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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta ( B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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2
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Tamada Y, Takeuchi K, Kusama T, Maeda M, Murata F, Osaka K, Fukuda H. Effectiveness of COVID-19 vaccines against infection in Japan: A test-negative study from the VENUS study. Vaccine 2023; 41:5447-5453. [PMID: 37487845 DOI: 10.1016/j.vaccine.2023.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/03/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Although the effectiveness of coronavirus disease 2019 (COVID-19) vaccines is a crucial public health concern, evidence from Western Pacific countries is limited, including Japan. This study aimed to estimate the COVID-19 vaccines effectiveness (VE) against infection during the Delta variant predominance (July-September 2021) in Japan. METHODS We performed a test-negative study using COVID-19 test data of ≥20-year-old residents in four municipalities who were tested in medical institutions between July 1 and September 30, 2021. We extracted COVID-19 test data from healthcare claims data, and the vaccination status at the testing date was ascertained using the Vaccination Record System data. Confirmed positive cases were identified using data from the national system for COVID-19, Health Center Real-time Information-sharing System on COVID-19. Logistic regression analyses were conducted to estimate the odds of testing positive according to vaccination status. VE was calculated as (1 - odds ratio) × 100%. RESULTS This study included 530 positive and 15,650 negative results. Adjusted manufacturer-unspecified VE was 4.1% (95% confidence interval [CI], -36.5-32.6) at 0-13 days after the first dose, 45.2% (95% CI, 13.4-65.3) at ≥14 days after the first dose, 85.2% (95% CI, 69.9-92.7) at 0-13 days after the second dose, and 79.6% (95% CI, 72.6-84.8) at ≥14 days after the second dose. In addition, the VE after the second dose was highest at 14-34 days after the dose (VE, 89.1%; 95% CI, 80.5-93.9). CONCLUSIONS High real-world effectiveness of COVID-19 vaccines, especially two doses, against infection during the Delta variant predominance in Japan was confirmed.
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Affiliation(s)
- Yudai Tamada
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry, Miyagi, Japan; Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kenji Takeuchi
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry, Miyagi, Japan; Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan; Division of Statistics and Data Science, Liaison Center for Innovative Dentistry, Tohoku University Graduate School of Dentistry, Miyagi, Japan.
| | - Taro Kusama
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry, Miyagi, Japan; Division of Statistics and Data Science, Liaison Center for Innovative Dentistry, Tohoku University Graduate School of Dentistry, Miyagi, Japan
| | - Megumi Maeda
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Fumiko Murata
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Ken Osaka
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry, Miyagi, Japan
| | - Haruhisa Fukuda
- Department of Health Care Administration and Management, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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Pang CJ, Delamater PL. Spatiotemporal characteristics of the SARS-CoV-2 Delta wave in North Carolina. Spat Spatiotemporal Epidemiol 2023; 45:100566. [PMID: 37301588 PMCID: PMC9838034 DOI: 10.1016/j.sste.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/18/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
We constructed county-level models to examine properties of the SARS-CoV-2 B.1.617.2 (Delta) variant wave of infections in North Carolina and assessed immunity levels (via prior infection, via vaccination, and overall) prior to the Delta wave. To understand how prior immunity shaped Delta wave outcomes, we assessed relationships among these characteristics. Peak weekly infection rate and total percent of the population infected during the Delta wave were negatively correlated with the proportion of people with vaccine-derived immunity prior to the Delta Wave, signaling that places with higher vaccine uptake had better outcomes. We observed a positive correlation between immunity via infection prior to Delta and percent of the population infected during the Delta wave, meaning that counties with poor pre-Delta outcomes also had poor Delta wave outcomes. Our findings illustrate geographic variation in outcomes during the Delta wave in North Carolina, highlighting regional differences in population characteristics and infection dynamics.
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Affiliation(s)
- Cindy J Pang
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul L Delamater
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Peterson S, Daigle J, Dueck C, Nagasawa A, Mulvey M, Mangat CS. Real-time quantitative reverse transcription polymerase chain reaction detection of SARS-CoV-2 Delta variant in Canadian wastewater. Can Commun Dis Rep 2023; 49:213-220. [PMID: 38414535 PMCID: PMC10898651 DOI: 10.14745/ccdr.v49i05a07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are associated with increased infectivity, severity, and mortality of coronavirus disease 2019 (COVID-19) and have been increasingly detected in clinical and wastewater surveillance in Canada and internationally. In this study, we present a real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay for detection of the N gene D377Y mutation associated with the SARS-CoV-2 Delta variant in wastewater. Methods Wastewater samples (n=980) were collected from six cities and 17 rural communities across Canada from July to November 2021 and screened for the D377Y mutation. Results The Delta variant was detected in all major Canadian cities and northern remote regions, and half of the southern rural communities. The sensitivity and specificity of this assay were sufficient for detection and quantitation of the Delta variant in wastewater to aid in rapid population-level screening and surveillance. Conclusion This study demonstrates a novel cost-effective RT-qPCR assay for tracking the spread of the SARS-CoV-2 Delta variant. This rapid assay can be easily integrated into current wastewater surveillance programs to aid in population-level variant tracking.
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Affiliation(s)
- Shelley Peterson
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Jade Daigle
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Codey Dueck
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Audra Nagasawa
- Centre for Population Health Data, Statistics Canada, Ottawa, ON
| | - Michael Mulvey
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB
| | - Chand S Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
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Heinrich F, Huter T, Mertens S, Lange P, Vering J, Heinemann A, Nörz DS, Hoffmann A, Aepfelbacher M, Ondruschka B, Krasemann S, Lütgehetmann M. New Postmortem Perspective on Emerging SARS-CoV-2 Variants of Concern, Germany. Emerg Infect Dis 2023; 29:652-656. [PMID: 36787498 PMCID: PMC9973696 DOI: 10.3201/eid2903.221297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
We performed autopsies on persons in Germany who died from COVID-19 and observed higher nasopharyngeal SARS-CoV-2 viral loads for variants of concern (VOC) compared with non-VOC lineages. Pulmonary inflammation and damage appeared higher in non-VOC than VOC lineages until adjusted for vaccination status, suggesting COVID-19 vaccination may mitigate pulmonary damage.
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Jeican II, Inișca P, Gheban D, Anton V, Lazăr M, Vică ML, Mironescu D, Rebeleanu C, Crivii CB, Aluaș M, Albu S, Siserman CV. Histopathological Lung Findings in COVID-19 B.1.617.2 SARS-CoV-2 Delta Variant. J Pers Med 2023; 13:jpm13020279. [PMID: 36836513 PMCID: PMC9961426 DOI: 10.3390/jpm13020279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The Delta variant (Pango lineage B.1.617.2) is one of the most significant and aggressive variants of SARS-CoV-2. To the best of our knowledge, this is the first paper specifically studying pulmonary morphopathology in COVID-19 caused by the B.1.617.2 Delta variant. METHODS The study included 10 deceased patients (40-83 years) with the COVID-19 Delta variant. The necrotic lung fragments were obtained either by biopsy (six cases) or autopsy (four cases). Tissue samples were subjected to virology analysis for identification of the SARS-CoV-2 variant, histopathology, and immunohistochemistry (anti-SARS coronavirus mouse anti-virus antibody). RESULTS Virology analysis identified B.1.617.2 through genetic sequencing in eight cases, and in two cases, specific mutations of B.1.617.2 were identified. Macroscopically, in all autopsied cases, the lung had a particular appearance, purple in color, with increased consistency on palpation and abolished crepitations. Histopathologically, the most frequently observed lesions were acute pulmonary edema (70%) and diffuse alveolar damage at different stages. The immunohistochemical examination was positive for proteins of SARS-CoV-2 in 60% of cases on alveolocytes and in endothelial cells. CONCLUSIONS The histopathological lung findings in the B.1.617.2 Delta variant are similar to those previously described in COVID-19. Spike protein-binding antibodies were identified immunohistochemically both on alveolocytes and in the endothelial cells, showing the potential of indirect damage from thrombosis.
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Affiliation(s)
- Ionuț Isaia Jeican
- Department of Anatomy and Embryology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Patricia Inișca
- Department of Pathology, County Emergency Hospital Deva, 330084 Deva, Romania
| | - Dan Gheban
- Department of Pathology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
- Department of Pathology, Emergency Clinical Hospital for Children, 400370 Cluj-Napoca, Romania
| | - Vlad Anton
- Department of Medical Biochemistry, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | - Mihaela Lazăr
- Viral Respiratory Infections Laboratory, Cantacuzino National Military-Medical Institute for Research and Development, 050096 Bucharest, Romania
| | - Mihaela Laura Vică
- Institute of Legal Medicine, 400006 Cluj-Napoca, Romania
- Department of Cell and Molecular Biology, Iuliu Hatieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania
| | | | - Codrin Rebeleanu
- Department of Legal Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Carmen Bianca Crivii
- Department of Anatomy and Embryology, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
| | - Maria Aluaș
- Department of Oral Health, Iuliu Hatieganu University of Medicine and Pharmacy, Victor Babeș Str., No. 15, 400012 Cluj-Napoca, Romania
- Correspondence: (M.A.); (S.A.)
| | - Silviu Albu
- Department of Head and Neck Surgery and Otorhinolaryngology, University Clinical Hospital of Railway Company, Iuliu Hatieganu University of Medicine and Pharmacy, 400015 Cluj-Napoca, Romania
- Correspondence: (M.A.); (S.A.)
| | - Costel Vasile Siserman
- Institute of Legal Medicine, 400006 Cluj-Napoca, Romania
- Department of Legal Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania
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Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. Int J Biol Macromol 2023; 226:1116-1140. [PMID: 36435470 PMCID: PMC9683856 DOI: 10.1016/j.ijbiomac.2022.11.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran,Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Shadi Abkhiz
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mohamadzadeh
- Department of Chemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak 3848177584, Iran
| | - Esmaeil Sadroddiny
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia,Correspondence to: V.N. Uversky, Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 16802, USA,Corresponding author
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8
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Kuhlmeier E, Chan T, Agüí CV, Willi B, Wolfensberger A, Beisel C, Topolsky I, Beerenwinkel N, Stadler T, Jones S, Tyson G, Hosie MJ, Reitt K, Hüttl J, Meli ML, Hofmann-Lehmann R. Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 2023; 15:245. [PMID: 36680285 PMCID: PMC9864232 DOI: 10.3390/v15010245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
In human beings, there are five reported variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). However, in contrast to human beings, descriptions of infections of animals with specific variants are still rare. The aim of this study is to systematically investigate SARS-CoV-2 infections in companion animals in close contact with SARS-CoV-2-positive owners ("COVID-19 households") with a focus on the Delta variant. Samples, obtained from companion animals and their owners were analyzed using a real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and next-generation sequencing (NGS). Animals were also tested for antibodies and neutralizing activity against SARS-CoV-2. Eleven cats and three dogs in nine COVID-19-positive households were RT-qPCR and/or serologically positive for the SARS-CoV-2 Delta variant. For seven animals, the genetic sequence could be determined. The animals were infected by one of the pangolin lineages B.1.617.2, AY.4, AY.43 and AY.129 and between zero and three single-nucleotide polymorphisms (SNPs) were detected between the viral genomes of animals and their owners, indicating within-household transmission between animal and owner and in multi-pet households also between the animals. NGS data identified SNPs that occur at a higher frequency in the viral sequences of companion animals than in viral sequences of humans, as well as SNPs, which were exclusively found in the animals investigated in the current study and not in their owners. In conclusion, our study is the first to describe the SARS-CoV-2 Delta variant transmission to animals in Switzerland and provides the first-ever description of Delta-variant pangolin lineages AY.129 and AY.4 in animals. Our results reinforce the need of a One Health approach in the monitoring of SARS-CoV-2 in animals.
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Affiliation(s)
- Evelyn Kuhlmeier
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Tatjana Chan
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Cecilia Valenzuela Agüí
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Aline Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | | | - Sarah Jones
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Grace Tyson
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Margaret J. Hosie
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Katja Reitt
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland
| | - Julia Hüttl
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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Wang Q, Peng L, Nie Y, Shu Y, Zhang H, Song Z, Li Y, Hu H, Li L, Wang X, Liu J, Li J, Shi Z, Deng F, Guo Y, Zhou Y, Yan B, Hu Z, Wang M. Hybridoma-derived neutralizing monoclonal antibodies against Beta and Delta variants of SARS-CoV-2 in vivo. Virol Sin 2022; 38:257-267. [PMID: 36596381 PMCID: PMC9803610 DOI: 10.1016/j.virs.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
Neutralizing monoclonal antibodies (mAb) are a major therapeutic strategy for the treatment of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. The continuous emergence of new SARS-CoV-2 variants worldwide has increased the urgency for the development of new mAbs. In this study, we immunized mice with the receptor-binding domain (RBD) of the SARS-CoV-2 prototypic strain (WIV04) and screened 35 RBD-specific mAbs using hybridoma technology. Results of the plaque reduction neutralization test showed that 25 of the mAbs neutralized authentic WIV04 strain infection. The 25 mAbs were divided into three categories based on the competitive enzyme-linked immunosorbent assay results. A representative mAb was selected from each category (RD4, RD10, and RD14) to determine the binding kinetics and median inhibitory concentration (IC50) of WIV04 and two variants of concern (VOC): B.1.351 (Beta) and B.1.617.2 (Delta). RD4 neutralized the B.1.617.2 variant with an IC50 of 2.67 ng/mL; however, it completely lost neutralizing activity against the B.1.351 variant. RD10 neutralized both variants with an IC50 exceeding 100 ng/mL; whereas RD14 neutralized two variants with a higher IC50 (>1 mg/mL). Animal experiments were performed to evaluate the protective effects of RD4 and RD10 against various VOC infections. RD4 could protect Adv-hACE2 transduced mice from B.1.617.2 infection at an antibody concentration of 25 mg/kg, while RD10 could protect mice from B.1.351 infection at an antibody concentration of 75 mg/kg. These results highlight the potential for future modifications of the mAbs for practical use.
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Affiliation(s)
- Qianran Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Lu Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanqiu Nie
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanni Shu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Huajun Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zidan Song
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yufeng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hengrui Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Liushuai Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jia Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhengli Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yu Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yiwu Zhou
- Department of Forensic Medicine, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Bing Yan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China,Hubei Jiangxia Laboratory, Wuhan, 430200, China,Corresponding author
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10
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Liu WD, Wang JT, Chao TL, Ieong SM, Tsai YM, Kuo PH, Tsai MJ, Chen YJ, Li GC, Ho SY, Chen HH, Huang YS, Hung CC, Chen YC, Chang SY, Chang SC. Evolution of neutralizing antibodies and cross-activity against different variants of SARS-CoV-2 in patients recovering from COVID-19. J Formos Med Assoc 2022:S0929-6646(22)00436-3. [PMID: 36496300 PMCID: PMC9705194 DOI: 10.1016/j.jfma.2022.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Patients recovering from COVID-19 may need vaccination against SARS-CoV-2 because acquired immunity from primary infection may wane, given the emergence of new SARS-CoV-2 variants. Understanding the trends of anti-spike IgG and neutralizing antibody titers in patients recovering from COVID-19 may inform the decision made on the appropriate interval between recovery and vaccination. METHODS Participants aged 20 years or older and diagnosed with COVID-19 between January and December, 2020 were enrolled. Serum specimens were collected every three months from 10 days to 12 months after the onset of symptom for determinations of anti-spike IgG and neutralizing antibody titers against SARS-CoV-2 Wuhan strain with D614G mutation, alpha, gamma and delta variants. RESULTS Of 19 participants, we found a decreasing trend of geometric mean titers of anti-spike IgG from 560.9 to 217 and 92 BAU/mL after a 4-month and a 7-month follow-up, respectively. The anti-spike IgG titers declined more quickly in the ten participants with severe or critical disease than the nine participants with only mild to moderate disease between one month and seven months after SARS-CoV-2 infection (-8.49 vs - 2.34-fold, p < 0.001). The neutralizing activity of the convalescent serum specimens collected from participants recovering from wild-type SARS-CoV-2 infection against different variants was lower, especially against the delta variants (p < 0.01 for each variant with Wuhan strain as reference). CONCLUSION Acquired immunity from primary infection with SARS-CoV-2 waned within 4-7 months in COVID-19 patients, and neutralizing cross-activities against different SARS-CoV-2 variants were lower compared with those against wild-type strain.
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Affiliation(s)
- Wang-Da Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan,Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan,Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan,Corresponding author. Department of Internal Medicine, National Taiwan University Hospital, 7 Chung-Shan South Rd., Taipei City 10002, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Si-Man Ieong
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ya-Min Tsai
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Hsien Kuo
- Department of Internal Medicine, National Taiwan University Hospital Biomedical Park Hospital, Hsinchu, Taiwan
| | - Ming-Jui Tsai
- Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin County, Taiwan
| | - Yi-Jie Chen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Guei-Chi Li
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Yuan Ho
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hui-Hou Chen
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Shan Huang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan,Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin County, Taiwan,Department of Tropical Medicine and Parasitology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yee-Chun Chen
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan,Center of Infection Control, National Taiwan University Hospital, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan,Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan,Corresponding author. Department of Laboratory Medicine, National Taiwan University Hospital, 7 Chung-Shan South Rd., Taipei City 10002, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan,School of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
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11
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Experton B, Elena A, Hein CS, Nordenberg D, Walker P, Schwendiman B, Burrow CR. Enhanced Vaccine Effectiveness during the Delta Phase of the COVID-19 Pandemic in the Medicare Population Supports a Multilayered Prevention Approach. Biology (Basel) 2022; 11. [PMID: 36552210 DOI: 10.3390/biology11121700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Throughout the pandemic, individuals 65 years and older have contributed most COVID-19 related deaths. To best formulate effective vaccination and other prevention policies to protect older adults, large scale observational studies of these higher risk individuals are needed. We conducted a Vaccine Effectiveness (VE) study during the B.1.617.2 Delta variant phase of the pandemic in July and August 2021 in a cohort of 17 million Medicare beneficiaries of which 5.7 million were fully vaccinated. We found that individuals fully vaccinated with the Pfizer-BioNTech BNT162b2 and Moderna mRNA-1273 vaccines in January 2021 had 2.5 times higher breakthrough infections and hospitalizations than those fully vaccinated in March 2021, consistent with waning of vaccine-induced immunity. Measuring VE weekly, we found that VE against hospitalization, and even more so against infection, increased from July 2021 through August 2021, suggesting that in addition to the protective role of vaccination, increased masking or social distancing might have contributed to the unexpected increase in VE. Ongoing monitoring of Medicare beneficiaries should be a priority as new variants continue to emerge, and the VE of the new bivalent vaccines remains to be established. This could be accomplished with a large Medicare claims database and the analytics platform used for this study.
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12
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Arantes I, Gomes Naveca F, Gräf T, Miyajima F, Faoro H, Luz Wallau G, Delatorre E, Reis Appolinario L, Cavalcante Pereira E, Venas TMM, Sampaio Rocha A, Serrano Lopes R, Mendonça Siqueira M, Bello G, Cristina Resende P; COVID-19 Fiocruz Genomic Surveillance Network. Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta across Different Brazilian Regions. Microbiol Spectr 2022; 10:e0264121. [PMID: 36000897 DOI: 10.1128/spectrum.02641-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The SARS-CoV-2 variant of concern (VOC) Delta was first detected in India in October 2020. The first imported cases of the Delta variant in Brazil were identified in April 2021 in the southern region, followed by more cases in different regions during the following months. By early September 2021, Delta was already the dominant variant in the southeastern (87%), southern (73%), and northeastern (52%) Brazilian regions. This study aimed to understand the spatiotemporal dissemination dynamics of Delta in Brazil. To this end, we employed a combination of maximum likelihood (ML) and Bayesian methods to reconstruct the evolutionary relationship of 2,264 VOC Delta complete genomes (482 from this study) recovered across 21 of the 27 Brazilian federal units. Our phylogeographic analyses identified three major transmission clusters of Delta in Brazil. The clade BR-I (n = 1,560) arose in Rio de Janeiro in late April 2021 and was the major cluster behind the dissemination of the VOC Delta in the southeastern, northeastern, northern, and central-western regions. The AY.101 lineage (n = 207) that arose in the Paraná state in late April 2021 and aggregated the largest fraction of sampled genomes from the southern region. Lastly, the AY.46.3 lineage emerged in Brazil in the São Paulo state in early June 2021 and remained mostly restricted to this state. In the rapid turnover of viral variants characteristic of the SARS-CoV-2 pandemic, Brazilian regions seem to occupy different stages of an increasing prevalence of the VOC Delta in their epidemic profiles. This process demands continuous genomic and epidemiological surveillance toward identifying and mitigating new introductions, limiting their dissemination, and preventing the establishment of more significant outbreaks in a population already heavily affected by the COVID-19 pandemic. IMPORTANCE Amid the SARS-CoV-2 continuously changing epidemic profile, this study details the space-time dynamics of the emergence of the Delta lineage across Brazilian territories, pointing out its multiple introductions in the country and its most prevalent sublineages. Some of these sublineages have their emergence, alongside their genomic composition and geographic distribution, detailed here for the first time. A special focus is given to the emergence process of Delta outside the country's south and southeast regions, the most populated and subjects of most published SARS-CoV-2 studies in Brazil. In summary, the study allows a better comprehension of the evolution process of a SARS-CoV-2 lineage that would be associated with a significant recrudescence of the pandemic in Brazil.
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13
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Caserta LC, Martins M, Cronk B, Anderson R, Eldridge H, Gallow D, Kruppa F, Plocharczyk E, Diel DG. Infection and Transmission of SARS-CoV-2 B.1.617.2 Lineage (Delta Variant) among Fully Vaccinated Individuals. Microbiol Spectr 2022; 10:e0056322. [PMID: 36165775 DOI: 10.1128/spectrum.00563-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The emergence of the SARS-CoV-2 B.1.617.2 lineage (Delta variant) in 2021 was associated with increased case numbers and test positivity rates, including a large number of infections in fully vaccinated individuals. Here, we describe the findings of an investigation conducted in Tompkins County, New York, to evaluate factors underlying a significant uptick in the number of coronavirus disease 2019 (COVID-19) cases observed in the months of July and August 2021. We performed genomic surveillance and genotyping as well as virological assessments to determine infectivity of the virus in a select number of clinical diagnostic samples. Genomic sequence analyses revealed complete replacement of the B.1.1.7 lineage (Alpha variant) with the B.1.617.2 lineage (Delta variant) between July 1 and August 4 2021. We observed a strong association between viral RNA loads detected by real-time reverse transcriptase PCR and infectious virus detected in respiratory secretions by virus titration. A marked increase in positive cases among fully vaccinated individuals was observed. The sequence divergence between two index Delta variant cases in April and May, and the cases after July 1st, revealed independent Delta variant introductions in Tompkins County. Contact tracing information enabled the detection of clusters of connected cases within closely related phylogenetic clusters. We also found evidence of transmission between vaccinated individuals and between vaccinated and unvaccinated individuals. This was confirmed by detection and isolation of infectious virus from a group of individuals within epidemiologically connected transmission clusters, confirming shedding of high viral loads and transmission of the virus by fully vaccinated individuals. IMPORTANCE The SARS-CoV-2 lineage B.1.617.2 (Delta variant) emerged in Asia and rapidly spread to other countries, becoming the dominant circulating lineage. Worldwide infections with B.1.617.2 peaked at a time in which vaccination rates were increasing. In this study, we present data characterizing the emergence of SARS-CoV-2 lineage B.1.617.2 (Delta variant) in Tompkins County, New York, which has one of the highest vaccination rates in the state. We present evidence demonstrating infection, replication, and transmission of SARS-CoV-2 lineage B.1.617.2 (Delta variant) between fully vaccinated individuals. Importantly, infectious virus loads were determined in a subset of samples and demonstrated shedding of high viral titers in respiratory secretions of vaccinated individuals.
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14
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Plante JA, Machado RRG, Mitchell BM, Shinde DP, Walker J, Scharton D, McConnell A, Saada N, Liu J, Khan B, Campos RK, Johnson BA, Menachery VD, Levine CB, Ren P, McLellan SLF, Plante KS, Weaver SC. Vaccination Decreases the Infectious Viral Load of Delta Variant SARS-CoV-2 in Asymptomatic Patients. Viruses 2022; 14. [PMID: 36146877 DOI: 10.3390/v14092071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 02/08/2023] Open
Abstract
The Delta variant of SARS-CoV-2 has caused many breakthrough infections in fully vaccinated individuals. While vaccine status did not generally impact the number of viral RNA genome copies in nasopharyngeal swabs of breakthrough patients, as measured by Ct values, it has been previously found to decrease the infectious viral load in symptomatic patients. We quantified the viral RNA, infectious virus, and anti-spike IgA in nasopharyngeal swabs collected from individuals asymptomatically infected with the Delta variant of SARS-CoV-2. Vaccination decreased the infectious viral load, but not the amount of viral RNA. Furthermore, vaccinees with asymptomatic infections had significantly higher levels of anti-spike IgA in their nasal secretions compared to unvaccinated individuals with asymptomatic infections. Thus, vaccination may decrease the transmission risk of Delta, and perhaps other variants, despite not affecting the amount of viral RNA measured in nasopharyngeal swabs.
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15
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Mousa M, Albreiki M, Alshehhi F, AlShamsi S, Marzouqi NA, Alawadi T, Alrand H, Alsafar H, Fikri A. Similar effectiveness of the inactivated vaccine BBIBP-CorV (Sinopharm) and the mRNA vaccine BNT162b2 (Pfizer-BioNTech) against COVID-19 related hospitalizations during the Delta outbreak in the UAE. J Travel Med 2022; 29:taac036. [PMID: 35244687 PMCID: PMC8903474 DOI: 10.1093/jtm/taac036] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/29/2022]
Abstract
Inactivated vaccine BBIBP-CorV {Sinopharm; 95% [95% confidence interval (CI): 94, 97%]} and the mRNA vaccine BNT162b2 [Pfizer-BioNTech; 98% (95% CI: 86, 99%)] demonstrated protection against COVID-19 related hospitalizations from the Delta (B.1.617.2) variant. Ongoing efforts are necessary to target vaccine hesitancy and to promote booster shots for protection against severe COVID-19 disease and arising variants of concern.
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Affiliation(s)
- Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Nuffield Department of Women’s and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Mohammed Albreiki
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Fatima Alshehhi
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Safiya AlShamsi
- Laboratory Department, Emirates Health Services Establishment, Dubai, United Arab Emirates
| | - Nada Al Marzouqi
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Tayba Alawadi
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Hussain Alrand
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Asma Fikri
- Public Health Sector, Ministry of Health and Prevention, Dubai, United Arab Emirates
- National Center for Health Research, Ministry of Health and Prevention, United Arab Emirates
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16
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Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Engelbrecht S, Wasserman S, Schrueder N, Boloko L, Symons G, Raubenheimer P, Viljoen A, Parker A, Cohen C, Jasat W, Lessells R, Wilkinson RJ, Boulle A, Hsiao M. Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. Gates Open Res 2022; 6:117. [PMID: 37994361 PMCID: PMC10663174 DOI: 10.12688/gatesopenres.13654.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 11/24/2023] Open
Abstract
Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex TM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.
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Affiliation(s)
- Hannah Hussey
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Ziyaad Valley-Omar
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Diana Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Stephen Korsman
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Deelan Doolabh
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Wofgang Preiser
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Tongai Maponga
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | | | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Neshaad Schrueder
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Linda Boloko
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Greg Symons
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Peter Raubenheimer
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Abraham Viljoen
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Arifa Parker
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jasat
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu Natal, Durban, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Marvin Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
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17
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Wang Q, Anang S, Iketani S, Guo Y, Liu L, Katsamba PS, Shapiro L, Ho DD, Sodroski JG. Functional properties of the spike glycoprotein of the emerging SARS-CoV-2 variant B.1.1.529. Cell Rep 2022; 39:110924. [PMID: 35658975 PMCID: PMC9119962 DOI: 10.1016/j.celrep.2022.110924] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022] Open
Abstract
The recently emerged B.1.1.529 (Omicron) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant has a highly divergent spike (S) glycoprotein. We compared the functional properties of B.1.1.529 BA.1 S with those of previous globally prevalent SARS-CoV-2 variants, D614G and B.1.617.2. Relative to these variants, B.1.1.529 S exhibits decreases in processing, syncytium formation, virion incorporation, and ability to mediate infection of cells with high TMPRSS2 expression. B.1.1.529 and B.1.617.2 S glycoproteins bind ACE2 with higher affinity than D614G S. The unliganded B.1.1.529 S trimer is less stable at low temperatures than the other SARS-CoV-2 Ss, a property related to its more “open” S conformation. Upon ACE2 binding, the B.1.1.529 S trimer sheds S1 at 37°C, but not at 0°C. B.1.1.529 pseudoviruses are relatively resistant to neutralization by sera from patients with coronavirus disease 2019 (COVID-19) and vaccinees. These properties of the B.1.1.529 S glycoprotein likely influence the transmission, cytopathic effects, and immune evasion of this emerging variant.
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Affiliation(s)
- Qian Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA.
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yicheng Guo
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Phinikoula S Katsamba
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lawrence Shapiro
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Joseph G Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
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18
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Ray SK, Mukherjee S. Divulging Incipient SARS-CoV-2 Delta ( B.1.617.2) Variant: Possible Interference with Global Scenario. Infect Disord Drug Targets 2022; 23:e060622205636. [PMID: 35670341 DOI: 10.2174/1871526522666220606092243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 Delta variant, also known as lineage B.1.617.2, is a variant of lineage B.1.617 of SARS-CoV-2, the virus that causes COVID-19. The B.1.617.2 variant was first discovered in India in December 2020, and by mid-April 2021, it had become the most often reported variant. On May 31, 2021, the World Health Organization (WHO) designated it as the Delta variation. Delta is 40-60% more transmissible than Alpha and nearly twice as transmissible as the original Wuhan strain of SARSCoV- 2, according to data. According to some evidence, the Delta variation may cause more severe illness in unprotected people than prior variants. A rapid increase in instances of this variation has been observed in the United Kingdom, which has been linked to travel from India and community transmission. WHO reports that the Delta version of COVID-19 has already been found in different countries throughout the world. According to the available information, the Delta variant appears to increase transmissibility, secondary attack rate, hospitalization risk, and immune escape. Due to the lack of data, the possible effects of the Delta variation on vaccination and treatment effectiveness remain unknown. However, neutralization efficiency in vaccinated people and resistance to monoclonal antibody therapy of the Delta variant have been documented in recent investigations.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
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19
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Peng L, Renauer PA, Ökten A, Fang Z, Park JJ, Zhou X, Lin Q, Dong MB, Filler R, Xiong Q, Clark P, Lin C, Wilen CB, Chen S. Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2. Cell Rep Med 2022; 3:100634. [PMID: 35561673 PMCID: PMC9040489 DOI: 10.1016/j.xcrm.2022.100634] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/06/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
Lipid nanoparticle (LNP)-mRNA vaccines offer protection against COVID-19; however, multiple variant lineages caused widespread breakthrough infections. Here, we generate LNP-mRNAs specifically encoding wild-type (WT), B.1.351, and B.1.617 SARS-CoV-2 spikes, and systematically study their immune responses. All three LNP-mRNAs induced potent antibody and T cell responses in animal models; however, differences in neutralization activity have been observed between variants. All three vaccines offer potent protection against in vivo challenges of authentic viruses of WA-1, Beta, and Delta variants. Single-cell transcriptomics of WT- and variant-specific LNP-mRNA-vaccinated animals reveal a systematic landscape of immune cell populations and global gene expression. Variant-specific vaccination induces a systemic increase of reactive CD8 T cells and altered gene expression programs in B and T lymphocytes. BCR-seq and TCR-seq unveil repertoire diversity and clonal expansions in vaccinated animals. These data provide assessment of efficacy and direct systems immune profiling of variant-specific LNP-mRNA vaccination in vivo.
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Affiliation(s)
- Lei Peng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Paul A Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Arya Ökten
- Department of Immunobiology, Yale University, New Haven, CT, USA; Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Zhenhao Fang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Jonathan J Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
| | - Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Qianqian Lin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Department of Immunobiology, Yale University, New Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA; Immunobiology Program, Yale University, New Haven, CT, USA
| | - Renata Filler
- Department of Immunobiology, Yale University, New Haven, CT, USA; Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, New Haven, CT, USA
| | - Paul Clark
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, New Haven, CT, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale University, New Haven, CT, USA; Department of Laboratory Medicine, Yale University, New Haven, CT, USA.
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA; Immunobiology Program, Yale University, New Haven, CT, USA; Department of Cell Biology, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, New Haven, CT, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
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20
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Servellita V, Syed AM, Morris MK, Brazer N, Saldhi P, Garcia-Knight M, Sreekumar B, Khalid MM, Ciling A, Chen PY, Kumar GR, Gliwa AS, Nguyen J, Sotomayor-Gonzalez A, Zhang Y, Frias E, Prostko J, Hackett J, Andino R, Wadford DA, Hanson C, Doudna J, Ott M, Chiu CY. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell 2022; 185:1539-1548.e5. [PMID: 35429436 PMCID: PMC8930394 DOI: 10.1016/j.cell.2022.03.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Virus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity against Delta and Omicron SARS-CoV-2 variants in 259 samples from 128 vaccinated individuals. Following Delta breakthrough infection, titers against WT rose 57-fold and 3.1-fold compared with uninfected boosted and unboosted individuals, respectively, versus only a 5.8-fold increase and 3.1-fold decrease for Omicron breakthrough infection. Among immunocompetent, unboosted patients, Delta breakthrough infections induced 10.8-fold higher titers against WT compared with Omicron (p = 0.037). Decreased antibody responses in Omicron breakthrough infections relative to Delta were potentially related to a higher proportion of asymptomatic or mild breakthrough infections (55.0% versus 28.6%, respectively), which exhibited 12.3-fold lower titers against WT compared with moderate to severe infections (p = 0.020). Following either Delta or Omicron breakthrough infection, limited variant-specific cross-neutralizing immunity was observed. These results suggest that Omicron breakthrough infections are less immunogenic than Delta, thus providing reduced protection against reinfection or infection from future variants.
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Affiliation(s)
- Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Abdullah M Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mary Kate Morris
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Noah Brazer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Prachi Saldhi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Alison Ciling
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Pei-Yi Chen
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jenny Nguyen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yueyuan Zhang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | | | | | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Carl Hanson
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA.
| | - Jennifer Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
| | - Melanie Ott
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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21
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Abstract
Emerging severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, especially those of concern, may have an impact on the virus's transmissibility and pathogenicity, as well as diagnostic equipment performance and vaccine effectiveness. Even though the SARS-CoV-2 Delta variant (B.1.617.2) emerged during India's second wave of infections, Delta variants have grown dominant internationally and are still evolving. On November 26, 2021, World Health Organization identified the variant B.1.1.529 as a variant of concern, naming it Omicron, based on evidence that Omicron contains numerous mutations that may influence its behavior. However, the mode of transmission and severity of the Omicron variant remains unknown. We used computational studies to examine the Delta and Omicron variants in this study and found that the Omicron variant had a higher affinity for human angiotensin-converting enzyme 2 (ACE2) than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor-binding domain (RBD), indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein's core and are required for structural stability. We observed a disorder-order transition in the Omicron variant between spike protein RBD regions 468-473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.
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Affiliation(s)
- Suresh Kumar
- Department of Diagnostic & Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, Shah Alam, Selangor, Malaysia
| | - Thiviya S Thambiraja
- Department of Diagnostic & Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, Shah Alam, Selangor, Malaysia
| | - Kalimuthu Karuppanan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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22
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Cicchitto G, Cardillo L, de Martinis C, Sabatini P, Marchitiello R, Abate G, Rovetti A, Cavallera A, Apuzzo C, Ferrigno F, Fusco G. Effects of Casirivimab/Imdevimab Monoclonal Antibody Treatment among Vaccinated Patients Infected by SARS-CoV-2 Delta Variant. Viruses 2022; 14:v14030650. [PMID: 35337057 PMCID: PMC8950724 DOI: 10.3390/v14030650] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 02/04/2023] Open
Abstract
There is a growing interest in using monoclonal antibodies (mAbs) in the early stages of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection to prevent disease progression. Little is known about the efficacy of mAbs against the delta variant of concern and its clinical presentations. We evaluated the effect of casirivimab/imdevimab treatment among five delta vaccine breakthrough patients. Symptomatic non-hospitalized vaccinated patients were submitted to nasopharyngeal swabs for the detection of SARS-CoV-2 and Next-Generation Sequencing (NGS). Blood analysis and chest Computed Tomography were also performed. A cocktail of casirivimab/imdevimab was administrated, and patients were monitored weekly. Clinical evolution was evaluated by the regression of the symptoms, negative results by real-time RT-PCR, and by the need of hospitalization: these aspects were considered as significant outcomes. In four cases, symptom reversion and viral load reduction were observed within 2 days and 7 days after mAbs treatment, respectively. Only one case, suffering from thymoma, was hospitalized 2 days later because of respiratory failure, which reverted within 18 days. mAbs treatment seems to be safe and effective against the delta variant and its clinical manifestations.
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Affiliation(s)
- Gaetano Cicchitto
- Department of Pneumology, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (G.C.); (F.F.)
| | - Lorena Cardillo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Naples, Italy; (C.d.M.); (G.F.)
- Correspondence: ; Tel.: +39-0817865509
| | - Claudio de Martinis
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Naples, Italy; (C.d.M.); (G.F.)
| | - Paola Sabatini
- Unit of Virology and Microbiology, “Umberto I” Hospital, 84014 Nocera Inferiore, Salerno, Italy;
| | - Rosita Marchitiello
- Unit of Clinical Pathology Laboratory, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (R.M.); (G.A.); (A.R.)
| | - Giovanna Abate
- Unit of Clinical Pathology Laboratory, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (R.M.); (G.A.); (A.R.)
| | - Adele Rovetti
- Unit of Clinical Pathology Laboratory, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (R.M.); (G.A.); (A.R.)
| | - Antonietta Cavallera
- Department of Radiology, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (A.C.); (C.A.)
| | - Camillo Apuzzo
- Department of Radiology, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (A.C.); (C.A.)
| | - Francesco Ferrigno
- Department of Pneumology, COVID-19 Hospital “M. Scarlato”, 84018 Scafati, Salerno, Italy; (G.C.); (F.F.)
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Naples, Italy; (C.d.M.); (G.F.)
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23
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Muttineni R, Binitha RN, Putty K, Marpakala K, Sandra SP, Panyam J, Vemula A, Singh SM, Balachandran S, Viroji Rao ST, Kondapi AK. SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India. Transbound Emerg Dis 2022; 69:e1721-e1733. [PMID: 35266305 PMCID: PMC9115369 DOI: 10.1111/tbed.14508] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/17/2022] [Accepted: 03/03/2022] [Indexed: 10/26/2022]
Abstract
Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole-genome sequences of SARS-CoV-2 circulating in India from 1st January 2021 to 31st August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24,260 amino acid mutations in the S protein, based on which 265 Pango lineages could be categorized. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N = 112) such mutations were observed in the N-terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2 and cytoplasmic domains of the S protein. Interestingly, 13.39% (N = 15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2% (N = 3) were known to be vaccine breakthrough mutations, and 0.89% (N = 1) were known to escape neutralising antibodies. The biological significance of 82% (N = 92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Radhakrishna Muttineni
- Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India
| | - R N Binitha
- Department of Zoology, Mar Athanasius College (Autonomous), Kothamangalam, Kerala, India
| | - Kalyani Putty
- Department of Veterinary Biotechnology, PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Kavitha Marpakala
- Department of Chemistry, University College Science, Osmania University, Hyderabad, Telangana, India
| | - S P Sandra
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Telangana, India
| | - Jaslin Panyam
- Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India
| | - Aravind Vemula
- Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India
| | - Shashi Mohan Singh
- Virus Research Lab, Department of Zoology, Osmania University, Hyderabad, Telangana, India
| | - Subin Balachandran
- Department of Zoology, Mar Athanasius College (Autonomous), Kothamangalam, Kerala, India
| | - S T Viroji Rao
- Department of Animal Genetics and Breeding, PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Anand Kumar Kondapi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Telangana, India
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24
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Halfmann PJ, Kuroda M, Armbrust T, Accola M, Valdez R, Kowalski-Dobson T, Rehrauer W, Gordon A, Kawaoka Y. Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. Cell Rep 2022; 38:110394. [PMID: 35139368 PMCID: PMC8801307 DOI: 10.1016/j.celrep.2022.110394] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/16/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence of the SARS-CoV-2 Delta variant (B.1.617.2) raises concerns about potential reduced sensitivity of the virus to antibody neutralization and subsequent vaccine breakthrough infections. Here, we use a live virus neutralization assay with sera from Pfizer- and Moderna-vaccinated individuals to examine neutralizing antibody titers against SARS-CoV-2 and observe a 3.9- and 2.7-fold reduction, respectively, in neutralizing antibody titers against the Delta variant compared with an early isolate bearing only a D614G substitution in its spike protein. We observe similar reduced sensitivity with sera from hamsters that were previously infected with an early isolate of SARS-CoV-2. Despite this reduction in neutralizing antibody titers against the Delta variant, hamsters previously infected (up to 15 months earlier) with an early isolate are protected from infection with the Delta variant, suggesting that the immune response to the first infection is sufficient to provide protection against subsequent infection with the Delta variant.
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Affiliation(s)
- Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA.
| | - Makoto Kuroda
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
| | - Tammy Armbrust
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA
| | - Molly Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Theresa Kowalski-Dobson
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - William Rehrauer
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711, USA; Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.
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25
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Liu Q, Xiong Q, Mei F, Ma C, Zhang Z, Hu B, Xu J, Jiang Y, Zhan F, Zhou S, Tao L, Chen X, Guo M, Wang X, Fang Y, Shen S, Liu Y, Liu F, Zhou L, Xu K, Ke C, Deng F, Cai K, Yan H, Chen Y, Lan K. Antibody neutralization to SARS-CoV-2 and variants after 1 year in Wuhan, China. Innovation (N Y) 2022; 3:100181. [PMID: 34746904 PMCID: PMC8563080 DOI: 10.1016/j.xinn.2021.100181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022] Open
Abstract
Most COVID-19 convalescents can build effective anti-SARS-CoV-2 humoral immunity, but it remains unclear how long it can maintain and how efficiently it can prevent the reinfection of the emerging SARS-CoV-2 variants. Here, we tested the sera from 248 COVID-19 convalescents around 1 year post-infection in Wuhan, the earliest known epicenter. SARS-CoV-2 immunoglobulin G (IgG) was well maintained in most patients and potently neutralizes the infection of the original strain and the B.1.1.7 variant. However, varying degrees of immune escape was observed on the other tested variants in a patient-specific manner, with individuals showing remarkably broad neutralization potency. The immune escape can be largely attributed to several critical spike mutations. These results suggest that SARS-CoV-2 can elicit long-lasting immunity but this is escaped by the emerging variants.
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Affiliation(s)
- Qianyun Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qing Xiong
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fanghua Mei
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Chengbao Ma
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhen Zhang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bing Hu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Junqiang Xu
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Yongzhong Jiang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Faxian Zhan
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Suhua Zhou
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Li Tao
- Wuhan Jiang'an District Center for Disease Control and Prevention, Wuhan 430000, China
| | - Xianying Chen
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ming Guo
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Wang
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yaohui Fang
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shu Shen
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yingle Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fang Liu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ke Xu
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou 511430, China
| | - Fei Deng
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Kun Cai
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Huan Yan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu Chen
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ke Lan
- State Key Laboratory of Virology, Institute for Vaccine Research and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Novazzi F, Baj A, Pasciuta R, Genoni A, Ferrante FD, Tripiciano R, Catanoso G, Focosi D, Maggi F. A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. Int J Infect Dis 2022; 116:271-272. [PMID: 34995777 PMCID: PMC8731264 DOI: 10.1016/j.ijid.2021.12.362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
The Delta variant of concern (VOC) of SARS-CoV-2 has become dominant worldwide. In this article, we report a cluster caused by B.1.617.2 harboring the additional mutation of concern (MOC) F490S. We observed that 5 fully vaccinated subjects aged between 47 and 84 years were infected with this variant. The immune escape mutation F490S, first identified in the Lambda VOI, appears to impair vaccine efficacy and is rapidly increasing in prevalence worldwide.
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Affiliation(s)
| | - Andreina Baj
- Laboratory of Microbiology, ASST SetteLaghi, Varese, Italy; Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Renee Pasciuta
- Laboratory of Microbiology, ASST SetteLaghi, Varese, Italy
| | - Angelo Genoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | | | | | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Laboratory of Microbiology, ASST SetteLaghi, Varese, Italy; Department of Medicine and Surgery, University of Insubria, Varese, Italy
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27
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Shkurnikov MY, Averinskaya DA, Komarov AG, Karbyshev IA, Speshilov GI, Shtinova IA, Doroshenko DA, Vechorko VI. Relationship of Covid-19 Severity with SARS-CoV-2 NS8 Protein Mutations Depending on Virus Strain. DOKL BIOCHEM BIOPHYS 2022; 507:242-246. [PMID: 36786981 PMCID: PMC9926417 DOI: 10.1134/s1607672922060102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 02/15/2023]
Abstract
In mid-2021, the Delta strain of SARS-CoV-2 caused the third wave of the COVID-19 pandemic. Huge efforts have been devoted to studying the effect of its mutations on the effectiveness of neutralizing antibodies. Much less attention was paid to the individual features of the presentation of its peptides by molecules of the major histocompatibility complex class I (MCHC-I). In this study, the correlation of the HLA-I genotype of patients under the age of 60 years with the severity of COVID-19 caused by the two most common variants of the SARS-CoV-2 Delta strain in the summer of 2021: AY.122 and B.1.617.2 was studied. Analysis of the severity of the course of COVID-19 revealed a more severe course of the disease caused by the AY.122 variant. Comparison of the mutation profile of the two most common variants of the Delta strain showed that that the G8R mutation in the NS8 protein makes the greatest contribution to the ability of MHC-I to present viral peptides. Given that the NS8 protein is able to suppress the maturation of MHC-I molecules, the appearance of a mutation in one of its immunogenic epitopes could make a significant contribution to the prevalence of the AY.122 variant in the Russian population.
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Affiliation(s)
- M. Yu. Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia ,Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - D. A. Averinskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - A. G. Komarov
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - I. A. Karbyshev
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - G. I. Speshilov
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - I. A. Shtinova
- Moscow City Public Institution of Health Care Diagnostic Center (Laboratory Testing Center) of Moscow Health Department, Moscow, Russia
| | - D. A. Doroshenko
- Moscow City Public Institution of Health Care Filatov City Clinical Hospital of Moscow Health Department, Moscow, Russia
| | - V. I. Vechorko
- Moscow City Public Institution of Health Care Filatov City Clinical Hospital of Moscow Health Department, Moscow, Russia
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28
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Lee BU. A high attack rate of 90% of SARS-CoV-2 Delta variant infections in crew personnel on a single navy ship. J Travel Med 2021; 28:6404468. [PMID: 34668534 DOI: 10.1093/jtm/taab168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/27/2021] [Accepted: 10/12/2021] [Indexed: 11/14/2022]
Abstract
A total of 272 soldiers out of the 301 soldiers (90.4%) were infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) on a single navy ship. This outbreak provides three lessons for the pandemic. This incident clearly demonstrates the transmission characteristics of the SARS-CoV-2 Delta VOC.
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Affiliation(s)
- Byung Uk Lee
- Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
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29
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Groß R, Zanoni M, Seidel A, Conzelmann C, Gilg A, Krnavek D, Erdemci-Evin S, Mayer B, Hoffmann M, Pöhlmann S, Liu W, Hahn BH, Beil A, Kroschel J, Jahrsdörfer B, Schrezenmeier H, Kirchhoff F, Münch J, Müller JA. Heterologous ChAdOx1 nCoV-19 and BNT162b2 prime-boost vaccination elicits potent neutralizing antibody responses and T cell reactivity against prevalent SARS-CoV-2 variants. EBioMedicine 2021; 75:103761. [PMID: 34929493 PMCID: PMC8682749 DOI: 10.1016/j.ebiom.2021.103761] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/27/2021] [Accepted: 12/02/2021] [Indexed: 11/03/2022] Open
Abstract
Background Heterologous COVID-19 vaccination regimens combining vector- and mRNA-based vaccines are already administered, but data on solicited adverse reactions, immunological responses and elicited protection are limited. Methods To evaluate the reactogenicity and humoral as well as cellular immune responses towards most prevalent SARS-CoV-2 variants after a heterologous ChAdOx1 nCoV-19 BNT162b2 prime-boost vaccination, we analysed a cohort of 26 clinic employees aged 25-46 (median 30.5) years who received a ChAdOx1 nCoV-19 prime followed by a BNT162b2 boost after an 8-week interval. Serological data were compared to a cohort which received homologous BNT162b2 vaccination with a 3-week interval (14 individuals aged 25-65, median 42). Findings Self-reported solicited symptoms after ChAdOx1 nCoV-19 prime were in line with previous reports and more severe than after the BNT162b2 boost. Antibody titres increased significantly over time resulting in strong neutralization titres two weeks after the BNT162b2 boost and subsequently slightly decreased over the course of 17 weeks. At the latest time point measured, all analysed sera retained neutralizing activity against the currently dominant Delta (B.1.617.2) variant. Two weeks post boost, neutralizing activity against the Alpha (B.1.1.7) and immune-evading Beta (B.1.351) variant was ∼4-fold higher than in individuals receiving homologous BNT162b2 vaccination. No difference was observed in neutralization of Kappa (B.1.617.1). In addition, heterologous vaccination induced CD4+ and CD8+ T cells reactive to SARS-CoV-2 spike peptides of all analysed variants; Wuhan-Hu-1, Alpha, Beta, Gamma (P.1), and Delta. Interpretation In conclusion, heterologous ChAdOx1 nCoV-19 / BNT162b2 prime-boost vaccination is not associated with serious adverse events and induces potent humoral and cellular immune responses. The Alpha, Beta, Delta, and Kappa variants of spike are potently neutralized by sera from all participants and reactive T cells recognize spike peptides of all tested variants. These results suggest that this heterologous vaccination regimen is at least as immunogenic and protective as homologous vaccinations and also offers protection against current variants of concern. Funding This project has received funding from the European Union's Horizon 2020 research and innovation programme, the German Research Foundation, the BMBF, the Robert Koch Institute (RKI), the Baden-Württemberg Stiftung, the county of Lower Saxony, the Ministry for Science, Research and the Arts of Baden-Württemberg, Germany, and the National Institutes of Health.
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Affiliation(s)
- Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Michelle Zanoni
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Andrea Gilg
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Daniela Krnavek
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Sümeyye Erdemci-Evin
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Benjamin Mayer
- Institute for Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Weimin Liu
- Department of Microbiology and Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Beatrice H Hahn
- Department of Microbiology and Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Alexandra Beil
- Central Department for Clinical Chemistry, University Hospital Ulm, 89081, Ulm, Germany
| | - Joris Kroschel
- Central Department for Clinical Chemistry, University Hospital Ulm, 89081, Ulm, Germany
| | - Bernd Jahrsdörfer
- Institute for Transfusion Medicine, Ulm University, 89081, Ulm, Germany; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Services Baden-Württemberg-Hessen and University Hospital Ulm, 89081, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute for Transfusion Medicine, Ulm University, 89081, Ulm, Germany; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Services Baden-Württemberg-Hessen and University Hospital Ulm, 89081, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany; Core Facility Functional Peptidomics, Ulm University Medical Center, 89081, Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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Fernández-Bastit L, Rodon J, Pradenas E, Marfil S, Trinité B, Parera M, Roca N, Pou A, Cantero G, Lorca-Oró C, Carrillo J, Izquierdo-Useros N, Clotet B, Noguera-Julián M, Blanco J, Vergara-Alert J, Segalés J. First Detection of SARS-CoV-2 Delta ( B.1.617.2) Variant of Concern in a Dog with Clinical Signs in Spain. Viruses 2021; 13:v13122526. [PMID: 34960795 PMCID: PMC8704391 DOI: 10.3390/v13122526] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Several cases of naturally infected dogs with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported despite the apparently low susceptibility of this species. Here, we document the first reported case of infection caused by the Delta (B.1.617.2) variant of concern (VOC) in a dog in Spain that lived with several household members suffering from Coronavirus Infectious Disease 2019 (COVID-19). The animal displayed mild digestive and respiratory clinical signs and had a low viral load in the oropharyngeal swab collected at the first sampling. Whole-genome sequencing indicated infection with the Delta variant, coinciding with the predominant variant during the fifth pandemic wave in Spain. The dog seroconverted, as detected 21 days after the first sampling, and developed neutralizing antibodies that cross-neutralized different SARS-CoV-2 variants. This study further emphasizes the importance of studying the susceptibility of animal species to different VOCs and their potential role as reservoirs in the context of COVID-19.
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Affiliation(s)
- Leira Fernández-Bastit
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Jordi Rodon
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Edwards Pradenas
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
| | - Silvia Marfil
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
| | - Núria Roca
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Anna Pou
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Guillermo Cantero
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Cristina Lorca-Oró
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
- Infectious Diseases and Immunity, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Barcelona, Spain
| | - Marc Noguera-Julián
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
- Infectious Diseases and Immunity, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Barcelona, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain; (E.P.); (S.M.); (B.T.); (M.P.); (J.C.); (N.I.-U.); (B.C.); (M.N.-J.); (J.B.)
- IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916 Badalona, Spain
- Infectious Diseases and Immunity, Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Barcelona, Spain
| | - Júlia Vergara-Alert
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain; (L.F.-B.); (J.R.); (N.R.); (A.P.); (G.C.); (C.L.-O.); (J.V.-A.)
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca en Tecnologies Agroalimentaries (IRTA), Campus de la UAB, 08193 Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinaria, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Correspondence:
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Kumar S, Thambiraja TS, Karuppanan K, Subramaniam G. Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein. J Med Virol 2021; 94:1641-1649. [PMID: 34914115 DOI: 10.1002/jmv.27526] [Citation(s) in RCA: 326] [Impact Index Per Article: 108.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
Abstract
Emerging severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, especially those of concern, may have an impact on the virus's transmissibility and pathogenicity, as well as diagnostic equipment performance and vaccine effectiveness. Even though the SARS-CoV-2 Delta variant (B.1.617.2) emerged during India's second wave of infections, Delta variants have grown dominant internationally and are still evolving. On November 26, 2021, World Health Organization identified the variant B.1.1.529 as a variant of concern, naming it Omicron, based on evidence that Omicron contains numerous mutations that may influence its behavior. However, the mode of transmission and severity of the Omicron variant remains unknown. We used computational studies to examine the Delta and Omicron variants in this study and found that the Omicron variant had a higher affinity for human angiotensin-converting enzyme 2 (ACE2) than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor-binding domain (RBD), indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein's core and are required for structural stability. We observed a disorder-order transition in the Omicron variant between spike protein RBD regions 468-473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.
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Affiliation(s)
- Suresh Kumar
- Department of Diagnostic & Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, Shah Alam, Selangor, Malaysia
| | - Thiviya S Thambiraja
- Department of Diagnostic & Allied Health Science, Faculty of Health and Life Sciences, Management and Science University, Shah Alam, Selangor, Malaysia
| | - Kalimuthu Karuppanan
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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Sakai-Tagawa Y, Yamayoshi S, Halfmann PJ, Kawaoka Y. Comparative Sensitivity of Rapid Antigen Tests for the Delta Variant ( B.1.617.2) of SARS-CoV-2. Viruses 2021; 13:v13112183. [PMID: 34834991 PMCID: PMC8618251 DOI: 10.3390/v13112183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Rapid antigen tests (RATs) for COVID-19 based on lateral flow immunoassays are useful for rapid diagnosis in a variety of settings. Although many kinds of RATs are available, their respective sensitivity has not been compared. Here, we examined the sensitivity of 27 RATs available in Japan for the detection of the SARS-CoV-2 delta variant. All of the RATs tested detected the delta variant albeit with different sensitivities. Nine RATs (ESPLINE SARS-CoV-2, ALSONIC COVID-19 Ag, COVID-19 and Influenza A+B Antigen Combo Rapid Test, ImmunoArrow SARS-CoV-2, Fuji Dri-chem immuno AG cartridge COVID-19 Ag, 2019-nCoV Ag rapid detection kit, Saliva SARS-CoV-2(2019-nCoV) Antigen Test Kit, and Rabliss SARS-CoV-2 antigen detection kit COVID19 AG) showed superior sensitivity to the isolated delta variant. Although actual clinical specimens were not examined, the detection level of most of the RATs was 7500 pfu, indicating that individuals whose test samples contained less virus than that would be considered negative. Therefore, it is important to bear in mind that RATs may miss individuals shedding low levels of infectious virus.
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Affiliation(s)
- Yuko Sakai-Tagawa
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan;
- International Research Center for Infectious Diseases, Department of Special Pathogens, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan;
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Correspondence: (S.Y.); (Y.K.)
| | - Peter J. Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan;
- International Research Center for Infectious Diseases, Department of Special Pathogens, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Correspondence: (S.Y.); (Y.K.)
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Waldman SE, Buehring T, Escobar DJ, Gohil SK, Gonzales R, Huang SS, Olenslager K, Prabaker KK, Sandoval T, Yim J, Yokoe DS, Cohen SH. Secondary Cases of Delta Variant Coronavirus Disease 2019 Among Vaccinated Healthcare Workers With Breakthrough Infections is Rare. Clin Infect Dis 2021; 75:e895-e897. [PMID: 34694358 PMCID: PMC8574310 DOI: 10.1093/cid/ciab916] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Indexed: 01/19/2023] Open
Abstract
In a retrospective, cohort study at 4 medical centers with high coronavirus disease 2019 vaccination rates, we evaluated breakthrough severe acute respiratory syndrome coronavirus 2 Delta variant infections in vaccinated healthcare workers. Few work-related secondary cases were identified. Breakthrough cases were largely due to unmasked social activities outside of work.
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Affiliation(s)
- Sarah E Waldman
- Correspondence: S. E. Waldman, University of California-Davis, School of Medicine, Division of Infectious Diseases, 4150 V Street, Suite G500, Sacramento CA 95817 ()
| | - Tara Buehring
- Clinical Epidemiology and Infection Prevention, University of California Los Angeles, Los Angeles Health, Los Angeles, California, USA
| | - Daniel J Escobar
- Division of Infectious Disease, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Shruti K Gohil
- Division of Infectious Diseases and Health Policy Research Institute, University of California Irvine School of Medicine, Irvine, California, USA
| | - Ralph Gonzales
- Department of Medicine and Clinical Innovation Center, University of California San Francisco, San Francisco, California, USA
| | - Susan S Huang
- Division of Infectious Diseases and Health Policy Research Institute, University of California Irvine School of Medicine, Irvine, California, USA
| | - Keith Olenslager
- Epidemiology & Infection Prevention Program, University of California, Irvine Health, Irvine, California, USA
| | - Kavitha K Prabaker
- Division of Infectious Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Tessa Sandoval
- Clinical Epidemiology and Infection Prevention, University of California Los Angeles, Los Angeles Health, Los Angeles, California, USA
| | - Jennifer Yim
- Epidemiology & Infection Prevention Program, University of California, Irvine Health, Irvine, California, USA
| | - Deborah S Yokoe
- Division of Infectious Disease, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Stuart H Cohen
- Division of Infectious Diseases, Department of Medicine, University of California Davis, Sacramento, California, USA
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Shiehzadegan S, Alaghemand N, Fox M, Venketaraman V. Analysis of the Delta Variant B.1.617.2 COVID-19. Clin Pract 2021; 11:778-784. [PMID: 34698149 PMCID: PMC8544471 DOI: 10.3390/clinpract11040093] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
With the delta variant of COVID-19, known as B.1.617.2, quickly ramping up infections around the world, we need to understand what makes this variant more contagious. One study has reported that the delta variant is 60% more transmissible than the alpha variant. As of August 2021, the delta variant has quickly become the dominant strain. Despite countries like the US, where most of the population is vaccinated, COVID-19 has made a resurgence in infections. Collectively, as a country, we ask: is it more deadly? What makes it more "contagious" or "transmissible"? This review article delves into the information we already know about the delta variant and how it compares with the other SARS-CoV-2 variants. The current vaccine companies like AstraZeneca, Pfizer/BioNTech, and Moderna have reported that their vaccines can provide protection against this variant but with a slightly reduced efficacy. In this article, we do a comprehensive review and summary of the delta B.1.617.2 variant and what makes it more contagious.
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Affiliation(s)
- Shayan Shiehzadegan
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E 2nd St, Pomona, CA 91766, USA; (S.S.); (M.F.)
| | - Nazanin Alaghemand
- Department of Biology, University of California Irvine, Irvine, CA 92697, USA;
| | - Michael Fox
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E 2nd St, Pomona, CA 91766, USA; (S.S.); (M.F.)
| | - Vishwanath Venketaraman
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, 309 E 2nd St, Pomona, CA 91766, USA; (S.S.); (M.F.)
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Arora P, Sidarovich A, Krüger N, Kempf A, Nehlmeier I, Graichen L, Moldenhauer AS, Winkler MS, Schulz S, Jäck HM, Stankov MV, Behrens GMN, Pöhlmann S, Hoffmann M. B.1.617.2 enters and fuses lung cells with increased efficiency and evades antibodies induced by infection and vaccination. Cell Rep 2021; 37:109825. [PMID: 34614392 PMCID: PMC8487035 DOI: 10.1016/j.celrep.2021.109825] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/20/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022] Open
Abstract
The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), B.1.617.2, emerged in India and has spread to over 80 countries. B.1.617.2 replaced B.1.1.7 as the dominant virus in the United Kingdom, resulting in a steep increase in new infections, and a similar development is expected for other countries. Effective countermeasures require information on susceptibility of B.1.617.2 to control by antibodies elicited by vaccines and used for coronavirus disease 2019 (COVID-19) therapy. We show, using pseudotyping, that B.1.617.2 evades control by antibodies induced upon infection and BNT162b2 vaccination, although to a lesser extent as compared to B.1.351. We find that B.1.617.2 is resistant against bamlanivimab, a monoclonal antibody with emergency use authorization for COVID-19 therapy. Finally, we show increased Calu-3 lung cell entry and enhanced cell-to-cell fusion of B.1.617.2, which may contribute to augmented transmissibility and pathogenicity of this variant. These results identify B.1.617.2 as an immune evasion variant with increased capacity to enter and fuse lung cells.
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Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Anzhalika Sidarovich
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nadine Krüger
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | | | - Martin S Winkler
- Department of Anesthesiology, University of Göttingen Medical Center, Göttingen, Georg-August University of Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Sebastian Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054 Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054 Erlangen, Germany
| | - Metodi V Stankov
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany.
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073 Göttingen, Germany.
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Amatya B, Pandey P, Dawadi S, Manandhar S. COVID-19 in fully vaccinated Everest trekkers in Nepal. J Travel Med 2021; 28:6316239. [PMID: 34230969 PMCID: PMC8344616 DOI: 10.1093/jtm/taab098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/12/2022]
Abstract
COVID-19 in a fully mRNA-1273 vaccinated aspiring Everest summiteer and an Everest trekker who had two doses of ChAdOx1nCoV-19 are presented. Delta B.1.617.2 variant was sequenced in one of the cases. Travellers should be wary of starting up travel to under-vaccinated regions, particularly if they are at high risk for severe disease.
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Affiliation(s)
- Bhawana Amatya
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| | - Prativa Pandey
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| | - Suvash Dawadi
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| | - Shanta Manandhar
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
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Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf G, Chao H, Gingras MC, Avadhanula V, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections. BMC Med 2021; 19:255. [PMID: 34593004 PMCID: PMC8483940 DOI: 10.1186/s12916-021-02103-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND This study aims to identify the causative strain of SARS-CoV-2 in a cluster of vaccine breakthroughs. Vaccine breakthrough by a highly transmissible SARS-CoV-2 strain is a risk to global public health. METHODS Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) by qPCR (quantitative polymerase chain reaction) for Wuhan-Hu1 and alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. GATK (genome analysis toolkit) variants were filtered with allele fraction ≥80 and min read depth 30x. RESULTS Viral sequencing revealed an infection cluster of 6 vaccinated patients infected with the delta (B.1.617.2) SARS-CoV-2 variant. With no history of vaccine breakthrough, this suggests the delta variant may possess immune evasion in patients that received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152. CONCLUSIONS Delta variant may pose the highest risk out of any currently circulating SARS-CoV-2 variants, with previously described increased transmissibility over alpha variant and now, possible vaccine breakthrough. FUNDING Parts of this work was supported by the National Institute of Allergy and Infectious Diseases (1U19AI144297) and Baylor College of Medicine internal funding.
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Affiliation(s)
- Timothy Farinholt
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang Qin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vipin Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsu Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vasanthi Avadhanula
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Paige Farinholt
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Charu Agrawal
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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Gómez-Carballa A, Pardo-Seco J, Bello X, Martinón-Torres F, Salas A. Superspreading in the emergence of COVID-19 variants. Trends Genet 2021; 37:1069-1080. [PMID: 34556337 PMCID: PMC8423994 DOI: 10.1016/j.tig.2021.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022]
Abstract
Superspreading and variants of concern (VOC) of the human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the main catalyzers of the coronavirus disease 2019 (COVID-19) pandemic. However, measuring their individual impact is challenging. By examining the largest database of SARS-CoV-2 genomes The Global Initiative on Sharing Avian Influenza Data [GISAID; n >1.2 million high-quality (HQ) sequences], we present evidence suggesting that superspreading has had a key role in the epidemiological predominance of VOC. There are clear signatures in the database compatible with large superspreading events (SSEs) coinciding chronologically with the worst epidemiological scenarios triggered by VOC. The data suggest that, without the randomness effect of the genetic drift facilitated by superspreading, new VOC of SARS-CoV-2 would have had more limited chance of success.
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Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines, and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines, and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Xabier Bello
- Genetics, Vaccines, and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Federico Martinón-Torres
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines, and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain.
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Lee BU. Why Does the SARS-CoV-2 Delta VOC Spread So Rapidly? Universal Conditions for the Rapid Spread of Respiratory Viruses, Minimum Viral Loads for Viral Aerosol Generation, Effects of Vaccination on Viral Aerosol Generation, and Viral Aerosol Clouds. Int J Environ Res Public Health 2021; 18:9804. [PMID: 34574724 PMCID: PMC8470664 DOI: 10.3390/ijerph18189804] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022]
Abstract
This study analyzes the reasons the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) spreads so rapidly. Novel topics such as universal conditions for the rapid spread of respiratory viruses, minimum viral loads for viral aerosol generation, effects of vaccination on viral aerosol generation, and viral aerosol clouds were studied. The analyses were based on experimental results and analytic model studies. Four universal conditions, namely asymptomatic host, high viral load, stability of viruses in air, and binding affinity of viruses to human cells, need to be satisfied for the rapid spread of respiratory viruses. SARS-CoV-2 and its variants such as the Alpha VOC and Delta VOC satisfy the four fundamental conditions. In addition, there is an original principle of aerosol generation of respiratory viruses. Assuming that the aerosol-droplet cutoff particle diameter for distinguishing potential aerosols from earthbound respiratory particles is 100 μm, the minimum viral load required in respiratory fluids to generate viral aerosols is ~106 copies mL-1, which is within the range of the reported viral loads in the Alpha VOC cases and the Delta VOC cases. The daily average viral loads of the Delta VOC in hosts have been reported to be between ~109 copies mL-1 and ~1010 copies mL-1 during the four days after symptom onset in 1848 cases of the Delta VOC infection. Owing to the high viral load, the SARS-CoV-2 Delta VOC has the potential to effectively spread through aerosols. COVID-19 vaccination can decrease aerosol transmission of the SARS-CoV-2 Alpha VOC by reducing the viral load. The viral load can explain the conundrum of viral aerosol spreading. The SARS-CoV-2 Delta VOC aerosol clouds have been assumed to be formed in restricted environments, resulting in a massive numbers of infected people in a very short period with a high spreading speed. Strong control methods against bioaerosols should be considered in this SARS-CoV-2 Delta VOC pandemic. Large-scale environmental monitoring campaigns of SARS-CoV-2 Delta VOC aerosols in public places in many countries are necessary, and these activities could contribute to controlling the coronavirus disease pandemic.
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Affiliation(s)
- Byung Uk Lee
- Aerosol and Bioengineering Laboratory, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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40
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Baj A, Novazzi F, Pasciuta R, Genoni A, Ferrante FD, Valli M, Partenope M, Tripiciano R, Ciserchia A, Catanoso G, Focosi D, Maggi F. Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. Emerg Infect Dis 2021; 27:3180-3182. [PMID: 34499599 PMCID: PMC8632179 DOI: 10.3201/eid2712.211792] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The Delta variant of concern of severe acute respiratory syndrome coronavirus 2 is dominant worldwide. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11–July 29, 2021. This mutation appears to affect immune response and vaccine efficacy; monitoring its appearance is urgent.
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Mohandas S, Yadav PD, Shete A, Nyayanit D, Sapkal G, Lole K, Gupta N. SARS-CoV-2 Delta Variant Pathogenesis and Host Response in Syrian Hamsters. Viruses 2021; 13:1773. [PMID: 34578354 PMCID: PMC8473140 DOI: 10.3390/v13091773] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/22/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
B.1.617 is becoming a dominant Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) lineage worldwide with many sublineages, of which B.1.617.2 is designated as a variant of concern. The pathogenicity of B.1.617.2 (Delta) and B.1.617.3 lineage of SARS-CoV-2 was evaluated and compared with that of B.1, an early virus isolate with D614G mutation in a Syrian hamster model. Viral load, antibody response, and lung disease were studied. There was no significant difference in the virus shedding pattern among these variants. High levels of SARS-CoV-2 sub genomic RNA were detected in the respiratory tract of hamsters infected with the Delta variant for 14 days, which warrants further transmission studies. The Delta variant induced lung disease of moderate severity in about 40% of infected animals, which supports the attributed disease severity of the variant. Cross neutralizing antibodies were detected in animals infected with B.1, Delta, and B.1.617.3 variant, but neutralizing capacity was significantly lower with B.1.351 (Beta variant).
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Affiliation(s)
- Sreelekshmy Mohandas
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (S.M.); (A.S.); (D.N.); (G.S.); (K.L.)
| | - Pragya Dhruv Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (S.M.); (A.S.); (D.N.); (G.S.); (K.L.)
| | - Anita Shete
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (S.M.); (A.S.); (D.N.); (G.S.); (K.L.)
| | - Dimpal Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (S.M.); (A.S.); (D.N.); (G.S.); (K.L.)
| | - Gajanan Sapkal
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (S.M.); (A.S.); (D.N.); (G.S.); (K.L.)
| | - Kavita Lole
- Indian Council of Medical Research-National Institute of Virology, Pune 411021, India; (S.M.); (A.S.); (D.N.); (G.S.); (K.L.)
| | - Nivedita Gupta
- Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi 110029, India;
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Seppälä E, Veneti L, Starrfelt J, Danielsen AS, Bragstad K, Hungnes O, Taxt AM, Watle SV, Meijerink H. Vaccine effectiveness against infection with the Delta ( B.1.617.2) variant, Norway, April to August 2021. Euro Surveill 2021; 26:2100793. [PMID: 34477054 PMCID: PMC8414959 DOI: 10.2807/1560-7917.es.2021.26.35.2100793] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/02/2021] [Indexed: 11/20/2022] Open
Abstract
Some variants of SARS-CoV-2 are associated with increased transmissibility, increased disease severity or decreased vaccine effectiveness (VE). In this population-based cohort study (n = 4,204,859), the Delta variant was identified in 5,430 (0.13%) individuals, of whom 84 were admitted to hospital. VE against laboratory confirmed infection with the Delta variant was 22.4% among partly vaccinated (95% confidence interval (CI): 17.0-27.4) and 64.6% (95% CI: 60.6-68.2) among fully vaccinated individuals, compared with 54.5% (95% CI: 50.4-58.3) and 84.4% (95%CI: 81.8-86.5) against the Alpha variant.
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Affiliation(s)
- Elina Seppälä
- Department of infectious disease control and vaccines, Norwegian Institute of Public Health, Oslo, Norway
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Lamprini Veneti
- Department of infectious disease control and preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Jostein Starrfelt
- Department of infectious disease control and preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Anders Skyrud Danielsen
- Department of infectious disease control and preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Karoline Bragstad
- Department of virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Olav Hungnes
- Department of virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Arne Michael Taxt
- Department of infectious disease control and vaccines, Norwegian Institute of Public Health, Oslo, Norway
| | - Sara Viksmoen Watle
- Department of infectious disease control and vaccines, Norwegian Institute of Public Health, Oslo, Norway
| | - Hinta Meijerink
- Department of infectious disease control and vaccines, Norwegian Institute of Public Health, Oslo, Norway
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Essa RA, Ahmed SK, Bapir DH, Rasul SA, Khdir AA, Abubakr CP. Clinical features and laboratory findings first case of B. 1.617.2 (delta) variant concern (VOC) in Iraq. Ann Med Surg (Lond) 2021; 69:102814. [PMID: 34512963 PMCID: PMC8416700 DOI: 10.1016/j.amsu.2021.102814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022] Open
Abstract
Since the initial report of the severe acute respiratory syndrome (SARS CoV-2) in Wuhan, China, in 2019, the virus has constantly mutated, resulting in the appearance of novel variants. In December 2020, the B.1.617.2 (delta) variant concern (VOC) was first reported in India, and rapidly spread around the globe, is now the main brand in the United Kingdom, and it has grown dramatically. Here we present the clinical features and laboratory findings of the first case of B. 1.617.2 (delta) variant concern (VOC) in Iraq. A 6-year-old female child presented with severe abdominal pain, headache, severe vomiting, and diarrhea, runny nose, alerted mental status, loss of appetite, and fever. The patient was diagnosed with COVID-19 delta variant B.1.617.2 by RT-PCR. The patient was treated by administration of glucose saline 4% for 3 days, ceftriaxone vial 1 mg every 12 h for 6 days, and an acetaminophen bottle on a need to prevent fever followed by a Flagyl bottle every 24 h for 3 days. Vaccination and prevention the spread of the virus and against it are important preventive approaches for delta variant. Sore throat, runny nose, headache, and vomiting, diarrhea are the major clinical features of the delta variant. This was followed by an elevation of the leukocyte WBC, and blood platelets. To reduce the impact of new delta variant B.1.617.2 infection; handwashing, wearing a double mask, avoiding crowded and closed settings, social distancing, lockdown, and ensuring good ventilation are major significant options against this variant.
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Affiliation(s)
- Rawand A. Essa
- Ph.D. in Cardiothoracic and Vascular Surgery, Lecturer in the University of Raparin, College of Nursing, Department of Adult Nursing, Rania, Sulaimani, Kurdistan-region, Iraq
- European Society for Thoracic Surgery (ESTS) Active Member, Iraq
- Department of Adult Nursing, College of Nursing, University of Raparin, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Medical City Private Hospital, Rania, Sulaimani, kurdistan-region, Iraq
| | - Sirwan K. Ahmed
- Department of Adult Nursing, College of Nursing, University of Raparin, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Medical City Private Hospital, Rania, Sulaimani, kurdistan-region, Iraq
- Rania Pediatric & Maternity Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq
| | - Dunya H. Bapir
- Department of Medical Laboratory, College of Science, University of Raparin, Kurdistan-region, Iraq
| | - Shero A. Rasul
- Department of Adult Nursing, College of Nursing, University of Raparin, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq
| | - Awat A. Khdir
- Department of Adult Nursing, College of Nursing, University of Raparin, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq
- Rania Pediatric & Maternity Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq
| | - Chawan P. Abubakr
- Department of Critical Care Nursing, College of Nursing, Urmia University of Medical Science, Iran
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Wilhelm A, Toptan T, Pallas C, Wolf T, Goetsch U, Gottschalk R, Vehreschild MJGT, Ciesek S, Widera M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021; 13:v13091693. [PMID: 34578275 DOI: 10.1101/2021.08.09.21261704] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 05/24/2023] Open
Abstract
The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.51-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which, however, might be circumvented by combination therapy with casirivimab together.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Rene Gottschalk
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
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45
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Wilhelm A, Toptan T, Pallas C, Wolf T, Goetsch U, Gottschalk R, Vehreschild MJGT, Ciesek S, Widera M. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Viruses 2021; 13:1693. [PMID: 34578275 PMCID: PMC8473269 DOI: 10.3390/v13091693] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/22/2021] [Indexed: 12/23/2022] Open
Abstract
The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.51-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. In conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which, however, might be circumvented by combination therapy with casirivimab together.
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Affiliation(s)
- Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Tuna Toptan
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Christiane Pallas
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
| | - Timo Wolf
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (T.W.); (M.J.G.T.V.)
| | - Udo Goetsch
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany; (U.G.); (R.G.)
| | - Rene Gottschalk
- Health Protection Authority of the City of Frankfurt am Main, 60313 Frankfurt am Main, Germany; (U.G.); (R.G.)
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (T.W.); (M.J.G.T.V.)
- University Center for Infectious Diseases (UCI), University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Branch Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 60596 Frankfurt am Main, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany; (A.W.); (T.T.); (C.P.); (S.C.)
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Kumar V, Singh J, Hasnain SE, Sundar D. Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Int J Mol Sci 2021; 22:9131. [PMID: 34502041 PMCID: PMC8431609 DOI: 10.3390/ijms22179131] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 01/19/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 has caused a global pandemic. The rapid mutation rate in the virus has created alarming situations worldwide and is being attributed to the false negativity in RT-PCR tests. It has also increased the chances of reinfection and immune escape. Recently various lineages namely, B.1.1.7 (Alpha), B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3 have caused rapid infection around the globe. To understand the biophysical perspective, we have performed molecular dynamic simulations of four different spikes (receptor binding domain)-hACE2 complexes, namely wildtype (WT), Alpha variant (N501Y spike mutant), Kappa (L452R, E484Q) and Delta (L452R, T478K), and compared their dynamics, binding energy and molecular interactions. Our results show that mutation has caused significant increase in the binding energy between the spike and hACE2 in Alpha and Kappa variants. In the case of Kappa and Delta variants, the mutations at L452R, T478K and E484Q increased the stability and intra-chain interactions in the spike protein, which may change the interaction ability of neutralizing antibodies to these spike variants. Further, we found that the Alpha variant had increased hydrogen interaction with Lys353 of hACE2 and more binding affinity in comparison to WT. The current study provides the biophysical basis for understanding the molecular mechanism and rationale behind the increase in the transmissivity and infectivity of the mutants compared to wild-type SARS-CoV-2.
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Affiliation(s)
- Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India; (V.K.); (J.S.)
| | - Jasdeep Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India; (V.K.); (J.S.)
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India; (V.K.); (J.S.)
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida 201301, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi 110016, India; (V.K.); (J.S.)
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47
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Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh MPHS, Lim YD, Lee PH, Lee TH, Chia PY, Maurer-Stroh S, Lin RTP, Leo YS, Lee VJ, Lye DC, Young BE. Clinical and Virological Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta). Clin Infect Dis 2021; 75:e1128-e1136. [PMID: 34423834 PMCID: PMC8522361 DOI: 10.1093/cid/ciab721] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective study, we compared the outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with wild-type strains from early 2020. METHODS National surveillance data from January to May 2021 were obtained and outcomes in relation to VOCs were explored. Detailed patient-level data from all patients with VOC infection admitted to our center between December 2020 and May 2021 were analyzed. Clinical outcomes were compared with a cohort of 846 patients admitted from January to April 2020. RESULTS A total of 829 patients in Singapore in the study period were infected with these 3 VOCs. After adjusting for age and sex, B.1.617.2 was associated with higher odds of oxygen requirement, intensive care unit admission, or death (adjusted odds ratio [aOR], 4.90; 95% confidence interval [CI]: 1.43-30.78). Of these patients, 157 were admitted to our center. After adjusting for age, sex, comorbidities, and vaccination, the aOR for pneumonia with B.1.617.2 was 1.88 (95% CI: .95-3.76) compared with wild-type. These differences were not seen with B.1.1.7 and B.1.351. Vaccination status was associated with decreased severity. B.1.617.2 was associated with significantly lower polymerase chain reaction cycle threshold (Ct) values and longer duration of Ct value ≤30 (median duration 18 days for B.1.617.2, 13 days for wild-type). CONCLUSIONS B.1.617.2 was associated with increased severity of illness, and with lower Ct values and longer viral shedding. These findings provide impetus for the rapid implementation of vaccination programs.
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Affiliation(s)
- Sean Wei Xiang Ong
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Calvin J Chiew
- National Centre for Infectious Diseases, Singapore, Singapore,Ministry of Health, Singapore, Singapore
| | - Li Wei Ang
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Tze Minn Mak
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Lin Cui
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Matthias Paul H S Toh
- National Centre for Infectious Diseases, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Pei Hua Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tau Hong Lee
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Po Ying Chia
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Singapore,A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore,Department of Biological Sciences, National University of Singapore, Singapore
| | - Raymond T P Lin
- National Centre for Infectious Diseases, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vernon J Lee
- Ministry of Health, Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - David Chien Lye
- National Centre for Infectious Diseases, Singapore, Singapore,Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barnaby Edward Young
- Correspondence: Barnaby Young, National Centre for Infectious Diseases, 16 Jln Tan Tock Seng, Singapore 308442 ()
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Kannan SR, Spratt AN, Cohen AR, Naqvi SH, Chand HS, Quinn TP, Lorson CL, Byrareddy SN, Singh K. Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. J Autoimmun 2021; 124:102715. [PMID: 34399188 DOI: 10.1016/j.jaut.2021.102715] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been rapidly evolving in the form of new variants. At least eleven known variants have been reported. The objective of this study was to delineate the differences in the mutational profile of Delta and Delta Plus variants. High-quality sequences (n = 1756) of Delta (B.1.617.2) and Delta Plus (AY.1 or B.1.617.2.1) variants were used to determine the prevalence of mutations (≥20 %) in the entire SARS-CoV-2 genome, their co-existence, and change in prevalence over a period of time. Structural analysis was conducted to get insights into the impact of mutations on antibody binding. A Sankey diagram was generated using phylogenetic analysis coupled with sequence-acquisition dates to infer the migration of the Delta Plus variant and its presence in the United States. The Delta Plus variant had a significant number of high-prevalence mutations (≥20 %) than in the Delta variant. Signature mutations in Spike (G142D, A222V, and T95I) existed at a more significant percentage in the Delta Plus variant than the Delta variant. Three mutations in Spike (K417N, V70F, and W258L) were exclusively present in the Delta Plus variant. A new mutation was identified in ORF1a (A1146T), which was only present in the Delta Plus variant with ~58 % prevalence. Furthermore, five key mutations (T95I, A222V, G142D, R158G, and K417N) were significantly more prevalent in the Delta Plus than in the Delta variant. Structural analyses revealed that mutations alter the sidechain conformation to weaken the interactions with antibodies. Delta Plus, which first emerged in India, reached the United States through England and Japan, followed by its spread to more than 20 the United States. Based on the results presented here, it is clear that the Delta and Delta Plus variants have unique mutation profiles, and the Delta Plus variant is not just a simple addition of K417N to the Delta variant. Highly correlated mutations may have emerged to keep the structural integrity of the virus.
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49
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Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, Rakshit P, Singh S, Abraham P, Panda S, Team NIC. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms 2021; 9:1542. [PMID: 34361977 PMCID: PMC8307577 DOI: 10.3390/microorganisms9071542] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/12/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of "variants of concern" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.
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Affiliation(s)
- Sarah Cherian
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Varsha Potdar
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Santosh Jadhav
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Pragya Yadav
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Nivedita Gupta
- Indian Council of Medical Research, New Delhi 110029, India; (N.G.); (S.P.)
| | - Mousumi Das
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Partha Rakshit
- National Centre for Disease Control, New Delhi 110054, India; (P.R.); (S.S.)
| | - Sujeet Singh
- National Centre for Disease Control, New Delhi 110054, India; (P.R.); (S.S.)
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India; (N.G.); (S.P.)
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Connor BA, Couto-Rodriguez M, Barrows JE, Gardner M, Rogova M, O'Hara NB, Nagy-Szakal D. Monoclonal Antibody Therapy in a Vaccine Breakthrough SARS-CoV-2 Hospitalized Delta ( B.1.617.2) Variant Case. Int J Infect Dis 2021; 110:232-234. [PMID: 34271202 PMCID: PMC8276551 DOI: 10.1016/j.ijid.2021.07.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022] Open
Abstract
We present two Delta (B.1.617.2) vaccine breakthrough individuals, a father and son living in separate households. The older, 63-year-old patient's symptoms were severe enough to require hospitalization. Despite having a high titer of anti-spike IgG in his serum, his symptoms resolved within 24 hours following monoclonal antibody (bamlanivimab/etesevimab) therapy.
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Affiliation(s)
- Bradley A Connor
- Weill Cornell Medicine, New York, NY, USA; The New York Center for Travel and Tropical Medicine, New York, NY, USA; GeoSentinel, New York, NY, USA.
| | | | | | - Morgan Gardner
- The New York Center for Travel and Tropical Medicine, New York, NY, USA; GeoSentinel, New York, NY, USA
| | - Marina Rogova
- The New York Center for Travel and Tropical Medicine, New York, NY, USA; GeoSentinel, New York, NY, USA
| | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA; SUNY Downstate Health Sciences University, The Department Cell Biology/College of Medicine, New York, NY, USA
| | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA; SUNY Downstate Health Sciences University, The Department Cell Biology/College of Medicine, New York, NY, USA
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