - Richard Odame Phillips
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Michael Owusu
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Africa Health Research Institute, Durban, South Africa
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Mykytyn AZ, Fouchier RA, Haagmans BL. Antigenic evolution of SARS coronavirus 2. Curr Opin Virol 2023; 62:101349. [PMID: 37647851 DOI: 10.1016/j.coviro.2023.101349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.
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Affiliation(s)
- Anna Z Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron Am Fouchier
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart L Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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Ma S, Xiao G, Deng X, Tong M, Huang J, Li Q, Zhang Y. CovidShiny: An Integrated Web Tool for SARS-CoV-2 Mutation Profiling and Molecular Diagnosis Assay Evaluation In Silico. Viruses 2023; 15:2017. [PMID: 37896794 PMCID: PMC10611021 DOI: 10.3390/v15102017] [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: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is still ongoing, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continuing to evolve and accumulate mutations. While various bioinformatics tools have been developed for SARS-CoV-2, a well-curated mutation-tracking database integrated with in silico evaluation for molecular diagnostic assays is currently unavailable. To address this, we introduce CovidShiny, a web tool that integrates mutation profiling, in silico evaluation, and data download capabilities for genomic sequence-based SARS-CoV-2 assays and data download. It offers a feasible framework for surveilling the mutation of SARS-CoV-2 and evaluating the coverage of the molecular diagnostic assay for SARS-CoV-2. With CovidShiny, we examined the dynamic mutation pattern of SARS-CoV-2 and evaluated the coverage of commonly used assays on a large scale. Based on our in silico analysis, we stress the importance of using multiple target molecular diagnostic assays for SARS-CoV-2 to avoid potential false-negative results caused by viral mutations. Overall, CovidShiny is a valuable tool for SARS-CoV-2 mutation surveillance and in silico assay design and evaluation.
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Affiliation(s)
- Shaoqian Ma
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Gezhi Xiao
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Xusheng Deng
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Mengsha Tong
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Jialiang Huang
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Qingge Li
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
| | - Yongyou Zhang
- The State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine Engineering, Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen 361100, China; (S.M.); (G.X.); (X.D.); (M.T.); (J.H.); (Q.L.)
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361100, China
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Andre M, Lau LS, Pokharel MD, Ramelow J, Owens F, Souchak J, Akkaoui J, Ales E, Brown H, Shil R, Nazaire V, Manevski M, Paul NP, Esteban-Lopez M, Ceyhan Y, El-Hage N. From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World. BIOLOGY 2023; 12:1267. [PMID: 37759666 PMCID: PMC10525159 DOI: 10.3390/biology12091267] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient transmission, severity, and immune evasion properties. The World Health Organization has given these variants names according to the letters of the Greek Alphabet, starting with the Alpha (B.1.1.7) variant, which emerged in 2020, followed by the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. This review explores the genetic variation among different VOCs of SARS-CoV-2 and how the emergence of variants made a global impact on the pandemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nazira El-Hage
- Herbert Wertheim College of Medicine, Biomedical Sciences Program Florida International University, Miami, FL 33199, USA; (M.A.); (L.-S.L.); (M.D.P.); (J.R.); (F.O.); (J.S.); (J.A.); (E.A.); (H.B.); (R.S.); (V.N.); (M.M.); (N.P.P.); (M.E.-L.); (Y.C.)
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37
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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Scheuermann SE, Goff K, Rowe LA, Beddingfield BJ, Maness NJ. Real-Time Analysis of SARS-CoV-2-Induced Cytolysis Reveals Distinct Variant-Specific Replication Profiles. Viruses 2023; 15:1937. [PMID: 37766343 PMCID: PMC10537736 DOI: 10.3390/v15091937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The ability of each new SARS-CoV-2 variant to evade host humoral immunity is the focus of intense research. Each variant may also harbor unique replication capabilities relevant for disease and transmission. Here, we demonstrate a new approach to assessing viral replication kinetics using real-time cell analysis (RTCA). Virus-induced cell death is measured in real time as changes in electrical impedance through cell monolayers while images are acquired at defined intervals via an onboard microscope and camera. Using this system, we quantified replication kinetics of five clinically important viral variants: WA1/2020 (ancestral), Delta, and Omicron subvariants BA.1, BA.4, and BA.5. Multiple measures proved useful in variant replication comparisons, including the elapsed time to, and the slope at, the maximum rate of cell death. Important findings include significantly weaker replication kinetics of BA.1 by all measures, while BA.5 harbored replication kinetics at or near ancestral levels, suggesting evolution to regain replicative capacity, and both an altered profile of cell killing and enhanced fusogenicity of the Delta variant. Together, these data show that RTCA is a robust method to assess replicative capacity of any given SARS-CoV-2 variant rapidly and quantitatively, which may be useful in assessment of newly emerging variants.
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Affiliation(s)
- Sarah E. Scheuermann
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Lori A. Rowe
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
| | - Brandon J. Beddingfield
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Nicholas J. Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA 70433, USA; (S.E.S.); (K.G.); (L.A.R.)
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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Li X, Yan H, Wong G, Ouyang W, Cui J. Identifying featured indels associated with SARS-CoV-2 fitness. Microbiol Spectr 2023; 11:e0226923. [PMID: 37698427 PMCID: PMC10580940 DOI: 10.1128/spectrum.02269-23] [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: 06/01/2023] [Accepted: 07/14/2023] [Indexed: 09/13/2023] Open
Abstract
As an RNA virus, severe acute respiratory coronavirus 2 (SARS-CoV-2) is known for frequent substitution mutations, and substitutions in important genome regions are often associated with viral fitness. However, whether indel mutations are related to viral fitness is generally ignored. Here we developed a computational methodology to investigate indels linked to fitness occurring in over 9 million SARS-CoV-2 genomes. Remarkably, by analyzing 31,642,404 deletion records and 1,981,308 insertion records, our pipeline identified 26,765 deletion types and 21,054 insertion types and discovered 65 indel types with a significant association with Pango lineages. We proposed the concept of featured indels representing the population of specific Pango lineages and variants as substitution mutations and termed these 65 indels as featured indels. The selective pressure of all indel types is assessed using the Bayesian model to explore the importance of indels. Our results exhibited higher selective pressure of indels like substitution mutations, which are important for assessing viral fitness and consistent with previous studies in vitro. Evaluation of the growth rate of each viral lineage indicated that indels play key roles in SARS-CoV-2 evolution and deserve more attention as substitution mutations. IMPORTANCE The fitness of indels in pathogen genome evolution has rarely been studied. We developed a computational methodology to investigate the severe acute respiratory coronavirus 2 genomes and analyze over 33 million records of indels systematically, ultimately proposing the concept of featured indels that can represent specific Pango lineages and identifying 65 featured indels. Machine learning model based on Bayesian inference and viral lineage growth rate evaluation suggests that these featured indels exhibit selection pressure comparable to replacement mutations. In conclusion, indels are not negligible for evaluating viral fitness.
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Affiliation(s)
- Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongliang Yan
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Wanli Ouyang
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
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40
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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [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: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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Zhan Q, Solo-Gabriele HM, Sharkey ME, Amirali A, Beaver CC, Boone MM, Comerford S, Cooper D, Cortizas EM, Cosculluela GA, Currall BB, Grills GS, Kobetz E, Kumar N, Laine J, Lamar WE, Lyu J, Mason CE, Reding BD, Roca MA, Schürer SC, Shukla BS, Solle NS, Suarez MM, Stevenson M, Tallon JJ, Thomas C, Vidović D, Williams SL, Yin X, Zarnegarnia Y, Babler KM. Correlative analysis of wastewater trends with clinical cases and hospitalizations through five dominant variant waves of COVID-19. ACS ES&T WATER 2023; 3:2849-2862. [PMID: 38487696 PMCID: PMC10936583 DOI: 10.1021/acsestwater.3c00032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Wastewater-based epidemiology (WBE) has been utilized to track community infections of Coronavirus Disease 2019 (COVID-19) by detecting RNA of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), within samples collected from wastewater. The correlations between community infections and wastewater measurements of the RNA can potentially change as SARS-CoV-2 evolves into new variations by mutating. This study analyzed SARS-CoV-2 RNA, and indicators of human waste in wastewater from two sewersheds of different scales (University of Miami (UM) campus and Miami-Dade County Central District wastewater treatment plant (CDWWTP)) during five internally defined COVID-19 variant dominant periods (Initial, Pre-Delta, Delta, Omicron and Post-Omicron wave). SARS-CoV-2 RNA quantities were compared against COVID-19 clinical cases and hospitalizations to evaluate correlations with wastewater SARS-CoV-2 RNA. Although correlations between documented clinical cases and hospitalizations were high, prevalence for a given wastewater SARS-CoV-2 level varied depending upon the variant analyzed. The correlative relationship was significantly steeper (more cases per level found in wastewater) for the Omicron-dominated period. For hospitalization, the relationships were steepest for the Initial wave, followed by the Delta wave with flatter slopes during all other waves. Overall results were interpreted in the context of SARS-CoV-2 virulence and vaccination rates among the community.
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Affiliation(s)
- Qingyu Zhan
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Helena Maria Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Mark E. Sharkey
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Ayaaz Amirali
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Cynthia C. Beaver
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Melinda M. Boone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Samuel Comerford
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | | | - Elena M. Cortizas
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Gabriella A. Cosculluela
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Benjamin B. Currall
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Erin Kobetz
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Naresh Kumar
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Jennifer Laine
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Walter E. Lamar
- Division of Occupational Health, Safety & Compliance, University of Miami Health System, Miami, FL 33136 USA
| | - Jiangnan Lyu
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian D. Reding
- Environmental Health and Safety, University of Miami, Miami, FL 33136 USA
| | - Matthew A. Roca
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
- Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146 USA
| | - Bhavarth S. Shukla
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Natasha Schaefer Solle
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Maritza M. Suarez
- Department of Medicine, University of Miami Miller School of Medicine, Miami, 33136 FL USA
| | - Mario Stevenson
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - John J. Tallon
- Facilities and Operations, University of Miami, Coral Gables, FL 33146 USA
| | - Collette Thomas
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Dušica Vidović
- Department of Molecular & Cellular Pharmacology, University of Miami Miller School of Medicines, Miami, FL 33136 USA
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Xue Yin
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
| | - Yalda Zarnegarnia
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Kristina Marie Babler
- Department of Chemical, Environmental, and Materials Engineering, University of Miami, Coral Gables, FL 33146 USA
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Liang J, Ding Z, Liu K. Identification of critical SARS-CoV-2 amino acids associated with COVID-19 hospitalization rate using machine learning and statistical modeling: An observational study in the United States. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105480. [PMID: 37437768 DOI: 10.1016/j.meegid.2023.105480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/29/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND The COVID-19 pandemic has put many medical systems on the verge of collapse in the last two years. Virus mutation was one of the important factors affecting the COVID-19 infection severity and hospitalizations. Although over ten thousand SARS-CoV-2 mutations being reported since the beginning of the COVID-19 pandemic, only a small percentage of mutations are likely to affect the virus phenotype and change its severity. Finding out which amino acids have the greatest impact on COVID-19 hospitalization rate is an important research question. METHODS This observational study used the COVID-19 case hospitalization ratio (CHR) to represent the virus severity related with hospitalization. The database is based on the daily state-level epidemiological and genomic sequential data in the United States from the Alpha wave to the first Omicron wave. The critical amino acids that mostly affected the CHR were determined by using four types of models including extreme gradient boosting decision trees (XGBoost), artificial neural networks (ANNs), logistic regression and Lasso regression models. RESULTS The XGBoost, ANN, logistic regression, and Lasso regression models all produce excellent results (mean square error for all state-level models does not exceed 0.0008 using the testing dataset). Based on the rank of importance of all covariates, the critical amino acids most affecting the CHR were identified, including T19, L24, P25, P26, A27, A67, H69, V70, T95, G142, V143, Y145, E156, F157, N211, L212, V213, R214, D215, G339, R346, S373, L452, S477, T478, E484, N501, A570, P681, and T716. CONCLUSION This study identified critical amino acids that are most likely to affect the hospitalization rate, allowing public health workers to monitor these highly risky amino acids and raise an alarm immediately when more severe mutations occur. Furthermore, the methodology and results may be extended to other regions.
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Affiliation(s)
- Jingbo Liang
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China.
| | - Zhaojun Ding
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Kunmeng Liu
- Center for Medical Artificial Intelligence, Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
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43
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Liu Y, Kumblathan T, Joyce MA, Tyrrell DL, Tipples G, Pang X, Li XF, Le XC. Multiplex Assays Enable Simultaneous Detection and Identification of SARS-CoV-2 Variants of Concern in Clinical and Wastewater Samples. ACS MEASUREMENT SCIENCE AU 2023; 3:258-268. [PMID: 37600458 PMCID: PMC10152402 DOI: 10.1021/acsmeasuresciau.3c00005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 08/22/2023]
Abstract
The targeted screening and sequencing approaches for COVID-19 surveillance need to be adjusted to fit the evolving surveillance objectives which necessarily change over time. We present the development of variant screening assays that can be applied to new targets in a timely manner and enable multiplexing of targets for efficient implementation in the laboratory. By targeting the HV69/70 deletion for Alpha, K417N for Beta, K417T for Gamma, and HV69/70 deletion plus K417N for sub-variants BA.1, BA.3, BA.4, and BA.5 of Omicron, we achieved simultaneous detection and differentiation of Alpha, Beta, Gamma, and Omicron in a single assay. Targeting both T478K and P681R mutations enabled specific detection of the Delta variant. The multiplex assays used in combination, targeting K417N and T478K, specifically detected the Omicron sub-variant BA.2. The limits of detection for the five variants of concern were 4-16 copies of the viral RNA per reaction. Both assays achieved 100% clinical sensitivity and 100% specificity. Analyses of 377 clinical samples and 24 wastewater samples revealed the Delta variant in 100 clinical samples (nasopharyngeal and throat swab) collected in November 2021. Omicron BA.1 was detected in 79 nasopharyngeal swab samples collected in January 2022. Alpha, Beta, and Gamma variants were detected in 24 wastewater samples collected in May-June 2021 from two major cities of Alberta (Canada), and the results were consistent with the clinical cases of multiple variants reported in the community.
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Affiliation(s)
- Yanming Liu
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Teresa Kumblathan
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Michael A. Joyce
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - D. Lorne Tyrrell
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Graham Tipples
- Li
Ka Shing Institute of Virology, Department
of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
| | - Xiaoli Pang
- Provincial
Laboratory for Public Health, Alberta Precision Laboratories, University of Alberta Hospitals, 8440-112 Street, Edmonton, Alberta T6G 2J2, Canada
- Department
of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Xing-Fang Li
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division
of Analytical and Environmental Toxicology, Department of Laboratory
Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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44
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Yamamoto S, Yamayoshi S, Ito M, Sakai-Tagawa Y, Nakachi I, Baba R, Kamimoto S, Ogura T, Hagiwara S, Kato H, Nakajima H, Uwamino Y, Yagi K, Sugaya N, Nagai H, Saito M, Adachi E, Koga M, Tsutsumi T, Duong C, Okuda M, Murakami J, Furusawa Y, Ujie M, Iwatsuki-Horimoto K, Yotsuyanagi H, Kawaoka Y. Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination. iScience 2023; 26:107208. [PMID: 37448563 PMCID: PMC10290734 DOI: 10.1016/j.isci.2023.107208] [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: 02/15/2023] [Revised: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
SARS-CoV-2 has gradually acquired amino acid substitutions in its S protein that reduce the potency of neutralizing antibodies, leading to decreased vaccine efficacy. Here, we attempted to obtain mutant viruses by passaging SARS-CoV-2 in the presence of plasma samples from convalescent patients or vaccinees to determine which amino acid substitutions affect the antigenicity of SARS-CoV-2. Several amino acid substitutions in the S2 region, as well as the N-terminal domain (NTD) and receptor-binding domain (RBD), affected the neutralization potency of plasma samples collected from vaccinees, indicating that amino acid substitutions in the S2 region as well as those in the NTD and RBD affect neutralization by vaccine-induced antibodies. Furthermore, the neutralizing potency of vaccinee plasma samples against mutant viruses we obtained or circulating viruses differed among individuals. These findings suggest that genetic backgrounds of vaccinees influence the recognition of neutralizing epitopes.
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Affiliation(s)
- Shinya Yamamoto
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Mutsumi Ito
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigenobu Kamimoto
- Pulmonary Division, Department of Internal Medicine, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Takayuki Ogura
- Department of Emergency and Intensive Care, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Shigehiro Hagiwara
- Department of Clinical Laboratory, Saiseikai Utsunomiya Hospital, Tochigi 321-0974, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuma Yagi
- Department of Pulmonary Medicine, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Norio Sugaya
- Department of Pediatrics, Keiyu Hospital, Kanagawa 220-8521, Japan
| | - Hiroyuki Nagai
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Eisuke Adachi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Calvin Duong
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Moe Okuda
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jurika Murakami
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yuri Furusawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Michiko Ujie
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
- The University of Tokyo, Pandemic Preparedness, Infection and Advanced Research Center, Tokyo 108-8639, Japan
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45
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Khetran SR, Mustafa R. Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e43906. [PMID: 37485046 PMCID: PMC10353769 DOI: 10.2196/43906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/02/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023]
Abstract
Background COVID-19 and Middle East Respiratory Syndrome are two pandemic respiratory diseases caused by coronavirus species. The novel disease COVID-19 caused by SARS-CoV-2 was first reported in Wuhan, Hubei Province, China, in December 2019, and became a pandemic within 2-3 months, affecting social and economic platforms worldwide. Despite the rapid development of vaccines, there have been obstacles to their distribution, including a lack of fundamental resources, poor immunization, and manual vaccine replication. Several variants of the original Wuhan strain have emerged in the last 3 years, which can pose a further challenge for control and vaccine development. Objective The aim of this study was to comprehensively analyze mutations in SARS-CoV-2 variants of concern (VoCs) using a bioinformatics approach toward identifying novel mutations that may be helpful in developing new vaccines by targeting these sites. Methods Reference sequences of the SARS-CoV-2 spike (YP_009724390) and nucleocapsid (YP_009724397) proteins were compared to retrieved sequences of isolates of four VoCs from 14 countries for mutational and evolutionary analyses. Multiple sequence alignment was performed and phylogenetic trees were constructed by the neighbor-joining method with 1000 bootstrap replicates using MEGA (version 6). Mutations in amino acid sequences were analyzed using the MultAlin online tool (version 5.4.1). Results Among the four VoCs, a total of 143 nonsynonymous mutations and 8 deletions were identified in the spike and nucleocapsid proteins. Multiple sequence alignment and amino acid substitution analysis revealed new mutations, including G72W, M2101I, L139F, 209-211 deletion, G212S, P199L, P67S, I292T, and substitutions with unknown amino acid replacement, reported in Egypt (MW533289), the United Kingdom (MT906649), and other regions. The variants B.1.1.7 (Alpha variant) and B.1.617.2 (Delta variant), characterized by higher transmissibility and lethality, harbored the amino acid substitutions D614G, R203K, and G204R with higher prevalence rates in most sequences. Phylogenetic analysis among the novel SARS-CoV-2 variant proteins and some previously reported β-coronavirus proteins indicated that either the evolutionary clade was weakly supported or not supported at all by the β-coronavirus species. Conclusions This study could contribute toward gaining a better understanding of the basic nature of SARS-CoV-2 and its four major variants. The numerous novel mutations detected could also provide a better understanding of VoCs and help in identifying suitable mutations for vaccine targets. Moreover, these data offer evidence for new types of mutations in VoCs, which will provide insight into the epidemiology of SARS-CoV-2.
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Affiliation(s)
- Saima Rehman Khetran
- Department of Life Sciences Sardar Bahadur Khan Women's University Quetta Pakistan
| | - Roma Mustafa
- Department of Life Sciences Sardar Bahadur Khan Women's University Quetta Pakistan
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46
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Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548464. [PMID: 37502853 PMCID: PMC10369864 DOI: 10.1101/2023.07.10.548464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence the ~30,000 nucleotide SARS-CoV-2 genome that use a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with 'Ns' inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). This study uses seven long-range PCR primers with an amplicon size of ~4500 bp to tile across the complete SARS-CoV-2 genome. One of these regions includes the full-length S-gene by using a set of flanking primers. Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias.
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Affiliation(s)
- Sangam Kandel
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 782), Little Rock, AR 72205, USA
| | - Susanna L. Hartzell
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
| | - Ashton K. Ingold
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
| | - Grace A. Turner
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
| | - Joshua L. Kennedy
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - David W. Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 782), Little Rock, AR 72205, USA
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47
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Sinha A, Sangeet S, Roy S. Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective. ACS OMEGA 2023; 8:23283-23304. [PMID: 37426203 PMCID: PMC10324094 DOI: 10.1021/acsomega.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023]
Abstract
Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure-function and passed through several variants of concern. Recent advances in high-resolution structure determination and multiscale imaging techniques, cost-effective next-generation sequencing, and development of new computational methods (including information theory, statistical methods, machine learning, and many other artificial intelligence-based techniques) have hugely contributed to the characterization of sequence, structure, function of spike proteins, and its different variants to understand viral pathogenesis, evolutions, and transmission. Laying on the foundation of the sequence-structure-function paradigm, this review summarizes not only the important findings on structure/function but also the structural dynamics of different spike components, highlighting the effects of mutations on them. As dynamic fluctuations of three-dimensional spike structure often provide important clues for functional modulation, quantifying time-dependent fluctuations of mutational events over spike structure and its genetic/amino acidic sequence helps identify alarming functional transitions having implications for enhanced fusogenicity and pathogenicity of the virus. Although these dynamic events are more difficult to capture than quantifying a static, average property, this review encompasses those challenging aspects of characterizing the evolutionary dynamics of spike sequence and structure and their implications for functions.
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48
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Miteva D, Kitanova M, Batselova H, Lazova S, Chervenkov L, Peshevska-Sekulovska M, Sekulovski M, Gulinac M, Vasilev GV, Tomov L, Velikova T. The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice. Vaccines (Basel) 2023; 11:1181. [PMID: 37514997 PMCID: PMC10385722 DOI: 10.3390/vaccines11071181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Although the chief of the World Health Organization (WHO) has declared the end of the coronavirus disease 2019 (COVID-19) as a global health emergency, the disease is still a global threat. To be able to manage such pandemics in the future, it is necessary to develop proper strategies and opportunities to protect human life. The data on the SARS-CoV-2 virus must be continuously analyzed, and the possibilities of mutation and the emergence of new, more infectious variants must be anticipated, as well as the options of using different preventive and therapeutic techniques. This is because the fast development of severe acute coronavirus 2 syndrome (SARS-CoV-2) variants of concern have posed a significant problem for COVID-19 pandemic control using the presently available vaccinations. This review summarizes data on the SARS-CoV-2 variants that are responsible for severe COVID-19 and the clinical efficacy of the most commonly used vaccines in clinical practice. The consequences after the disease (long COVID or post-COVID conditions) continue to be the subject of studies and research, and affect social and economic life worldwide.
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Affiliation(s)
- Dimitrina Miteva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Meglena Kitanova
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Hristiana Batselova
- Department of Epidemiology and Disaster Medicine, University Hospital "Saint George", Medical University, 6000 Plovdiv, Bulgaria
| | - Snezhina Lazova
- Pediatric Department, University Hospital "N. I. Pirogov," 21 "General Eduard I. Totleben" Blvd, 1606 Sofia, Bulgaria
- Department of Healthcare, Faculty of Public Health "Prof. Tsekomir Vodenicharov, MD, DSc", Medical University of Sofia, Bialo More 8 str., 1527 Sofia, Bulgaria
| | - Lyubomir Chervenkov
- Department of Diagnostic Imaging, Medical University Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, 1407 Sofia, Bulgaria
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Metodija Sekulovski
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
- Department of Anesthesiology and Intensive Care, University Hospital Lozenetz, 1 Kozyak str., 1407 Sofia, Bulgaria
| | - Milena Gulinac
- Department of General and Clinical Pathology, Medical University of Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Georgi V Vasilev
- Clinic of Endocrinology and Metabolic Disorders, UMHAT "Sv. Georgi", 4000 Plovdiv, Bulgaria
| | - Luchesar Tomov
- Department of Informatics, New Bulgarian University, Montevideo 21 str., 1618 Sofia, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
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49
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Márquez-Costa R, Montagud-Martínez R, Marqués MC, Albert E, Navarro D, Daròs JA, Ruiz R, Rodrigo G. Multiplexable and Biocomputational Virus Detection by CRISPR-Cas9-Mediated Strand Displacement. Anal Chem 2023; 95:9564-9574. [PMID: 37204239 PMCID: PMC10255568 DOI: 10.1021/acs.analchem.3c01041] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
Recurrent disease outbreaks caused by different viruses, including the novel respiratory virus SARS-CoV-2, are challenging our society at a global scale; so versatile virus detection methods would enable a calculated and faster response. Here, we present a novel nucleic acid detection strategy based on CRISPR-Cas9, whose mode of action relies on strand displacement rather than on collateral catalysis, using the Streptococcus pyogenes Cas9 nuclease. Given a preamplification process, a suitable molecular beacon interacts with the ternary CRISPR complex upon targeting to produce a fluorescent signal. We show that SARS-CoV-2 DNA amplicons generated from patient samples can be detected with CRISPR-Cas9. We also show that CRISPR-Cas9 allows the simultaneous detection of different DNA amplicons with the same nuclease, either to detect different SARS-CoV-2 regions or different respiratory viruses. Furthermore, we demonstrate that engineered DNA logic circuits can process different SARS-CoV-2 signals detected by the CRISPR complexes. Collectively, this CRISPR-Cas9 R-loop usage for the molecular beacon opening (COLUMBO) platform allows a multiplexed detection in a single tube, complements the existing CRISPR-based methods, and displays diagnostic and biocomputing potential.
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Affiliation(s)
- Rosa Márquez-Costa
- Institute
for Integrative Systems Biology (I2SysBio), CSIC − University
of Valencia, 46980 Paterna, Spain
| | - Roser Montagud-Martínez
- Institute
for Integrative Systems Biology (I2SysBio), CSIC − University
of Valencia, 46980 Paterna, Spain
| | - María-Carmen Marqués
- Institute
for Integrative Systems Biology (I2SysBio), CSIC − University
of Valencia, 46980 Paterna, Spain
| | - Eliseo Albert
- Microbiology
Service, Clinic University Hospital, INCLIVA
Biomedical Research Institute, 46010 Valencia, Spain
| | - David Navarro
- Microbiology
Service, Clinic University Hospital, INCLIVA
Biomedical Research Institute, 46010 Valencia, Spain
- Department
of Microbiology, School of Medicine, University
of Valencia, 46010 Valencia, Spain
| | - José-Antonio Daròs
- Instituto
de Biología Molecular y Celular de Plantas (IBMCP), CSIC − Universitat Politècnica de València, 46022 Valencia, Spain
| | - Raúl Ruiz
- Institute
for Integrative Systems Biology (I2SysBio), CSIC − University
of Valencia, 46980 Paterna, Spain
| | - Guillermo Rodrigo
- Institute
for Integrative Systems Biology (I2SysBio), CSIC − University
of Valencia, 46980 Paterna, Spain
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50
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Nabaes Jodar MS, Torres C, Mojsiejczuk L, Acuña D, Valinotto LE, Goya S, Natale M, Lusso S, Alexay S, Amadio A, Irazoqui M, Fernandez F, Acevedo ME, Alvarez Lopez C, Angelletti A, Aulicino P, Bolatti E, Brusés B, Cacciahue M, Cavatorta A, Cerri A, Cordero A, Debat H, Dus Santos MJ, Eberhardt MF, Ercole R, Espul C, Farber M, Fay F, Fernandez A, Ferrini F, Formichelli L, Ceballos S, Gallego F, Giri A, Gismondi M, Acevedo RM, Gramundi I, Ibañez ME, Konig G, Leiva V, Lorenzini Campos M, Lucero H, Marquez N, Mazzeo M, Mistchenko AS, Montoto L, Muñoz M, Nadalich V, Nardi C, Ortiz B, Pianciola L, Pintos C, Puebla A, Rastellini C, Rojas AE, Sfalcin J, Suarez A, Theaux C, Thomas G, Tittarelli E, Toro R, Villanova V, Wenk G, Ziehm C, Zimmermann MC, Zunino S, Pais P, Viegas M. The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37. Viruses 2023; 15:1382. [PMID: 37376681 DOI: 10.3390/v15061382] [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: 05/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial--temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.
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Affiliation(s)
- Mercedes Soledad Nabaes Jodar
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigaciones En Bacteriologia y Virologia Molecular (IbaViM), Junín 956, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Laura Mojsiejczuk
- Instituto de Investigaciones En Bacteriologia y Virologia Molecular (IbaViM), Junín 956, Ciudad Autómoma de Buenos Aires 1113, Argentina
| | - Dolores Acuña
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
| | - Laura Elena Valinotto
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
| | - Stephanie Goya
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Monica Natale
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Silvina Lusso
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Sofia Alexay
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Ariel Amadio
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigación de La Cadena Lactea (IDICAL) INTA-CONICET, Ruta 34 Km 227, Rafaela 2300, Argentina
| | - Matias Irazoqui
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigación de La Cadena Lactea (IDICAL) INTA-CONICET, Ruta 34 Km 227, Rafaela 2300, Argentina
| | - Franco Fernandez
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba 5020, Argentina
| | - Maria Elina Acevedo
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Cristina Alvarez Lopez
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Andres Angelletti
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Paula Aulicino
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Laboratorio de Biología Celular y Retrovirus, Hospital de Pediatría Prof. Juan P. Garrahan, Avenida Brasil 1175, Ciudad Autónoma de Buenos Aires 1260, Argentina
| | - Elisa Bolatti
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina
| | - Bettina Brusés
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Marco Cacciahue
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Ana Cavatorta
- Centro de Tecnología En Salud Pública, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario 2000, Argentina
| | - Agustina Cerri
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina
| | - Andres Cordero
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Humberto Debat
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba 5020, Argentina
| | - Maria Jose Dus Santos
- Instituto de Virología e Innovaciones Tecnológicas (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
- Laboratorio de Diagnostico-UNIDAD COVID, Universidad Nacional de Hurlingham, Hurlingham 1686, Argentina
| | - Maria Florencia Eberhardt
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Investigación de La Cadena Lactea (IDICAL) INTA-CONICET, Ruta 34 Km 227, Rafaela 2300, Argentina
| | - Regina Ercole
- Laboratorio de Virología, HIEAyC San Juan de Dios, Calles 27 y 70, La Plata 1900, Argentina
| | - Carlos Espul
- Dirección de Epidemiologia y Red de Laboratorios Del Ministerio de Salud de La Provincia de Mendoza, Mendoza 5500, Argentina
| | - Marisa Farber
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Fabián Fay
- CIBIC Laboratorio, Pte. Roca 746, Rosario 2000, Argentina
| | - Ailen Fernandez
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Florencia Ferrini
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Laboratorio de Medicina Genómica, Facultad de Medicina, Universidad Nacional Del Nordeste, Córdoba 1430, Argentina
| | - Laura Formichelli
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Santiago Ceballos
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Cadic-Conicet, Universidad Nacional de Tierra del Fuego, Houssay 200, Ushuaia 9410, Argentina
| | - Fernando Gallego
- Hospital Regional Ushuaia, Av. 12 de Octubre y Maipú, Ushuaia 9410, Argentina
| | - Adriana Giri
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina
| | - Maria Gismondi
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Raul Maximiliano Acevedo
- Instituto de Botánica Del Nordeste-UNNE, Sargento Juan Bautista Cabral 2131, Corrientes 3400, Argentina
| | - Ivan Gramundi
- Hospital Regional Ushuaia, Av. 12 de Octubre y Maipú, Ushuaia 9410, Argentina
| | - María Eugenia Ibañez
- Biología Molecular-Laboratorio Central, Hospital Alemán, Av. Pueyrredón 1640, Cuidad Autónoma de Buenos Aires 1118, Argentina
| | - Guido Konig
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Viviana Leiva
- Laboratorio de Salud Pública, Talcahuano 2194, Godoy Cruz 5501, Argentina
| | - Melina Lorenzini Campos
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Horacio Lucero
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Av. Las Heras 727, Resistencia 3500, Argentina
| | - Nathalie Marquez
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba 5020, Argentina
| | - Melina Mazzeo
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Alicia Susana Mistchenko
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
- Comisión Investigaciones Científicas de La Provincia de Buenos Aires, Camino General Belgrano y 526, La Plata 1900, Argentina
| | - Luciana Montoto
- Laboratorio de Biología Molecular Hospital Pedro de Elizalde, Avenida Manuel A Montes de Oca 1402, Cuidad Autónoma de Buenos Aires 1270, Argentina
| | - Marianne Muñoz
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Victoria Nadalich
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Cristina Nardi
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA) de La Universidad Nacional de Tierra Del Fuego (UNTDF), Houssay 200, Ushuaia 9410, Argentina
| | - Belén Ortiz
- Laboratorio de Salud Pública, Talcahuano 2194, Godoy Cruz 5501, Argentina
| | - Luis Pianciola
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Carolina Pintos
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Andrea Puebla
- Instituto de Biotecnología, Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), De Los Reseros y N. Repetto s/No, Hurlingham 1686, Argentina
| | - Carolina Rastellini
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Alejandro Ezequiel Rojas
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales (ICPA) de La Universidad Nacional de Tierra Del Fuego (UNTDF), Houssay 200, Ushuaia 9410, Argentina
| | - Javier Sfalcin
- CIBIC Laboratorio, Pte. Roca 746, Rosario 2000, Argentina
| | - Ariel Suarez
- Departamento de Biología y Genética Molecular, IACA Laboratorios, San Martín 68, Bahía Blanca 8000, Argentina
| | - Clara Theaux
- Laboratorio de Biología Molecular Del Hospital General de Agudos, Carlos G. Durand, Diaz Vélez 5044, Cuidad Autónoma de Buenos Aires 1405, Argentina
| | - Guillermo Thomas
- Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Estefania Tittarelli
- Departamento de Biología y Genética Molecular, IACA Laboratorios, San Martín 68, Bahía Blanca 8000, Argentina
| | - Rosana Toro
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
| | - Vanina Villanova
- Laboratorio Mixto de Biotecnología Acuática, Av. Eduardo Carrasco y Cordiviola, Rosario 2000, Argentina
| | - Gretel Wenk
- Laboratorio de Biología Molecular Hospital Pedro de Elizalde, Avenida Manuel A Montes de Oca 1402, Cuidad Autónoma de Buenos Aires 1270, Argentina
| | - Cecilia Ziehm
- Laboratorio Central Ciudad de Neuquén, Ministerio de Salud, Gregorio Martínez 65, Neuquén 8300, Argentina
| | - Maria Carla Zimmermann
- Laboratorio de Medicina Genómica, Facultad de Medicina, Universidad Nacional Del Nordeste, Córdoba 1430, Argentina
| | - Sebastian Zunino
- Laboratorio de Virología Molecular, Hospital Blas L. Dubarry, Calle 12 825, Mercedes 6600, Argentina
| | - Proyecto Pais
- Consorcio Argentino de Genómica de SARS-CoV-2, Proyecto Argentino Interinstitucional de Genómica de SARS-CoV-2, Gallo 1330, Ciudad Autónoma de Buenos Aires 1425, Argentina
| | - Mariana Viegas
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Godoy Cruz 2390, Ciudad Autónoma de Buenos Aires 2915, Argentina
- Laboratorio de Salud Pública, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 1 y 47, La Plata 1900, Argentina
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