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Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [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: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
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Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
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Jiang M, Fang C, Ma Y. Deciphering the rule of antigen-antibody amino acid interaction. Front Immunol 2023; 14:1269916. [PMID: 38111576 PMCID: PMC10725943 DOI: 10.3389/fimmu.2023.1269916] [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: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Purpose Antigenic drift is the biggest challenge for mutagenic RNA virus vaccine development. The primary purpose is to determine the IEMM (immune escape mutation map) of 20 amino acids' replacement to reveal the rule of the viral immune escape. Methods To determine the relationship between epitope mutation and immune escape, we use universal protein tags as a linear epitope model. To describe and draw amino acid linkage diagrams, mutations of protein tags are classified into four categories: IEM (immune escape mutation), ADERM (antibody-dependent enhancement risk mutation), EQM (equivalent mutation), and IVM (invalid mutation). To overcome the data limitation, a general antigen-antibody (Ag-Ab) interaction map was constructed by analyzing the published three-dimensional (3D) Ag-Ab interaction patterns. Results (i) One residue interacts with multiple amino acids in antigen-antibody interaction. (ii) Most amino acid replacements are IVM and EQM. (iii) Once aromatic amino acids replace non-aromatic amino acids, the mutation is often IEM. (iv) Substituting residues with the same physical and chemical properties easily leads to IVM. Therefore, this study has important theoretical significance for future research on antigenic drift, antibody rescue, and vaccine renewal design. Conclusion The antigenic epitope mutations were typed into IEM, ADERM, EQM, and IVM types to describe and quantify the results of antigenic mutations. The antigen-antibody interaction rule was summarized as a one-to-many interaction rule. To sum up, the epitope mutation rules were defined as IVM and EQM predomination rules and the aryl mutation escape rule.
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Affiliation(s)
| | | | - Yongping Ma
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Basical Medical Collage, Chongqing Medical University, Chongqing, China
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He X, He C, Hong W, Yang J, Wei X. Research progress in spike mutations of SARS-CoV-2 variants and vaccine development. Med Res Rev 2023. [PMID: 36929527 DOI: 10.1002/med.21941] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 09/27/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic can hardly end with the emergence of different variants over time. In the past 2 years, several variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), such as the Delta and Omicron variants, have emerged with higher transmissibility, immune evasion and drug resistance, leading to higher morbidity and mortality in the population. The prevalent variants of concern (VOCs) share several mutations on the spike that can affect virus characteristics, including transmissibility, antigenicity, and immune evasion. Increasing evidence has demonstrated that the neutralization capacity of sera from COVID-19 convalescent or vaccinated individuals is decreased against SARS-CoV-2 variants. Moreover, the vaccine effectiveness of current COVID-19 vaccines against SARS-CoV-2 VOCs is not as high as that against wild-type SARS-CoV-2. Therefore, more attention might be paid to how the mutations impact vaccine effectiveness. In this review, we summarized the current studies on the mutations of the SARS-CoV-2 spike, particularly of the receptor binding domain, to elaborate on how the mutations impact the infectivity, transmissibility and immune evasion of the virus. The effects of mutations in the SARS-CoV-2 spike on the current therapeutics were highlighted, and potential strategies for future vaccine development were suggested.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingyun Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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4
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Halfmann PJ, Minor NR, Haddock III LA, Maddox R, Moreno GK, Braun KM, Baker DA, Riemersa KK, Prasad A, Alman KJ, Lambert MC, Florek K, Bateman A, Westergaard R, Safdar N, Andes DR, Kawaoka Y, Fida M, Yao JD, Friedrich TC, O’Connor DH. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual. Virus Evol 2022; 9:veac104. [PMID: 37692895 PMCID: PMC10491860 DOI: 10.1093/ve/veac104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 09/12/2023] Open
Abstract
Prolonged infections in immunocompromised individuals may be a source for novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Nicholas R Minor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Luis A Haddock III
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Robert Maddox
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kasen K Riemersa
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Ankur Prasad
- Division of Allergy, Pulmonary and Critical Care Medicine, School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705-2281, USA
| | - Kirsten J Alman
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Matthew C Lambert
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Allen Bateman
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Ryan Westergaard
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Nasia Safdar
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - David R Andes
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Madiha Fida
- Division of Infectious Diseases, Mayo Clinic, 200 First St. SW, Rochester, Rochester, Minnesota 55905, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
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5
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Discovery and mechanism of action of Thonzonium bromide from an FDA-approved drug library with potent and broad-spectrum inhibitory activity against main proteases of human coronaviruses. Bioorg Chem 2022; 130:106264. [PMCID: PMC9643332 DOI: 10.1016/j.bioorg.2022.106264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
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Deminco F, Vaz SN, Santana DS, Pedroso C, Tadeu J, Stoecker A, Vieira SM, Netto E, Brites C. A Simplified Sanger Sequencing Method for Detection of Relevant SARS-CoV-2 Variants. Diagnostics (Basel) 2022; 12:2609. [PMID: 36359452 PMCID: PMC9689870 DOI: 10.3390/diagnostics12112609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 08/26/2023] Open
Abstract
Molecular surveillance of the new coronavirus through new genomic sequencing technologies revealed the circulation of important variants of SARS-CoV-2. Sanger sequencing has been useful in identifying important variants of SARS-CoV-2 without the need for whole-genome sequencing. A sequencing protocol was constructed to cover a region of 1000 base pairs, from a 1120 bp product generated after a two-step RT-PCR assay in samples positive for SARS-CoV-2. Consensus sequence construction and mutation identification were performed. Of all 103 samples sequenced, 69 contained relevant variants represented by 20 BA.1, 13 delta, 22 gamma, and 14 zeta, identified between June 2020 and February 2022. All sequences found were aligned with representative sequences of the variants. Using the Sanger sequencing methodology, we were able to develop a more accessible protocol to assist viral surveillance with a more accessible platform.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Carlos Brites
- Laboratório de Pesquisa em Infectologia, Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia (UFBA)/EBSERH, Salvador 40170-110, Bahia, Brazil
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7
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Chetta M, Tarsitano M, Oro M, Rivieccio M, Bukvic N. An in silico pipeline approach uncovers a potentially intricate network involving spike SARS-CoV-2 RNA, RNA vaccines, host RNA-binding proteins (RBPs), and host miRNAs at the cellular level. J Genet Eng Biotechnol 2022; 20:129. [PMID: 36066672 PMCID: PMC9446605 DOI: 10.1186/s43141-022-00413-5] [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: 03/25/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the last 2 years, we have been fighting against SARS-CoV-2 viral infection, which continues to claim victims all over the world. The entire scientific community has been mobilized in an attempt to stop and eradicate the infection. A well-known feature of RNA viruses is their high mutational rate, particularly in specific gene regions. The SARS-CoV-2 S protein is also affected by these changes, allowing viruses to adapt and spread more easily. The vaccines developed using mRNA coding protein S undoubtedly contributed to the "fight" against the COVID-19 pandemic even though the presence of new variants in the spike protein could result in protein conformational changes, which could affect vaccine immunogenicity and thus vaccine effectiveness. RESULTS The study presents the findings of an in silico analysis using various bioinformatics tools finding conserved sequences inside SARS-CoV-2 S protein (encoding mRNA) same as in the vaccine RNA sequences that could be targeted by specific host RNA-binding proteins (RBPs). According to the results an interesting scenario emerges involving host RBPs competition and subtraction. The presence of viral RNA in cytoplasm could be a new tool in the virus's armory, allowing it to improve its chances of survival by altering cell gene expression and thus interfering with host cell processes. In silico analysis was used also to evaluate the presence of similar human miRNA sequences within RBPs motifs that can modulate human RNA expression. Increased cytoplasmic availability of exogenous RNA fragments derived from RNA physiological degradation could potentially mimic the effect of host human miRNAs within the cell, causing modulation of the host cell network. CONCLUSIONS Our in silico analysis could aid in shedding light on the potential effects of exogenous RNA (i.e. viruses and vaccines), thereby improving our understanding of the cellular interactions between virus and host biomolecules. Finally, using the computational approach, it is possible to obtain a safety assessment of RNA-based vaccines as well as indications for use in specific clinical conditions.
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Affiliation(s)
- Massimiliano Chetta
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy.
| | - Marina Tarsitano
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy
| | - Maria Oro
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy
| | - Maria Rivieccio
- AORN A. Cardarelli-Dipartimento delle Tecnologie Avanzate Diagnostico-Terapeutiche e dei Servizi sanitari-U.O.C. Genetica Medica e di Laboratorio, Via A. Cardarelli 9, 80131, Napoli, Italy
| | - Nenad Bukvic
- AOUC "Policlinico di Bari"-UOC Lab. di Genetica Medica, Piazza Giulio Cesare 11, 70124, Bari, Italy
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Cer RZ, Voegtly LJ, Adhikari BN, Pike BL, Lueder MR, Glang LA, Malagon F, Ana ES, Regeimbal JM, Potts-Szoke MF, Schully KL, Smith DR, Bishop-Lilly KA. Genomic and virologic characterization of samples from a shipboard outbreak of COVID-19 reveals distinct variants within limited temporospatial parameters. Front Microbiol 2022; 13:960932. [PMID: 36033872 PMCID: PMC9399806 DOI: 10.3389/fmicb.2022.960932] [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: 06/03/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Early in the pandemic, in March of 2020, an outbreak of COVID-19 occurred aboard the aircraft carrier USS Theodore Roosevelt (CVN-71), during deployment in the Western Pacific. Out of the crew of 4,779 personnel, 1,331 service members were suspected or confirmed to be infected with SARS-CoV-2. The demographic, epidemiologic, and laboratory findings of service members from subsequent investigations have characterized the outbreak as widespread transmission of virus with relatively mild symptoms and asymptomatic infection among mostly young healthy adults. At the time, there was no available vaccination against COVID-19 and there was very limited knowledge regarding SARS-CoV-2 mutation, dispersal, and transmission patterns among service members in a shipboard environment. Since that time, other shipboard outbreaks from which data can be extracted have occurred, but these later shipboard outbreaks have occurred largely in settings where the majority of the crew were vaccinated, thereby limiting spread of the virus, shortening duration of the outbreaks, and minimizing evolution of the virus within those close quarters settings. On the other hand, since the outbreak on the CVN-71 occurred prior to widespread vaccination, it continued over the course of roughly two months, infecting more than 25% of the crew. In order to better understand genetic variability and potential transmission dynamics of COVID-19 in a shipboard environment of immunologically naïve, healthy individuals, we performed whole-genome sequencing and virus culture from eighteen COVID-19-positive swabs collected over the course of one week. Using the unique variants identified in those genomes, we detected seven discrete groups of individuals within the population aboard CVN-71 infected with viruses of distinct genomic signature. This is in stark contrast to a recent outbreak aboard another U.S. Navy ship with >98% vaccinated crew after a port visit in Reykjavik, Iceland, where the outbreak lasted only approximately 2 weeks and the virus was clonal. Taken together, these results demonstrate the utility of sequencing from complex clinical samples for molecular epidemiology and they also suggest that a high rate of vaccination among a population in close communities may greatly reduce spread, thereby restricting evolution of the virus.
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Affiliation(s)
- Regina Z. Cer
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Logan J. Voegtly
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Bishwo N. Adhikari
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Defense Threat Reduction Agency, Ft. Belvoir, VA, United States
| | - Brian L. Pike
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Matthew R. Lueder
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Lindsay A. Glang
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Francisco Malagon
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- Leidos, Reston, VA, United States
| | - Ernesto Santa Ana
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - James M. Regeimbal
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Maria F. Potts-Szoke
- Department of Operations, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kevin L. Schully
- The Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Darci R. Smith
- Department of Microbiology and Immunology, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | - Kimberly A. Bishop-Lilly
- Department of Genomics and Bioinformatics, Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
- *Correspondence: Kimberly A. Bishop-Lilly,
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Gopi P, Gurnani M, Singh S, Sharma P, Pandya P. Structural aspects of SARS-CoV-2 mutations: Implications to plausible infectivity with ACE-2 using computational modeling approach. J Biomol Struct Dyn 2022:1-16. [PMID: 35938696 DOI: 10.1080/07391102.2022.2108901] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Some of the SARS-CoV-2 variants are said to be more infectious than the previous others and are causing panic around the globe. Cases related to Delta plus (δ+) and omicron (ο) variants are on the rise worldwide. This sudden surge warrants an investigation into the reasons for its binding with ACE-2. The present study attempts to find out the structural basis of binding interactions of SARS-CoV-2 mutants based on computational modeling and comparative analysis. In silico strategies including protein-protein docking, mutation analysis, molecular dynamics, and binding energy calculations were used to study the binding of the 'receptor binding domain' (RBD) of the seven 'variants of concern' which include Alpha (α), Beta (β), Gamma (γ), Kappa (κ), Delta (δ), Delta plus (δ+) and omicron (ο) with ACE-2 (human angiotensin-converting enzyme-2) and with antibodies. Among all the variants dealt with in this study, Delta plus and omicron were found to be binding more strongly to ACE-2 than others due to inherent mutations and the consequent change in the hydrophilic and hydrophobic environment of the binding site. Furthermore, molecular dynamic (MD) simulations and subsequent MM/PBSA calculations provided useful structural insights into key residues participating in the interaction. Infectivity of a virus could be dependent on the interplay of evading antibodies and simultaneously attaching strongly with the host receptor. A cross-correlation between mutant spike proteins' binding with ACE-2 and antibodies provides a holistic assessment of the binding nature of these mutants vis-à-vis native virus and offers opportunities for designing potential therapeutics against these new mutants.
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Affiliation(s)
- Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Manisha Gurnani
- Amity Institute of Environmental Science, Amity University, Noida, Uttar Pradesh, India
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Palak Sharma
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
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Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela. Viruses 2022; 14:v14071378. [PMID: 35891359 PMCID: PMC9317613 DOI: 10.3390/v14071378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Some of the lineages of SARS-CoV-2, the new coronavirus responsible for COVID-19, exhibit higher transmissibility or partial resistance to antibody-mediated neutralization and were designated by WHO as Variants of Interests (VOIs) or Concern (VOCs). The aim of this study was to monitor the dissemination of VOIs and VOCs in Venezuela from March 2021 to February 2022. A 614 nt genomic fragment was sequenced for the detection of some relevant mutations of these variants. Their presence was confirmed by complete genome sequencing, with a correlation higher than 99% between both methodologies. After the introduction of the Gamma VOC since the beginning of the year 2021, the variants Alpha VOC and Lambda VOI were detected as early as March 2021, at a very low frequency. In contrast, the Mu VOI, detected in May 2021, was able to circulate throughout the country. After the detection of the Delta VOC in June 2021, it became the predominant circulating variant. With the arrival of the Omicron VOC in December, this variant was able to displace the Delta one in less than one month.
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11
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Molina-Mora JA. Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. GENE REPORTS 2022; 27:101554. [PMID: 35155843 PMCID: PMC8824091 DOI: 10.1016/j.genrep.2022.101554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/29/2022] [Accepted: 02/04/2022] [Indexed: 10/28/2022]
Abstract
Emerging mutations and genotypes of the SARS-CoV-2 virus, responsible for the COVID-19 pandemic, have been reported globally. In Costa Rica during the year 2020, a predominant genotype carrying the mutation T1117I in the spike (S:T1117I) was previously identified. To investigate the possible effects of this mutation on the function of the spike, i.e. the biology of the virus, different bioinformatic pipelines based on phylogeny, natural selection, and co-evolutionary models, molecular docking, and epitopes prediction were implemented. Results of the phylogeny of sequences carrying the S:T1117I worldwide showed a polyphyletic group, with the emergence of local lineages. In Costa Rica, the mutation is found in the lineage B.1.1.389 and it is suggested to be a product of positive/adaptive selection. Different changes in the function of the spike protein and more stable interaction with a ligand (nelfinavir drug) were found. Only one epitope out 742 in the spike was affected by the mutation, with some different properties, but suggesting scarce changes in the immune response and no influence on the vaccine effectiveness. Jointly, these results suggest a partial benefit of the mutation for the spread of the virus with this genotype during the year 2020 in Costa Rica, although possibly not strong enough with the introduction of new lineages during early 2021 which became predominant later. In addition, the bioinformatic analyses used here can be applied as an in silico strategy to eventually study other mutations of interest for the SARS-CoV-2 virus and other pathogens.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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12
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Rayati Damavandi A, Dowran R, Al Sharif S, Kashanchi F, Jafari R. Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy. Med Microbiol Immunol 2022; 211:79-103. [PMID: 35235048 PMCID: PMC8889515 DOI: 10.1007/s00430-022-00729-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/09/2022] [Indexed: 12/30/2022]
Abstract
An ongoing pandemic of newly emerged SARS-CoV-2 has puzzled many scientists and health care policymakers around the globe. The appearance of the virus was accompanied by several distinct antigenic changes, specifically spike protein which is a key element for host cell entry of virus and major target of currently developing vaccines. Some of these mutations enable the virus to attach to receptors more firmly and easily. Moreover, a growing number of trials are demonstrating higher transmissibility and, in some of them, potentially more serious forms of illness related to novel variants. Some of these lineages, especially the Beta variant of concern, were reported to diminish the neutralizing activity of monoclonal and polyclonal antibodies present in both convalescent and vaccine sera. This could imply that these independently emerged variants could make antiviral strategies prone to serious threats. The rapid changes in the mutational profile of new clades, especially escape mutations, suggest the convergent evolution of the virus due to immune pressure. Nevertheless, great international efforts have been dedicated to producing efficacious vaccines with cutting-edge technologies. Despite the partial decrease in vaccines efficacy against worrisome clades, most current vaccines are still effective at preventing mild to severe forms of disease and hospital admission or death due to coronavirus disease 2019 (COVID-19). Here, we summarize existing evidence about newly emerged variants of SARS-CoV-2 and, notably, how well vaccines work against targeting new variants and modifications of highly flexible mRNA vaccines that might be required in the future.
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Affiliation(s)
- Amirmasoud Rayati Damavandi
- Students’ Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Razieh Dowran
- Students’ Scientific Research Center, Exceptional Talents Development Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarah Al Sharif
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA USA
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA USA
| | - Reza Jafari
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
- Hematology, Immune Cell Therapy, and Stem Cell Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
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13
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Gröhs Ferrareze PA, Zimerman RA, Franceschi VB, Caldana GD, Netz PA, Thompson CE. Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations. J Biomol Struct Dyn 2022; 41:3110-3128. [PMID: 35594172 DOI: 10.1080/07391102.2022.2076154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has reached by February 2022 more than 380 million cases and 5.5 million deaths worldwide since its beginning in late 2019, leading to enhanced concern in the scientific community and the general population. One of the most important pieces of this host-pathogen interaction is the spike protein, which binds to the hACE2 cell receptor, mediates the membrane fusion and is the major target of neutralizing antibodies against SARS-CoV-2. The multiple amino acid substitutions observed in this region, specially in RBD have enhanced the hACE2 binding affinity and led to several modifications in the mechanisms of SARS-CoV-2 pathogenesis, improving the viral fitness and/or promoting immune evasion, with potential impact in the vaccine development. In this work, we identified 48 sites under selective pressures, 17 of them with the strongest evidence by the HyPhy tests, including VOC related mutation sites 138, 142, 222, 262, 484, 681, and 845, among others. The coevolutionary analysis identified 28 sites found not to be conditionally independent, such as E484K-N501Y. The molecular dynamics and free energy estimates showed the structural stabilizing effect and the higher impact of E484K for enhanced binding affinity between the spike RBD and hACE2 in P.1 and P.2 lineages (specially with L452V). Structural changes were also identified in the hACE molecule when interacting with B.1.1.7 RDB. Despite some destabilizing substitutions, a stabilizing effect was identified for the majority of the positively selected mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | | | - Vinícius Bonetti Franceschi
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Gabriel Dickin Caldana
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Paulo Augusto Netz
- Graduate Program in Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.,Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
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14
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Ortiz-Pineda PA, Sierra-Torres CH. Evolutionary Traits and Genomic Surveillance of SARS-CoV-2 in South America. Glob Health Epidemiol Genom 2022; 2022:8551576. [PMID: 35655960 PMCID: PMC9132712 DOI: 10.1155/2022/8551576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/12/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Abstract
Since the zoonotic event from which SARS-CoV-2 started infecting humans late in 2019, the virus has caused more than 5 million deaths and has infected over 500 million people around the world. The pandemic has had a severe impact on social and economic activities, with greater repercussions in low-income countries. South America, with almost 5% of the world's population, has reckoned with almost a fifth of the total people infected and more than 26% (>1/4) of the deceased. Fortunately, the full genome structure and sequence of SARS-CoV-2 have been rapidly obtained and studied thanks to all the scientific efforts and data sharing around the world. Such molecular analysis of SARS-CoV-2 dynamics showed that rates of mutation, similar to other members of the Coronaviridae family, along with natural selection forces, could result in the emergence of new variants; few of them might be of high consequence. However, this is a serious threat to controlling the pandemic and, of course, enduring the process of returning to normalization with the implicit monetary cost of such a contingency. The lack of updated knowledge in South America justifies the need to develop a structured genomic surveillance program of current and emerging SARS-CoV-2 variants. The modeling of the molecular events and microevolution of the virus will contribute to making better decisions on public health management of the pandemic and developing accurate treatments and more efficient vaccines.
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Affiliation(s)
- Pablo A. Ortiz-Pineda
- Laboratory of Molecular Biology and Genomics, InnovaGen Foundation, Popayán, Colombia
| | - Carlos H. Sierra-Torres
- Laboratory of Molecular Biology and Genomics, InnovaGen Foundation, Popayán, Colombia
- Human Genetics Laboratory, Department of Physiological Sciences, Faculty of Health Sciences, University of Cauca, Popayán, Colombia
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Yang Z, Zhang S, Tang YP, Zhang S, Xu DQ, Yue SJ, Liu QL. Clinical Characteristics, Transmissibility, Pathogenicity, Susceptible Populations, and Re-infectivity of Prominent COVID-19 Variants. Aging Dis 2022; 13:402-422. [PMID: 35371608 PMCID: PMC8947836 DOI: 10.14336/ad.2021.1210] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
In addition to the rapid, global spread of SARS-CoV-2, new and comparatively more contagious variants are of considerable concern. These emerging mutations have become a threat to the global public health, creating COVID-19 surges in different countries. However, information on these emerging variants is limited and scattered. In this review, we discuss new variants that have emerged worldwide and identify several variants of concern, such as B.1.1.7, B.1.351, P.1, B.1.617.2 and B.1.1.529, and their basic characteristics. Other significant variants such as C.37, B.1.621, B.1.525, B.1.526, AZ.5, C.1.2, and B.1.617.1 are also discussed. This review highlights the clinical characteristics of these variants, including transmissibility, pathogenicity, susceptible population, and re-infectivity. It provides the latest information on the recent variants of SARS-CoV-2. The summary of this information will help researchers formulate reasonable strategies to curb the ongoing COVID-19 pandemic.
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Affiliation(s)
- Zhen Yang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
- 2School of Public Health, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Shuo Zhang
- 3School of Clinical Medicine (Guang'anmen Hospital), Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Ping Tang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Sai Zhang
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Ding-Qiao Xu
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Shi-Jun Yue
- 1Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, and State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), and Shaanxi Key Laboratory of Chinese Medicine Fundamentals and New Drugs Research, and Shaanxi Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
| | - Qi-Ling Liu
- 2School of Public Health, Shaanxi University of Chinese Medicine, Xi'an, Shaanxi, China
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Mostefai F, Gamache I, N'Guessan A, Pelletier J, Huang J, Murall CL, Pesaranghader A, Gaonac'h-Lovejoy V, Hamelin DJ, Poujol R, Grenier JC, Smith M, Caron E, Craig M, Wolf G, Krishnaswamy S, Shapiro BJ, Hussin JG. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Front Med (Lausanne) 2022; 9:826746. [PMID: 35265640 PMCID: PMC8899026 DOI: 10.3389/fmed.2022.826746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
The genome of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), has been sequenced at an unprecedented scale leading to a tremendous amount of viral genome sequencing data. To assist in tracing infection pathways and design preventive strategies, a deep understanding of the viral genetic diversity landscape is needed. We present here a set of genomic surveillance tools from population genetics which can be used to better understand the evolution of this virus in humans. To illustrate the utility of this toolbox, we detail an in depth analysis of the genetic diversity of SARS-CoV-2 in first year of the COVID-19 pandemic. We analyzed 329,854 high-quality consensus sequences published in the GISAID database during the pre-vaccination phase. We demonstrate that, compared to standard phylogenetic approaches, haplotype networks can be computed efficiently on much larger datasets. This approach enables real-time lineage identification, a clear description of the relationship between variants of concern, and efficient detection of recurrent mutations. Furthermore, time series change of Tajima's D by haplotype provides a powerful metric of lineage expansion. Finally, principal component analysis (PCA) highlights key steps in variant emergence and facilitates the visualization of genomic variation in the context of SARS-CoV-2 diversity. The computational framework presented here is simple to implement and insightful for real-time genomic surveillance of SARS-CoV-2 and could be applied to any pathogen that threatens the health of populations of humans and other organisms.
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Affiliation(s)
- Fatima Mostefai
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Isabel Gamache
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Arnaud N'Guessan
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Justin Pelletier
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Jessie Huang
- Department of Computer Science, Yale University, New Haven, CT, United States
| | - Carmen Lia Murall
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | | | - Vanda Gaonac'h-Lovejoy
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
| | - David J. Hamelin
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
| | - Raphaël Poujol
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Martin Smith
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
| | - Etienne Caron
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
- Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC, Canada
| | - Morgan Craig
- Research Centre, CHU Sainte-Justine, Montreal, QC, Canada
- Département de Mathématiques et Statistique, Université de Montréal, Montreal, QC, Canada
| | - Guy Wolf
- Mila – Quebec AI institute, Montreal, QC, Canada
- Département de Mathématiques et Statistique, Université de Montréal, Montreal, QC, Canada
| | - Smita Krishnaswamy
- Department of Computer Science, Yale University, New Haven, CT, United States
- Department of Genetics, Yale University, New Haven, CT, United States
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Julie G. Hussin
- Research Centre, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médecine, Université de Montréal, Montreal, QC, Canada
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Zimerman RA, Ferrareze PAG, Cadegiani FA, Wambier CG, Fonseca DDN, de Souza AR, Goren A, Rotta LN, Ren Z, Thompson CE. Comparative Genomics and Characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern From Amazonas, Brazil. Front Med (Lausanne) 2022; 9:806611. [PMID: 35242782 PMCID: PMC8885995 DOI: 10.3389/fmed.2022.806611] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/12/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND P.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, in the end of 2020, and has emerged as a very important variant of concern (VOC) of SARS-CoV-2 worldwide. P.1 has been linked to increased infectivity, higher mortality, and immune evasion, leading to reinfections and potentially reduced efficacy of vaccines and neutralizing antibodies. METHODS The samples of 276 patients from the State of Amazonas were sent to a central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global and regional phylogenetic analyses of the successfully sequenced genomes were conducted through maximum likelihood method. Multiple alignments were obtained including previously obtained unique human SARS-CoV-2 sequences. The evolutionary histories of spike and non-structural proteins from ORF1a of northern genomes were described and their molecular evolution was analyzed for detection of positive (FUBAR, FEL, and MEME) and negative (FEL and SLAC) selective pressures. To further evaluate the possible pathways of evolution leading to the emergence of P.1, we performed specific analysis for copy-choice recombination events. A global phylogenomic analysis with subsampled P.1 and B.1.1.28 genomes was applied to evaluate the relationship among samples. RESULTS Forty-four samples from the State of Amazonas were successfully sequenced and confirmed as P.1 (Gamma) lineage. In addition to previously described P.1 characteristic mutations, we find evidence of continuous diversification of SARS-CoV-2, as rare and previously unseen P.1 mutations were detected in spike and non-structural protein from ORF1a. No evidence of recombination was found. Several sites were demonstrated to be under positive and negative selection, with various mutations identified mostly in P.1 lineage. According to the Pango assignment, phylogenomic analyses indicate all samples as belonging to the P.1 lineage. CONCLUSION P.1 has shown continuous evolution after its emergence. The lack of clear evidence for recombination and the positive selection demonstrated for several sites suggest that this lineage emergence resulted mainly from strong evolutionary forces and progressive accumulation of a favorable signature set of mutations.
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Affiliation(s)
| | | | | | - Carlos Gustavo Wambier
- Department of Dermatology, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | | | | | - Andy Goren
- Applied Biology, Inc., Irvine, CA, United States
| | - Liane Nanci Rotta
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Zhihua Ren
- Suzhou Kintor Pharmaceutical, Inc., Suzhou, China
| | - Claudia Elizabeth Thompson
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
- Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front Immunol 2022; 13:801522. [PMID: 35222380 PMCID: PMC8863680 DOI: 10.3389/fimmu.2022.801522] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants' immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants' partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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Colson P, Fantini J, Yahi N, Delerce J, Levasseur A, Fournier PE, Lagier JC, Raoult D, La Scola B. Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. Arch Virol 2022; 167:583-589. [PMID: 35083577 PMCID: PMC8791675 DOI: 10.1007/s00705-021-05331-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 01/01/2023]
Abstract
We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. Eleven other sequences in France and 8,831 worldwide were available from GISAID, 92% originating from Japan. The three genome sequences from our institute were phylogenetically closest to another from Guinea-Conakry, where one of the patients had travelled. These viruses did not exhibit any unusual features in cell culture. Spike structural predictions indicated a 1.3-time higher transmissibility index than for the globally spread B.1.1.7 variant but also an affinity loss for gangliosides that might have slowed dissemination. The spread of new SARS-CoV-2 mutants/variants is still not well understood and therefore difficult to predict, and this hinders implementation of effective preventive measures, including adapted vaccines.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005, Marseille, France.
| | - Jacques Fantini
- Aix-Marseille Univ., INSERM U_1072, 13015, Marseille, France
| | - Nouara Yahi
- Aix-Marseille Univ., INSERM U_1072, 13015, Marseille, France
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 boulevard Jean Moulin, 13005, Marseille, France
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20
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Park G, Hwang BH. SARS-CoV-2 Variants: Mutations and Effective Changes. BIOTECHNOL BIOPROC E 2021; 26:859-870. [PMID: 34975266 PMCID: PMC8713537 DOI: 10.1007/s12257-021-0327-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 11/26/2022]
Abstract
One of the primary threats to the goal of controlling and eventually defeating SARS-CoV-2 is that of mutation. Recognizing this, a great amount of effort and dedicated study is being given to the matter. Due to the novel coronavirus's general prevalence and rate of mutation, this is an extremely dynamic area with constant new developments. Therefore, understanding the virus's pathogenesis and how mutations affect it is crucial. This review attempts to aid in understanding the currently most important strains and what primary changes they entail in connection to more specific mutations, and how they each affect infectivity, antigen resistance, and other properties. In an attempt to maintain relevance to the time at which this paper will be published, priority has been given to variants classified by the WHO and the CDC as of Sep. 23, 2021, as "Variants of Concern". Of particular interest in B.1.1.7, B.1.351, B.1.617.2, P.1 are the mutations affecting the Spike protein and Receptor Binding Domain, as they directly affect infectivity and susceptibility to neutralization. Certain mutations (D614G, E484K, N501Y, K417N, L452R and P681R) have appeared across several different strains, often accompanied by others that may be complementary working together to confer increased infectivity, fitness, or resistance to neutralization. We anticipate that the understanding of such COVID-19 mutations will, in the near future, prove important for diagnosis, treatment development, and vaccine development.
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Affiliation(s)
- Gene Park
- Whitmore School, Morgantown, WV 26505 USA
| | - Byeong Hee Hwang
- Division of Bioengineering, Incheon National University, Incheon, 22012 Korea
- Department of Bio·nanobioengineering, Incheon National University, Incheon, 22012 Korea
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21
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Zhao Y, Lee A, Composto K, Cunningham MH, Mediavilla JR, Fennessey S, Corvelo A, Chow KF, Zody M, Chen L, Kreiswirth BN, Perlin DS. A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Emerg Microbes Infect 2021; 10:994-997. [PMID: 33977858 PMCID: PMC8168736 DOI: 10.1080/22221751.2021.1929504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 12/12/2022]
Abstract
Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. While the concerning variants are fast spreading in various geographical areas, identification and monitoring of these variants are lagging far behind, due in large part to the slow speed and insufficient capacity of viral sequencing. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. Using this tool, we screened a total of 1135 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey between late December 2020 and March 2021. Our data revealed dramatic increases in the frequencies of both E484K and N501Y over time, underscoring the need for continuous epidemiological monitoring.
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Affiliation(s)
- Yanan Zhao
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Annie Lee
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Kaelea Composto
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Marcus H. Cunningham
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Jose R. Mediavilla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | | | | | - Kar Fai Chow
- Core Laboratory, Department of Pathology, Hackensack University Medical Center, Hackensack, NJ, USA
| | | | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
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22
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Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021; 22:757-773. [PMID: 34535792 PMCID: PMC8447121 DOI: 10.1038/s41576-021-00408-x] [Citation(s) in RCA: 642] [Impact Index Per Article: 214.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ravindra K Gupta
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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23
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Jaspe RC, Loureiro CL, Sulbaran Y, Moros ZC, D'Angelo P, Rodríguez L, Zambrano JL, Hidalgo M, Vizzi E, Alarcón V, Aguilar M, Garzaro DJ, Rangel HR, Pujol FH. Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105147. [PMID: 34800714 PMCID: PMC8596652 DOI: 10.1016/j.meegid.2021.105147] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/22/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
In less than two years since SARS-CoV-2 emerged, the new coronavirus responsible for COVID-19, has accumulated a great number of mutations. Many of these mutations are located in the Spike protein and some of them confer to the virus higher transmissibility or partial resistance to antibody mediated neutralization. Viral variants with such confirmed abilities are designated by WHO as Variants of Concern (VOCs). The aim of this study was to monitor the introduction of variants and VOCs in Venezuela. A small fragment of the viral genome was sequenced for the detection of the most relevant mutations found in VOCs. This approach allowed the detection of Gamma VOC. Its presence was confirmed by complete genome sequencing. The Gamma VOC was detected in Venezuela since January 2021, and in March 2021 was predominant in the East and Central side of the country, representing more than 95% of cases sequenced in all the country in April–May 2021. In addition to the Gamma VOC, other isolates carrying the mutation E484K were also detected. The frequency of this mutation has been increasing worldwide, as shown in a survey of sequences carrying E484K mutation in GISAID, and was detected in Venezuela in many probable cases of reinfection. Complete genome sequencing of these cases allowed us to identify E484K mutation in association with Gamma VOC and other lineages. In conclusion, the strategy adopted in this study is suitable for genomic surveillance of variants for countries lacking robust genome sequencing capacities. In the period studied, Gamma VOC seems to have rapidly become the dominant variant throughout the country.
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Affiliation(s)
- Rossana C Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Carmen L Loureiro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Yoneira Sulbaran
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Zoila C Moros
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Pierina D'Angelo
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Lieska Rodríguez
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - José Luis Zambrano
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Mariana Hidalgo
- Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Esmeralda Vizzi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Víctor Alarcón
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Marwan Aguilar
- Instituto Nacional de Higiene "Rafael Rangel", Caracas, Miranda, Venezuela
| | - Domingo J Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | | | - Héctor R Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Miranda, Venezuela.
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24
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Capozzi L, Simone D, Bianco A, Del Sambro L, Rondinone V, Pace L, Manzulli V, Iacobellis M, Parisi A. Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. Life (Basel) 2021; 11:1259. [PMID: 34833135 PMCID: PMC8625042 DOI: 10.3390/life11111259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 isolates from long-term COVID-19 patients play a significant role in understanding the mechanisms of infection and virus persistence. This study describes a SARS-CoV-2 isolate from a 53-year-old woman from Apulia (Italy), who was COVID-19 positive for approximately four months. In this paper we aimed to investigate any potential correlation between genetic mutations and clinical features of this case of infection. The viral isolate was assigned to lineage B.1.177.51 through whole-genome sequencing (WGS) and harbored a novel set of mutations on the Spike protein (V143D, del144/145 and E484K); furthermore, seroneutralization assays showed impaired response of the surveyed strain to BNT162b2 (Comirnaty) Pfizer/BioNTech vaccine-induced (average reduction of 70%) and convalescent sera (average reduction of 19.04%), when compared to VOC P.1. This study highlights the importance of genomic surveillance for the management of the COVID-19 pandemic, the relevance of monitoring of emerging SARS-CoV-2 mutations in all lineages, and the necessity of testing the response of emerging variants to available therapies and vaccines.
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Affiliation(s)
- Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Valeria Rondinone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Lorenzo Pace
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
| | - Michela Iacobellis
- Cytopathology Department of the Hospital Di Venere, Via Ospedale di Venere 1, 70131 Bari, Italy;
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia 20, 71121 Foggia, Italy; (L.C.); (D.S.); (A.B.); (L.D.S.); (V.R.); (L.P.); (V.M.)
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25
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Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Virus Res 2021; 308:198629. [PMID: 34780883 PMCID: PMC8585963 DOI: 10.1016/j.virusres.2021.198629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022]
Abstract
The E484K mutation at the SARS-CoV-2 Spike protein emerged independently in different variants around the world and has been widely associated with immune escape from neutralizing antibodies generated during previous infection or vaccination. In this work, the B.1 + L249S+E484K lineage was isolated along with A.1, B.1.420, and B.1.111 SARS-CoV-2 lineages without the E484K mutation and the neutralizing titer of convalescent sera was compared using microneutralization assays. While no significant differences in the neutralizing antibody titers were found between A.1 and B.lineages without the E484K mutation, the neutralizing titers against B.1 + L249S+E484K were 1.5, 1.9, 2.1, and 1.3-fold lower than against A.1, B.1.420, B.1.111-I, and B.1.111-II, respectively. However, molecular epidemiological data indicate that there is no increase in the transmissibility rate associated with this new lineage. This study supports the capability of new variants with the E484K mutation to be resistant to neutralization by humoral immunity, and therefore the need to intensify surveillance programs to determine if these lineages represent a risk for public health.
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26
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Focosi D, Maggi F. Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Rev Med Virol 2021; 31:e2231. [PMID: 33724631 PMCID: PMC8250244 DOI: 10.1002/rmv.2231] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022]
Abstract
The Spike protein is the target of both antibody-based therapeutics (convalescent plasma, polyclonal serum, monoclonal antibodies) and vaccines. Mutations in Spike could affect efficacy of those treatments. Hence, monitoring of mutations is necessary to forecast and readapt the inventory of therapeutics. Different phylogenetic nomenclatures have been used for the currently circulating SARS-CoV-2 clades. The Spike protein has different hotspots of mutation and deletion, the most dangerous for immune escape being the ones within the receptor binding domain (RBD), such as K417N/T, N439K, L452R, Y453F, S477N, E484K, and N501Y. Convergent evolution has led to different combinations of mutations among different clades. In this review we focus on the main variants of concern, that is, the so-called UK (B.1.1.7), South African (B.1.351) and Brazilian (P.1) strains.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/chemistry
- Antibodies, Viral/metabolism
- Antibodies, Viral/therapeutic use
- Brazil/epidemiology
- COVID-19/epidemiology
- COVID-19/immunology
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- Gene Expression
- Humans
- Immune Evasion
- Immunization, Passive/methods
- Mutation
- Phylogeny
- Protein Binding
- Risk Assessment
- SARS-CoV-2/classification
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- South Africa/epidemiology
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- United Kingdom/epidemiology
- COVID-19 Serotherapy
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Affiliation(s)
- Daniele Focosi
- North‐Western Tuscany Blood BankPisa University HospitalPisaItaly
| | - Fabrizio Maggi
- Department of Medicine and SurgeryUniversity of InsubriaVareseItaly
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27
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Martin S, Heslan C, Jégou G, Eriksson LA, Le Gallo M, Thibault V, Chevet E, Godey F, Avril T. SARS-CoV-2 integral membrane proteins shape the serological responses of patients with COVID-19. iScience 2021; 24:103185. [PMID: 34604721 PMCID: PMC8479324 DOI: 10.1016/j.isci.2021.103185] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/16/2021] [Accepted: 09/24/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has elicited a unique mobilization of the scientific community to develop efficient tools to understand and combat the infection. Like other coronavirae, SARS-CoV-2 hijacks host cell secretory machinery to produce viral proteins that compose the nascent virions; including spike (S), envelope (E), and membrane (M) proteins, the most exposed transmembrane proteins to the host immune system. As antibody response is part of the anti-viral immune arsenal, we investigate the immunogenic potential of S, E, and M using a human cell-based system to mimic membrane insertion and N-glycosylation. Both S and M elicit specific Ig production in patients with SARS-CoV-2. Patients with moderate and severe diseases exhibit elevated Ig responses. Finally, reduced Ig binding was observed with spike G614 compared to D614 variant. Altogether, our assay points toward an unexpected immune response against M and represents a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.
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Affiliation(s)
- Sophie Martin
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | | | - Gwénaële Jégou
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | - Leif A. Eriksson
- Department of Chemistry & Molecular Biology, University of Gothenburg, 41390 Göteborg, Sweden
| | - Matthieu Le Gallo
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | | | - Eric Chevet
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | - Florence Godey
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | - Tony Avril
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
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28
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Franceschi VB, Ferrareze PAG, Zimerman RA, Cybis GB, Thompson CE. Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Virus Res 2021; 304:198532. [PMID: 34363852 PMCID: PMC8654641 DOI: 10.1016/j.virusres.2021.198532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has already reached more than 110 million people and is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. International efforts have been established to share information about Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology and evolution to support the development of effective strategies for public health and disease management. We aimed to analyze the high-quality genome sequences from Brazil from February 2020-2021 to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages by using phylogenetics and phylodynamics analyses. We describe heterogeneous sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of specific lineages across different Brazilian regions. We found at least seven major (1-7) and two minor clades related to the six most prevalent lineages in the country and described its spatial distribution and dynamics. The emergence and recent frequency shift of lineages (P.1 and P.2) carrying mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers about better decisions to fight the COVID-19 pandemic.
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Affiliation(s)
- Vinícius Bonetti Franceschi
- Graduate Program in Cell and Molecular Biology (PPGBCM), Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Ricardo Ariel Zimerman
- Department of Infection Control and Prevention, Hospital da Brigada Militar, Porto Alegre, RS, Brazil
| | - Gabriela Bettella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Claudia Elizabeth Thompson
- Graduate Program in Cell and Molecular Biology (PPGBCM), Center of Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), 245/200C Sarmento Leite St, Porto Alegre, RS 90050-170, Brazil.
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29
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Nag A, Paul S, Banerjee R, Kundu R. In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021; 137:104818. [PMID: 34481181 PMCID: PMC8401086 DOI: 10.1016/j.compbiomed.2021.104818] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND This world is currently witnessing a pandemic outbreak of 'COVID-19' caused by a positive-strand RNA virus 'SARS-CoV-2'. Millions have succumbed globally to the disease, and the numbers are increasing day by day. The viral genome enters into the human host through interaction between the spike protein (S) and host angiotensin-converting enzyme-2 (ACE2) proteins. S is the common target for most recently rolled-out vaccines across regions. A recent surge in single/multiple mutations in S region is of great concern as it may escape vaccine induced immunity. So far, the treatment regime with repurposed drugs has not been too successful. HYPOTHESIS Natural compounds are capable of targeting mutated spike protein by binding to its active site and destabilizing the spike-host ACE2 interaction. MATERIALS AND METHODS A hypothetical mutated spike protein was constructed by incorporating twelve different mutations from twelve geographical locations simultaneously into the receptor-binding domain (RBD) and docked with ACE2 and seven phytochemicals namely allicin, capsaicin, cinnamaldehyde, curcumin, gingerol, piperine and zingeberene. Molecular Dynamic (MD) simulation and Principal Component Analysis (PCA) were finally used for validation of the docking results. RESULT The docking results showed that curcumin and piperine were most potent to bind ACE2, mutated spike, and mutated spike-ACE2 complex, thereby restricting viral entry. ADME analysis also proved their drug candidature. The docking complexes were found to be stable by MD simulation. CONCLUSION This result provides a significant insight about the phytochemicals' role, namely curcumin and piperine, as the potential therapeutic entities against mutated spike protein of SARS-CoV-2.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to Be University), Bangalore 560029, India
| | - Subhabrata Paul
- School of Biotechnology, Presidency University, Canal Bank Rd, DG Block, Action Area 1D, New Town, West Bengal 700156, India
| | - Ritesh Banerjee
- School of Biological and Environmental Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Rita Kundu
- Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India.
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In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021. [DOI: 10.1016/j.compbiomed.2021.104818
expr 849028860 + 881472580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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31
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Lennerstrand J, Palanisamy N. Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Viruses 2021; 13:1974. [PMID: 34696404 PMCID: PMC8538289 DOI: 10.3390/v13101974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called 'adaptive mutations' and 'mutations identified in the prolonged infections', in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections' mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.
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Affiliation(s)
- Johan Lennerstrand
- Department of Medical Sciences, Section of Clinical Microbiology, Uppsala University, 751 85 Uppsala, Sweden;
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Halaji M, Heiat M, Faraji N, Ranjbar R. Epidemiology of COVID-19: An updated review. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2021; 26:82. [PMID: 34759999 PMCID: PMC8548902 DOI: 10.4103/jrms.jrms_506_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/30/2020] [Accepted: 04/25/2021] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a zoonotic infection, is responsible for COVID-19 pandemic and also is known as a public health concern. However, so far, the origin of the causative virus and its intermediate hosts is yet to be fully determined. SARS-CoV-2 contains nearly 30,000 letters of RNA that allows the virus to infect cells and hijack them to make new viruses. On the other hand, among 14 detected mutations in the SARS-CoV-2 S protein that provide advantages to virus for transmission and evasion form treatment, the D614G mutation (substitution of aspartic acid [D] with glycine [G] in codon 614 was particular which could provide the facilitation of the transmission of the virus and virulence. To date, in contrary to the global effort to come up with various aspects of SARS-CoV-2, there are still great pitfalls in the knowledge of this disease and many angles remain unclear. That's why, the monitoring and periodical investigation of this emerging infection in an epidemiological study seems to be essential. The present study characterizes the current epidemiological status (i.e., possible transmission route, mortality and morbidity risk, emerging SARS-CoV-2 variants, and clinical feature) of the SARS-CoV-2 in the world during these pandemic.
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Affiliation(s)
- Mehrdad Halaji
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Niloofar Faraji
- Department of Medical Laboratory Sciences, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Wu L, Peng C, Yang Y, Shi Y, Zhou L, Xu Z, Zhu W. Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Brief Bioinform 2021; 23:6374062. [PMID: 34553217 PMCID: PMC8500006 DOI: 10.1093/bib/bbab383] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/23/2022] Open
Abstract
Although the current coronavirus disease 2019 (COVID-19) vaccines have been used worldwide to halt spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the emergence of new SARS-CoV-2 variants with E484K mutation shows significant resistance to the neutralization of vaccine sera. To better understand the resistant mechanism, we calculated the binding affinities of 26 antibodies to wild-type (WT) spike protein and to the protein harboring E484K mutation, respectively. The results showed that most antibodies (~85%) have weaker binding affinities to the E484K mutated spike protein than to the WT, indicating the high risk of immune evasion of the mutated virus from most of current antibodies. Binding free energy decomposition revealed that the residue E484 forms attraction with most antibodies, while the K484 has repulsion from most antibodies, which should be the main reason of the weaker binding affinities of E484K mutant to most antibodies. Impressively, a monoclonal antibody (mAb) combination was found to have much stronger binding affinity with E484K mutant than WT, which may work well against the mutated virus. Based on binding free energy decomposition, we predicted that the mutation of four more residues on receptor-binding domain (RBD) of spike protein, viz., F490, V483, G485 and S494, may have high risk of immune evasion, which we should pay close attention on during the development of new mAb therapeutics.
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Affiliation(s)
- Leyun Wu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Cheng Peng
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yanqing Yang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yulong Shi
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Liping Zhou
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Zhijian Xu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
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Istifli ES, Netz PA, Sihoglu Tepe A, Sarikurkcu C, Tepe B. Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). J Biomol Struct Dyn 2021; 40:12760-12771. [PMID: 34495817 PMCID: PMC8442754 DOI: 10.1080/07391102.2021.1975569] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/29/2021] [Indexed: 12/27/2022]
Abstract
Covid-19 is a viral disease caused by the virus SARS-CoV-2 that spread worldwide and caused more than 4.3 million deaths. Moreover, SARS-CoV-2 still continues to evolve, and specifically the E484K, N501Y, and South Africa triple (K417N + E484K + N501Y) spike protein mutants remain as the 'escape' phenotypes. The aim of this study was to compare the interaction between the receptor binding domain (RBD) of the E484K, N501Y and South Africa triple spike variants and ACE2 with the interaction between wild-type spike RBD-ACE2 and to show whether the obtained binding affinities and conformations corraborate clinical findings. The structures of the RBDs of the E484K, N501Y and South Africa triple variants were generated with DS Studio v16 and energetically minimized using the CHARMM22 force field. Protein-protein dockings were performed in the HADDOCK server and the obtained wild-type and mutant spike-ACE2 complexes were submitted to 200-ns molecular dynamics simulations with subsequent free energy calculations using GROMACS. Based on docking binding affinities and free energy calculations the E484K, N501Y and triple mutant variants were found to interact stronger with the ACE2 than the wild-type spike. Interestingly, molecular dynamics and MM-PBSA results showed that E484K and spike triple mutant complexes were more stable than the N501Y one. Moreover, the E484K and South Africa triple mutants triggered greater conformational changes in the spike glycoprotein than N501Y. The E484K variant alone, or the combination of K417N + E484K + N501Y mutations induce significant conformational transitions in the spike glycoprotein, while increasing the spike-ACE2 binding affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Erman Salih Istifli
- Department of Biology, Faculty of Science and Literature, Cukurova University, Adana, Turkey
| | - Paulo A. Netz
- Theoretical Chemistry Group, Institute of Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Arzuhan Sihoglu Tepe
- Department of Pharmacy Services, Vocational High School of Health Services, Kilis 7 Aralık University, Kilis, Turkey
| | - Cengiz Sarikurkcu
- Department of Analytical Chemistry, Faculty of Pharmacy, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Bektas Tepe
- Department of Molecular Biology and Genetics, Faculty of Science and Literature, Kilis 7 Aralik University, Kilis, Turkey
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35
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Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Virol J 2021; 18:166. [PMID: 34389034 PMCID: PMC8361246 DOI: 10.1186/s12985-021-01633-w] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.
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Affiliation(s)
- Jalen Singh
- School of Interdisciplinary Science, McMaster University, Hamilton, ON, Canada
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
| | - Karen Mossman
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.
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36
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Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clin Proteomics 2021; 18:19. [PMID: 34384361 PMCID: PMC8358260 DOI: 10.1186/s12014-021-09325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.
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Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Alenquer M, Ferreira F, Lousa D, Valério M, Medina-Lopes M, Bergman ML, Gonçalves J, Demengeot J, Leite RB, Lilue J, Ning Z, Penha-Gonçalves C, Soares H, Soares CM, Amorim MJ. Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. PLoS Pathog 2021; 17:e1009772. [PMID: 34352039 PMCID: PMC8341613 DOI: 10.1371/journal.ppat.1009772] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/30/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics.
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Affiliation(s)
- Marta Alenquer
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Diana Lousa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Oeiras, Portugal
| | - Mariana Valério
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Oeiras, Portugal
| | - Mónica Medina-Lopes
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | | | - Juliana Gonçalves
- CEDOC NOVA, Centro de Estudos de Doenças Crónicas, Nova Medical School, Universidade Nova de Lisboa; Lisboa, Portugal
| | - Jocelyne Demengeot
- Lymphocyte Physiology Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Ricardo B. Leite
- Genomics Unit, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Jingtao Lilue
- Bioinformatics Unit, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Zemin Ning
- The Wellcome Trust Sanger Institute; Hinxton, United Kingdom
| | | | - Helena Soares
- CEDOC NOVA, Centro de Estudos de Doenças Crónicas, Nova Medical School, Universidade Nova de Lisboa; Lisboa, Portugal
| | - Cláudio M. Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Oeiras, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
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Tauzin A, Nayrac M, Benlarbi M, Gong SY, Gasser R, Beaudoin-Bussières G, Brassard N, Laumaea A, Vézina D, Prévost J, Anand SP, Bourassa C, Gendron-Lepage G, Medjahed H, Goyette G, Niessl J, Tastet O, Gokool L, Morrisseau C, Arlotto P, Stamatatos L, McGuire AT, Larochelle C, Uchil P, Lu M, Mothes W, De Serres G, Moreira S, Roger M, Richard J, Martel-Laferrière V, Duerr R, Tremblay C, Kaufmann DE, Finzi A. A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses. Cell Host Microbe 2021; 29:1137-1150.e6. [PMID: 34133950 PMCID: PMC8175625 DOI: 10.1016/j.chom.2021.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/06/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022]
Abstract
While the standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered 3 weeks apart, some public health authorities are spacing these doses, raising concerns about efficacy. However, data indicate that a single dose can be up to 90% effective starting 14 days post-administration. To assess the mechanisms contributing to protection, we analyzed humoral and T cell responses three weeks after a single BNT162b2 dose. We observed weak neutralizing activity elicited in SARS-CoV-2 naive individuals but strong anti-receptor binding domain and spike antibodies with Fc-mediated effector functions and cellular CD4+ T cell responses. In previously infected individuals, a single dose boosted all humoral and T cell responses, with strong correlations between T helper and antibody immunity. Our results highlight the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support for spacing doses to vaccinate more individuals in conditions of vaccine scarcity.
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Affiliation(s)
- Alexandra Tauzin
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Manon Nayrac
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | - Annemarie Laumaea
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, Canada
| | | | | | | | | | - Julia Niessl
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, USA
| | - Olivier Tastet
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada
| | - Laurie Gokool
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada
| | | | | | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Catherine Larochelle
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département des Neurosciences, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Pradeep Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Gaston De Serres
- Institut National de Santé Publique du Québec, Quebec, QC, H2P 1E2, Canada
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Michel Roger
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Valérie Martel-Laferrière
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Cécile Tremblay
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada.
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Médecine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, USA.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2BA, Canada.
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39
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Vega-Magaña N, Sánchez-Sánchez R, Hernández-Bello J, Venancio-Landeros AA, Peña-Rodríguez M, Vega-Zepeda RA, Galindo-Ornelas B, Díaz-Sánchez M, García-Chagollán M, Macedo-Ojeda G, García-González OP, Muñoz-Valle JF. RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Front Cell Infect Microbiol 2021; 11:672562. [PMID: 34123874 PMCID: PMC8195289 DOI: 10.3389/fcimb.2021.672562] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022] Open
Abstract
Background Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population. Methods Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico. Results In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. Conclusion This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.
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Affiliation(s)
- Natali Vega-Magaña
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - Jorge Hernández-Bello
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - Marcela Peña-Rodríguez
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | | | | | - Mariel García-Chagollán
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | - Gabriela Macedo-Ojeda
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | | | - José Francisco Muñoz-Valle
- Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara, Mexico
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