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Ellmen I, Overton AK, Knapp JJ, Nash D, Ho H, Hungwe Y, Prasla S, Nissimov JI, Charles TC. Reconstructing SARS-CoV-2 lineages from mixed wastewater sequencing data. Sci Rep 2024; 14:20273. [PMID: 39217200 PMCID: PMC11365997 DOI: 10.1038/s41598-024-70416-4] [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: 04/05/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Wastewater surveillance of SARS-CoV-2 has emerged as a critical tool for tracking the spread of COVID-19. In addition to estimating the relative case numbers using quantitative PCR, SARS-CoV-2 genomic RNA can be extracted from wastewater and sequenced. There are many existing techniques for using the sequenced RNA to determine the relative abundance of known lineages in a sample. However, it is very challenging to predict novel lineages from wastewater data due to its mixed composition and unreliable genomic coverage. In this work, we present a novel technique based on non-negative matrix factorization which is able to reconstruct lineage definitions by analyzing data from across different samples. We test the method both on synthetic and real wastewater sequencing data. We show that the technique is able to determine major lineages such as Omicron and Delta as well as sub-lineages such as BA.5.2.1. We provide a method for determining emerging lineages in wastewater without the need for genomic data from clinical samples. This could be used for routine monitoring of SARS-CoV-2 as well as other emerging viral pathogens in wastewater. Additionally, it may be used to determine more full-genome sequences for viruses with fewer available genomes.
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Affiliation(s)
- Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada.
- Department of Statistics, University of Oxford, Oxford, United Kingdom.
| | - Alyssa K Overton
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jennifer J Knapp
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
| | - Hannifer Ho
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Yemurayi Hungwe
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Samran Prasla
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jozef I Nissimov
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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Lebatteux D, Soudeyns H, Boucoiran I, Gantt S, Diallo AB. Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures. PLoS One 2024; 19:e0296627. [PMID: 38241279 PMCID: PMC10798494 DOI: 10.1371/journal.pone.0296627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 12/07/2023] [Indexed: 01/21/2024] Open
Abstract
Machine learning was shown to be effective at identifying distinctive genomic signatures among viral sequences. These signatures are defined as pervasive motifs in the viral genome that allow discrimination between species or variants. In the context of SARS-CoV-2, the identification of these signatures can assist in taxonomic and phylogenetic studies, improve in the recognition and definition of emerging variants, and aid in the characterization of functional properties of polymorphic gene products. In this paper, we assess KEVOLVE, an approach based on a genetic algorithm with a machine-learning kernel, to identify multiple genomic signatures based on minimal sets of k-mers. In a comparative study, in which we analyzed large SARS-CoV-2 genome dataset, KEVOLVE was more effective at identifying variant-discriminative signatures than several gold-standard statistical tools. Subsequently, these signatures were characterized using a new extension of KEVOLVE (KANALYZER) to highlight variations of the discriminative signatures among different classes of variants, their genomic location, and the mutations involved. The majority of identified signatures were associated with known mutations among the different variants, in terms of functional and pathological impact based on available literature. Here we showed that KEVOLVE is a robust machine learning approach to identify discriminative signatures among SARS-CoV-2 variants, which are frequently also biologically relevant, while bypassing multiple sequence alignments. The source code of the method and additional resources are available at: https://github.com/bioinfoUQAM/KEVOLVE.
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Affiliation(s)
- Dylan Lebatteux
- Department of Computer Science, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Centre, Montréal, Québec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Pediatrics, Faculty of Medicine, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Isabelle Boucoiran
- Department of Obstetrics and Gynecology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Soren Gantt
- CHU Sainte-Justine Research Centre, Montréal, Québec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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Ozhmegova EN, Savochkina TE, Prilipov AG, Tikhomirov E, Larichev VF, Sayfullin MA, Grebennikova TV. [Molecular epidemiological analysis of SARS-CoV-2 genovariants in Moscow and Moscow region]. Vopr Virusol 2023; 67:496-505. [PMID: 37264839 DOI: 10.36233/0507-4088-146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Indexed: 06/03/2023]
Abstract
INTRODUCTION SARS-CoV-2, a severe acute respiratory illness virus that emerged in China in late 2019, continues to spread rapidly around the world, accumulating mutations and thus causing serious concern. Five virus variants of concern are currently known: Alpha (lineage B.1.1.7), Beta (lineage B.1.351), Gamma (lineage P.1), Delta (lineage B.1.617.2), and Omicron (lineage B.1.1.529). In this study, we conducted a molecular epidemiological analysis of the most prevalent genovariants in Moscow and the region. The aim of the study is to estimate the distribution of various variants of SARS-CoV-2 in Moscow city and the Moscow Region. MATERIALS AND METHODS 227 SARS-CoV-2 sequences were used for analysis. Isolation of the SARS-CoV-2 virus was performed on Vero E6 cell culture. Sequencing was performed by the Sanger method. Bioinformatic analysis was carried out using software packages: MAFFT, IQ-TREE v1.6.12, jModelTest 2.1.7, Nextstrain, Auspice v2.34. RESULTS As a result of phylogenetic analysis, we have identified the main variants of the virus circulating in Russia that have been of concern throughout the existence of the pandemic, namely: variant B.1.1.7, which accounted for 30% (9/30), AY.122, which accounted for 16.7% (5/30), BA.1.1 with 20% (6/30) and B.1.1 with 33.3% (10/30). When examining Moscow samples for the presence of mutations in SARS-CoV-2 structural proteins of different genovariants, a significant percentage of the most common substitutions was recorded: S protein D614G (86.7%), P681H/R (63.3%), E protein T9I (20.0%); M protein I82T (30.0%), D3G (20.0%), Q19E (20.0%) and finally N protein R203K/M (90.0%), G204R/P (73.3 %). CONCLUSION The study of the frequency and impact of mutations, as well as the analysis of the predominant variants of the virus are important for the development and improvement of vaccines for the prevention of COVID-19. Therefore, ongoing molecular epidemiological studies are needed, as these data provide important information about changes in the genome of circulating SARS-CoV-2 variants.
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Affiliation(s)
- E N Ozhmegova
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
| | - T E Savochkina
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
| | - A G Prilipov
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
| | - E Tikhomirov
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
| | - V F Larichev
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
| | - M A Sayfullin
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
- Pirogov Russian National Research Medical University
| | - T V Grebennikova
- National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation
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Delshad M, Sanaei MJ, Pourbagheri-Sigaroodi A, Bashash D. Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination. Int Immunopharmacol 2022; 111:109128. [PMID: 35963158 PMCID: PMC9359488 DOI: 10.1016/j.intimp.2022.109128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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KAYA G, ALTINDİŞ M. Virological, Epidemiological Features and Prevention of SARS-CoV-2 Omicron (B.1.1.529) Variant: A Rewiev. KOCAELI ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.30934/kusbed.1060956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has been a cause for serious concern worldwide due to its high rate of transmission and number of mutations. During genomic studies in South Africa and Botswana in November 2021, a new variant of SARS-CoV-2 was identified associated with a rapid resurgence of infections in Gauteng Province, South Africa. Omicron variant was identified as a type of concern by the World Health Organization after sequence uploads of the first genome. It was subsequently identified in 87 countries within three weeks. The Omicron variant is a very exceptional virus carrying more than 30 mutations in the spike glycoprotein that are predicted to affect antibody neutralization and spike function. Omicron is highly contagious and spreads faster than previous variants, but may cause less severe symptoms than previous variants. Omicron variant can evade the immune system. It can also evade the vaccine responses developed against COVID-19. Rapid and careful preventive steps, including vaccination, will always be a key for suppression of the Omicron variant.
This review summarizes the highly mutated regions, core infectiousness, vaccine elimination, and antibody resistance of the Omicron variant of SARS-CoV-2.
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Affiliation(s)
- Gülsüm KAYA
- Sakarya Üniversitesi Eğitim ve Araştırma Hastanesi
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Manjunath R, Gaonkar SL, Saleh EAM, Husain K. A comprehensive review on Covid-19 Omicron (B.1.1.529) variant. Saudi J Biol Sci 2022; 29:103372. [PMID: 35855306 PMCID: PMC9284530 DOI: 10.1016/j.sjbs.2022.103372] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/05/2022] [Accepted: 06/27/2022] [Indexed: 12/05/2022] Open
Abstract
The world has been combating different variants of SARS-COV-19 since its first outbreak in Wuhan city. SARS-COV-19 is caused by the coronavirus. The corona virus mutates and becomes more transmissible than earlier variants as the day passes. Till 24 November 2021, SARS-COV-19 has four variants Alpha, Beta, Gamma, and Delta, respectively. Among them, the delta variant caused severe havoc across the world. South Africa registered a new variant with the World Health Organization (WHO) on 24 November 2021, which is much more transmissible than previous variants. The WHO classified it as a variant of concern (VOC) on 26 November 2021 and called it the Greek letter Omicron (B.1.1.529), the fifteenth letter in the alphabet. Here a serious attempt was made to comprehend the omicron variant's origin, nomenclature, characteristics, mutations, the difference between delta and omicron variant, epidemiology, transmission, clinical features, impact on immunity, immune evasion, vaccines efficacy, etc.
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Affiliation(s)
- R Manjunath
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Santosh L. Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ebraheem Abdu Musad Saleh
- Department of Chemistry, Prince Sattam Bin Abdulaziz University, College of Arts and Science, Wadi Al-Dawasir 11991, Saudi Arabia
| | - Kakul Husain
- Department of Chemistry, Prince Sattam Bin Abdulaziz University, College of Arts and Science, Wadi Al-Dawasir 11991, Saudi Arabia
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Das S, Kar SS, Samanta S, Banerjee J, Giri B, Dash SK. Immunogenic and reactogenic efficacy of Covaxin and Covishield: a comparative review. Immunol Res 2022; 70:289-315. [PMID: 35192185 PMCID: PMC8861611 DOI: 10.1007/s12026-022-09265-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/17/2022] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is an RNA virus that was identified for the first time in December 2019 in Wuhan, China. The World Health Organization (WHO) labeled the novel coronavirus (COVID-19) outbreak a worldwide pandemic on March 11, 2020, due to its widespread infectivity pattern. Because of the catastrophic COVID-19 outbreak, the development of safe and efficient vaccinations has become a key priority in every health sector throughout the globe. On the 13th of January 2021, the vaccination campaign against SARS-CoV-2 was launched in India and started the administration of two types of vaccines known as Covaxin and Covishield. Covishield is an adenovirus vector-based vaccine, and Covaxin was developed by a traditional method of vaccine formulation, which is composed of adjuvanted inactivated viral particles. Each vaccine's utility or efficiency is determined by its formulation, adjuvants, and mode of action. The efficacy of the vaccination depends on numeral properties like generation antibodies, memory cells, and cell-mediated immunity. According to the third-phase experiment, Covishield showed effectiveness of nearly 90%, whereas Covaxin has an effectiveness of about 80%. Both vaccination formulations in India have so far demonstrated satisfactory efficacy against numerous mutant variants of SARS-CoV-2. The efficacy of Covishield may be diminished if the structure of spike (S) protein changes dramatically in the future. In this situation, Covaxin might be still effective for such variants owing to its ability to produce multiple antibodies against various epitopes. This study reviews the comparative immunogenic and therapeutic efficacy of Covaxin and Covishield and also discussed the probable vaccination challenges in upcoming days.
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Affiliation(s)
- Swarnali Das
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Suvrendu Sankar Kar
- Department of Medicine, R.G.Kar Medical College, Kolkata, 700004, West Bengal, India
| | - Sovan Samanta
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Jhimli Banerjee
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Biplab Giri
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India
| | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda, 732103, West Bengal, India.
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Shao W, Zhang W, Fang X, Yu D, Wang X. Challenges of SARS-CoV-2 Omicron Variant and appropriate countermeasures. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:387-394. [PMID: 35501267 PMCID: PMC9040366 DOI: 10.1016/j.jmii.2022.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
The Omicron (B.1.1.529) variant was first reported in South Africa and rapidly spread worldwide in early November 2021. This caused panic in various countries, so it is necessary to understand Omicron Variant. This paper summarizes omicron variant-related research achievements. Studies have shown that Omicron Variant contains many mutations that make it more infectious and transmissible. At the same time, immune escape is also caused, resulting in reduced efficacy of existing vaccines, increased risk of reinfection, treatment failure or reduction of monoclonal antibody therapies, and detection failure. However, current data indicate that Omicron Variant causes mild clinical symptoms and few severe cases and deaths. Omicron Variant is valid for a range of nonpharmaceutical interventions against SARS-CoV-2. Improving diagnostic accuracy and enabling timely isolation and treatment of diagnosed cases is also critical to interrupting the spread of omicron variants. COVID-19 vaccine boosters could undoubtedly help control Omicron spread and infection. However, developing a vaccine specific to Omicron Variant is also imminent.
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Affiliation(s)
- Wenxia Shao
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Weiying Zhang
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiang Fang
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daojun Yu
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xianjun Wang
- Department of Laboratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Cosar B, Karagulleoglu ZY, Unal S, Ince AT, Uncuoglu DB, Tuncer G, Kilinc BR, Ozkan YE, Ozkoc HC, Demir IN, Eker A, Karagoz F, Simsek SY, Yasar B, Pala M, Demir A, Atak IN, Mendi AH, Bengi VU, Cengiz Seval G, Gunes Altuntas E, Kilic P, Demir-Dora D. SARS-CoV-2 Mutations and their Viral Variants. Cytokine Growth Factor Rev 2022; 63:10-22. [PMID: 34580015 PMCID: PMC8252702 DOI: 10.1016/j.cytogfr.2021.06.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022]
Abstract
Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed. Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications. The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein. In this review, a literature survey in the scope of the increasing SARS-CoV-2 mutations and the viral variations is conducted. In the light of current knowledge, the various disguises of the mutant SARS-CoV-2 forms and their apparent differences from the original strain are examined as they could possibly aid in finding the most appropriate therapeutic approaches.
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Affiliation(s)
- Begum Cosar
- Başkent University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, Ankara, Turkey
| | - Zeynep Yagmur Karagulleoglu
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Sinan Unal
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | | | - Dilruba Beyza Uncuoglu
- Ankara University, Graduate School of Natural and Applied Sciences, Department of Biology, Ankara, Turkey
| | - Gizem Tuncer
- Hacettepe University, Graduate School of Science and Engineering, General Biology Program, Ankara, Turkey; HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey
| | - Bugrahan Regaip Kilinc
- Kastamonu University, School of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey; Kastamonu University, School of Engineering and Architecture, Department of Biomedical Engineering, Kastamonu, Turkey
| | - Yunus Emre Ozkan
- Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, Kocaeli, Turkey
| | - Hikmet Ceyda Ozkoc
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey
| | | | - Ali Eker
- Akdeniz University, Faculty of Medicine, Antalya, Turkey
| | | | | | - Bunyamin Yasar
- Alanya Alaaddin Keykubat University, Department of Molecular Medicine, Antalya, Turkey
| | - Mehmetcan Pala
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, Sivas, Turkey
| | - Aysegul Demir
- Üsküdar University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Irem Naz Atak
- Ankara University, Faculty of Science, Department of Biology, Ankara, Turkey
| | - Aysegul Hanife Mendi
- Gazi University, Faculty of Dentistry, Department of Basic Sciences, Division of Medical Microbiology, Ankara, Turkey
| | - Vahdi Umut Bengi
- Gülhane Training and Research Hospital, Faculty of Dentistry, Department of Periodontology, Ankara, Turkey
| | - Guldane Cengiz Seval
- Ankara University, School of Medicine Department of Hematology, Cebeci, Ankara, Turkey
| | | | - Pelin Kilic
- HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey; Ankara University, Stem Cell Institute, Ankara, Turkey.
| | - Devrim Demir-Dora
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Gene and Cell Therapy, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Medical Biotechnology, Antalya, Turkey.
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Franke KR, Isett R, Robbins A, Paquette-Straub C, Shapiro CA, Lee MM, Crowgey EL. Genomic surveillance of SARS-CoV-2 in the state of Delaware reveals tremendous genomic diversity. PLoS One 2022; 17:e0262573. [PMID: 35045124 PMCID: PMC8769358 DOI: 10.1371/journal.pone.0262573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
The use of next generation sequencing is critical for the surveillance of severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, transmission, as single base mutations have been identified with differences in infectivity. A total of 1,459 high quality samples were collected, sequenced, and analyzed in the state of Delaware, a location that offers a unique perspective on transmission given its proximity to large international airports on the east coast. Pangolin and Nextclade were used to classify these sequences into 16 unique clades and 88 lineages. A total of 411 samples belonging to the Alpha 20I/501Y.V1 (B.1.1.7) strain of concern were identified, as well as one sample belonging to Beta 20H/501.V2 (B.1.351), thirteen belonging to Epsilon 20C/S:452R (B.1.427/B.1.429), two belonging to Delta 20A/S:478K (B.1.617.2), and 15 belonging to Gamma 20J/501Y.V3 (p.1). A total of 2217 unique coding mutations were observed with an average of 17.7 coding mutations per genome. These data paired with continued sample collection and sequencing will give a deeper understanding of the spread of SARS-CoV-2 strains within Delaware and its surrounding areas.
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Affiliation(s)
- Karl R. Franke
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
| | - Robert Isett
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
| | - Alan Robbins
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
| | - Carrie Paquette-Straub
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
| | - Craig A. Shapiro
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
| | - Mary M. Lee
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
| | - Erin L. Crowgey
- Research Department, Nemours Children’s Hospital Delaware, Wilmington, Delaware, United States of America
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Jiang H, Xi H, Juhas M, Zhang Y. Biosensors for Point Mutation Detection. Front Bioeng Biotechnol 2021; 9:797831. [PMID: 34976987 PMCID: PMC8714947 DOI: 10.3389/fbioe.2021.797831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Hanlin Jiang
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Hui Xi
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen, China
- *Correspondence: Yang Zhang,
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12
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He X, Hong W, Pan X, Lu G, Wei X. SARS-CoV-2 Omicron variant: Characteristics and prevention. MedComm (Beijing) 2021; 2:838-845. [PMID: 34957469 PMCID: PMC8693031 DOI: 10.1002/mco2.110] [Citation(s) in RCA: 279] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has brought about a great threat to global public health. Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.529 has been reported in South Africa and induced a rapid increase in COVID-19 cases. On November 24, 2021, B.1.1.529 named Omicron was designated as a variant under monitoring (VUM) by World Health Organization (WHO). Two days later, the Omicron variant was classified as a variant of concern (VOC). This variant harbors a high number of mutations, including 15 mutations in the receptor-binding domain (RBD) of spike. The Omicron variant also shares several mutations with the previous VOC Alpha, Beta, and Gamma variants, which immediately raised global concerns about viral transmissibility, pathogenicity, and immune evasion. Here we described the discovery and characteristics of the Omicron variant, compared the mutations of the spike in the five VOCs, and further raised possible strategies to prevent and overcome the prevalence of the Omicron variant.
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Affiliation(s)
- Xuemei He
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
| | - Xiangyu Pan
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
| | - Guangwen Lu
- West China Hospital Emergency DepartmentState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduChina
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13
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Figueroa-Pizano MD, Campa-Mada AC, Carvajal-Millan E, Martinez-Robinson KG, Chu AR. The underlying mechanisms for severe COVID-19 progression in people with diabetes mellitus: a critical review. AIMS Public Health 2021; 8:720-742. [PMID: 34786431 PMCID: PMC8568590 DOI: 10.3934/publichealth.2021057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
Diabetes mellitus (DM) has a high incidence of comorbidities among patients with severe coronavirus disease 2019 (COVID-19). The elevated prevalence of DM in the world population makes it a significant risk factor because diabetic individuals appear to be prone to clinical complications and have increased mortality rates. Here, we review the possible underlying mechanisms involved in DM that led to worse outcomes in COVID-19. The impacts of hyperglycemia side effects, secondary comorbidities, weakened innate and adaptive immunity, chronic inflammation, and poor nutritional status, commonly present in DM, are discussed. The role of the SARS-CoV-2 receptor and its polymorphic variations on higher binding affinity to facilitate viral uptake in people with DM were also considered. Clinical differences between individuals with type 1 DM and type 2 DM affected by COVID-19 and the potential diabetogenic effect of SARS-CoV-2 infection were addressed.
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Affiliation(s)
- María D Figueroa-Pizano
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Alma C Campa-Mada
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Elizabeth Carvajal-Millan
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Karla G Martinez-Robinson
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
| | - Agustin Rascon Chu
- Research Center for Food and Development, CIAD, AC, Carretera Gustavo Enrique Astiazarán Rosas No. 46, C.P. 83304, Hermosillo, Sonora, México
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14
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Chappleboim A, Joseph-Strauss D, Rahat A, Sharkia I, Adam M, Kitsberg D, Fialkoff G, Lotem M, Gershon O, Schmidtner AK, Oiknine-Djian E, Klochendler A, Sadeh R, Dor Y, Wolf D, Habib N, Friedman N. Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing. Sci Transl Med 2021; 13:eabj2266. [PMID: 34591660 PMCID: PMC9928115 DOI: 10.1126/scitranslmed.abj2266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests have relied on RNA extraction followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays. Whereas automation improved logistics and different pooling strategies increased testing capacity, highly multiplexed next-generation sequencing (NGS) diagnostics remain a largely untapped resource. NGS tests have the potential to markedly increase throughput while providing crucial SARS-CoV-2 variant information. Current NGS-based detection and genotyping assays for SARS-CoV-2 are costly, mostly due to parallel sample processing through multiple steps. Here, we have established ApharSeq, in which samples are barcoded in the lysis buffer and pooled before reverse transcription. We validated this assay by applying ApharSeq to more than 500 clinical samples from the Clinical Virology Laboratory at Hadassah hospital in a robotic workflow. The assay was linear across five orders of magnitude, and the limit of detection was Ct 33 (~1000 copies/ml, 95% sensitivity) with >99.5% specificity. ApharSeq provided targeted high-confidence genotype information due to unique molecular identifiers incorporated into this method. Because of early pooling, we were able to estimate a 10- to 100-fold reduction in labor, automated liquid handling, and reagent requirements in high-throughput settings compared to current testing methods. The protocol can be tailored to assay other host or pathogen RNA targets simultaneously. These results suggest that ApharSeq can be a promising tool for current and future mass diagnostic challenges.
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Affiliation(s)
- Alon Chappleboim
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayelet Rahat
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Israa Sharkia
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Miriam Adam
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daniel Kitsberg
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Gavriel Fialkoff
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Matan Lotem
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Omer Gershon
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Anna-Kristina Schmidtner
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Esther Oiknine-Djian
- Hadassah Hebrew University Medical Center, Jerusalem 9112001, Israel.,Lautenberg Centre for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ronen Sadeh
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Dana Wolf
- Hadassah Hebrew University Medical Center, Jerusalem 9112001, Israel.,Lautenberg Centre for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Naomi Habib
- Edmond and Lily Safra Center for Brain Sciences, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,Rachel and Selim Benin School of Computer Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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15
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Günl F, Mecate-Zambrano A, Rehländer S, Hinse S, Ludwig S, Brunotte L. Shooting at a Moving Target-Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development. Vaccines (Basel) 2021; 9:1052. [PMID: 34696160 PMCID: PMC8540924 DOI: 10.3390/vaccines9101052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/06/2023] Open
Abstract
Since late 2019 the newly emerged pandemic SARS-CoV-2, the causative agent of COVID-19, has hit the world with recurring waves of infections necessitating the global implementation of non-pharmaceutical interventions, including strict social distancing rules, the wearing of masks and the isolation of infected individuals in order to restrict virus transmissions and prevent the breakdown of our healthcare systems. These measures are not only challenging on an economic level but also have a strong impact on social lifestyles. Using traditional and novel technologies, highly efficient vaccines against SARS-CoV-2 were developed and underwent rapid clinical evaluation and approval to accelerate the immunization of the world population, aiming to end the pandemic and return to normality. However, the emergence of virus variants with improved transmission, enhanced fitness and partial immune escape from the first generation of vaccines poses new challenges, which are currently being addressed by scientists and pharmaceutical companies all over the world. In this ongoing pandemic, the evaluation of SARS-CoV-2 vaccines underlies diverse unpredictable dynamics, posed by the first broad application of the mRNA vaccine technology and their compliance, the occurrence of unexpected side effects and the rapid emergence of variations in the viral antigen. However, despite these hurdles, we conclude that the available SARS-CoV-2 vaccines are very safe and efficiently protect from severe COVID-19 and are thereby the most powerful tools to prevent further harm to our healthcare systems, economics and individual lives. This review summarizes the unprecedented pathways of vaccine development and approval during the ongoing SARS-CoV-2 pandemic. We focus on the real-world effectiveness and unexpected positive and negative side effects of the available vaccines and summarize the timeline of the applied adaptations to the recommended vaccination strategies in the light of emerging virus variants. Finally, we highlight upcoming strategies to improve the next generations of SARS-CoV-2 vaccines.
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Affiliation(s)
- Franziska Günl
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Angeles Mecate-Zambrano
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Selina Rehländer
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Saskia Hinse
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
| | - Stephan Ludwig
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
| | - Linda Brunotte
- Institute of Virology (IVM), University of Münster, 48149 Münster, Germany; (F.G.); (A.M.-Z.); (S.R.); (S.H.); (S.L.)
- Interdisciplinary Centre for Clinical Research (IZKF), Medical Faculty, University of Münster, 48149 Münster, Germany
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16
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Mor O, Mandelboim M, Fleishon S, Bucris E, Bar-Ilan D, Linial M, Nemet I, Kliker L, Lustig Y, Mendelson ES, Zuckerman NS. The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Vaccines (Basel) 2021; 9:937. [PMID: 34452062 PMCID: PMC8402656 DOI: 10.3390/vaccines9080937] [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: 07/07/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
Emerging SARS-CoV-2 variants may threaten global vaccination efforts and the awaited reduction in outbreak burden. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. The variant infected 270 individuals in Israel between December 2020 and March 2021, until diminishing due to the gain in dominance of the Alpha variant in February 2021. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread.
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Affiliation(s)
- Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Shay Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | - Yaniv Lustig
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
| | | | - Ella S. Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel; (O.M.); (M.M.); (S.F.); (E.B.); (D.B.-I.); (I.N.); (L.K.); (Y.L.); (E.S.M.)
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17
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Mor O, Mandelboim M, Fleishon S, Bucris E, Bar-Ilan D, Linial M, Nemet I, Kliker L, Lustig Y, Mendelson ES, Zuckerman NS. The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Vaccines (Basel) 2021; 9. [PMID: 34452062 DOI: 10.1101/2021.07.03.21259957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 05/20/2023] Open
Abstract
Emerging SARS-CoV-2 variants may threaten global vaccination efforts and the awaited reduction in outbreak burden. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. The variant infected 270 individuals in Israel between December 2020 and March 2021, until diminishing due to the gain in dominance of the Alpha variant in February 2021. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread.
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Affiliation(s)
- Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Shay Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ital Nemet
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Limor Kliker
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Yaniv Lustig
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
| | - Ella S Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Neta S Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Sheba Medical Center, Tel-Hashomer 52621, Israel
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18
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Trombetta CM, Marchi S, Viviani S, Manenti A, Benincasa L, Ruello A, Bombardieri E, Vicenti I, Zazzi M, Montomoli E. Serum Neutralizing Activity against B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants of Concern in Hospitalized COVID-19 Patients. Viruses 2021; 13:1347. [PMID: 34372553 PMCID: PMC8310013 DOI: 10.3390/v13071347] [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: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
The recent spreading of new SARS-CoV-2 variants, carrying several mutations in the spike protein, could impact immune protection elicited by natural infection or conferred by vaccination. In this study, we evaluated the neutralizing activity against the viral variants that emerged in the United Kingdom (B.1.1.7), Brazil (P.1), and South Africa (B.1.351) in human serum samples from hospitalized patients infected by SARS-CoV-2 during the first pandemic wave in Italy in 2020. Of the patients studied, 59.5% showed a decrease (≥2 fold) in neutralizing antibody titer against B.1.1.7, 83.3% against P.1, and 90.5% against B.1.351 with respect to the original strain. The reduction in antibody titers against all analyzed variants, and in particular P.1 and B.1.351, suggests that previous symptomatic infection might be not fully protective against exposure to SARS-CoV-2 variants carrying a set of relevant spike mutations.
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Affiliation(s)
- Claudia Maria Trombetta
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
| | - Simonetta Viviani
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
| | - Alessandro Manenti
- VisMederi srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
| | - Linda Benincasa
- VisMederi Research srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
| | - Antonella Ruello
- Humanitas Gavazzeni, Via Mauro Gavazzeni 21, 24125 Bergamo, Italy; (A.R.); (E.B.)
| | - Emilio Bombardieri
- Humanitas Gavazzeni, Via Mauro Gavazzeni 21, 24125 Bergamo, Italy; (A.R.); (E.B.)
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (M.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (M.Z.)
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
- VisMederi srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
- VisMederi Research srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
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19
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Janik E, Niemcewicz M, Podogrocki M, Majsterek I, Bijak M. The Emerging Concern and Interest SARS-CoV-2 Variants. Pathogens 2021; 10:633. [PMID: 34064143 PMCID: PMC8224338 DOI: 10.3390/pathogens10060633] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for coronavirus disease 2019 (COVID-19) was discovered in December 2019 in Wuhan, China. Since that time, the virus has spread around the world, which resulted in an announcement of the World Health Organization (WHO), dated in March 2020, that COVID-19 was a worldwide pandemic, and since then, the world has been struggling with this disease. SARS-CoV-2, similar to other RNA viruses, continually mutates, and new variants are appearing. Among large numbers of detected SARS-CoV-2 variants, only an insignificant amount of them are able to pose a risk to public health, as they are more contagious and cause more severe conditions. The emerged variants were classified by the Centers for Disease Control and Prevention (CDC) in collaboration with SARS-CoV-2 Interagency Group (SIG) according to strictly defined pattern. Variants were classified as variants of concern, variants of interest, and variants of high consequence. In the last few months, three variants of concern (B.1.1.7, B.1.351, and P.1) and four variants of interests (B.1.526, B.1.525, B.1.427/B.1.429, and P.2) were distinguished and are essential for close monitoring. This analysis summarizes the principal information concerning SARS-CoV-2 variants, such as their infectivity, severity, mutations, and immune susceptibility.
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Affiliation(s)
- Edyta Janik
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
| | - Marcin Niemcewicz
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
| | - Marcin Podogrocki
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, 90-419 Lodz, Poland;
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (E.J.); (M.N.); (M.P.)
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