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Anand A, Long C, Chandran K. NYC metropolitan wastewater reveals links between SARS-CoV-2 amino acid mutations and disease outcomes. Sci Total Environ 2024; 908:167971. [PMID: 37914132 DOI: 10.1016/j.scitotenv.2023.167971] [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] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Since late 2020, diverse SARS-CoV-2 variants with enhanced infectivity and transmissibility have emerged. In contrast to the focus on amino acid mutations in the spike protein, mutations in non-spike proteins and their associated impacts remain relatively understudied. New York City metropolitan wastewater revealed over 60 % of the most frequently occurring amino acid mutations in regions outside the spike protein. Strikingly, ~50 % of the mutations detected herein remain uncharacterized for functional impacts. Our results suggest that there are several understudied mutations within non-spike proteins N, ORF1a, ORF1b, ORF9b, and ORF9c, that could increase transmissibility, and infectivity among human populations. We also demonstrate significant correlations of P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, and P13L with documented mortality rates, hospitalization rates, and percent positivity suggesting that amino acid mutations are likely to be indicators of COVID-19 infection outcomes.
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Affiliation(s)
- Archana Anand
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, United States of America
| | - Chenghua Long
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, 500 W. 120th Street, New York, NY 10027, United States of America.
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Pilchová V, Gerhauser I, Armando F, Wirz K, Schreiner T, de Buhr N, Gabriel G, Wernike K, Hoffmann D, Beer M, Baumgärtner W, von Köckritz-Blickwede M, Schulz C. Characterization of young and aged ferrets as animal models for SARS-CoV-2 infection with focus on neutrophil extracellular traps. Front Immunol 2023; 14:1283595. [PMID: 38169647 PMCID: PMC10758425 DOI: 10.3389/fimmu.2023.1283595] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Neutrophil extracellular traps (NETs) are net-like structures released by activated neutrophils upon infection [e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] as part of the innate immune response that have protective effects by pathogen entrapment and immobilization or result in detrimental consequences for the host due to the massive release of NETs and their impaired degradation by nucleases like DNase-1. Higher amounts of NETs are associated with coronavirus disease 2019 (COVID-19) severity and are a risk factor for severe disease outcome. The objective of our study was to investigate NET formation in young versus aged ferrets to evaluate their value as translational model for SARS-CoV-2-infection and to correlate different NET markers and virological parameters. In each of the two groups (young and aged), nine female ferrets were intratracheally infected with 1 mL of 106 TCID50/mL SARS-CoV-2 (BavPat1/2020) and euthanized at 4, 7, or 21 days post-infection. Three animals per group served as negative controls. Significantly more infectious virus and viral RNA was found in the upper respiratory tract of aged ferrets. Interestingly, cell-free DNA and DNase-1 activity was generally higher in bronchoalveolar lavage fluid (BALF) but significantly lower in serum of aged compared to young ferrets. In accordance with these data, immunofluorescence microscopy revealed significantly more NETs in lungs of aged compared to young infected ferrets. The association of SARS-CoV-2-antigen in the respiratory mucosa and NET markers in the nasal conchae, but the absence of virus antigen in the lungs, confirms the nasal epithelium as the major location for virus replication as described for young ferrets. Furthermore, a strong positive correlation was found between virus shedding and cell-free DNA or the level of DNAse-1 activity in aged ferrets. Despite the increased NET formation in infected lungs of aged ferrets, the animals did not show a strong NET phenotype and correlation among tested NET markers. Therefore, ferrets are of limited use to study SARS-CoV-2 pathogenesis associated with NET formation. Nevertheless, the mild to moderate clinical signs, virus shedding pattern, and the lung pathology of aged ferrets confirm those animals as a relevant model to study age-dependent COVID-19 pathogenesis.
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Affiliation(s)
- Veronika Pilchová
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Institute of Biochemistry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Ingo Gerhauser
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Center for Systems Neuroscience Hannover (ZSN), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Federico Armando
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Katrin Wirz
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Institute of Biochemistry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Tom Schreiner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Center for Systems Neuroscience Hannover (ZSN), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Nicole de Buhr
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Institute of Biochemistry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Gülşah Gabriel
- Department for Viral Zoonoses-One Health, Leibniz Institute of Virology, Hamburg, Germany
- Institute for Virology, University for Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich Loeffler Institute, Greifswald, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Center for Systems Neuroscience Hannover (ZSN), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Maren von Köckritz-Blickwede
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Institute of Biochemistry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Claudia Schulz
- Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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Skuza K, Rutyna P, Krzowski L, Rabalski L, Lepionka T. Surveillance of SARS-CoV-2 Genetic Variants in the Polish Armed Forces Using Whole Genome Sequencing Analysis. Int J Mol Sci 2023; 24:14851. [PMID: 37834302 PMCID: PMC10573488 DOI: 10.3390/ijms241914851] [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] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Military operations involve the global movement of personnel and equipment, increasing the risk of spreading infectious pathogens such as SARS-CoV-2. Given the continuous engagement of the Polish Armed Forces in overseas operations, an active surveillance program targeting Variants of Concern (VOC) of SARS-CoV-2 was implemented among military personnel. Screening using RT-qPCR tests was conducted on 1699 soldiers between November 2021 and May 2022. Of these, 84 SARS-CoV-2 positive samples met the criteria for whole genome sequencing analysis and variant identification. Whole genome sequencing was performed using two advanced next-generation sequencing (NGS) technologies: sequencing by synthesis and nanopore sequencing. Our analysis revealed eleven SARS-CoV-2 lineages belonging to 21K, 21L, and 21J. The predominant lineage was BA.1.1 (57% of the samples), followed by BA.1 (23%) and BA.2 (6%). Notably, all identified lineages detected in post-deployment screening tests were classified as VOC and were already present in Poland, showing the effectiveness of the Military Sanitary Inspection measures in mitigating the COVID-19 spread. Pre-departure and post-mission screening and isolation successfully prevented SARS-CoV-2 VOC exportation and importation. Proactive measures are vital in minimizing the impact of COVID-19 in military settings, emphasizing the need for continued vigilance and response strategies.
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Affiliation(s)
- Katarzyna Skuza
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4, 24-100 Pulawy, Poland;
| | - Pawel Rutyna
- Chair and Department of Medical Microbiology, Medical University of Lublin, 1 Chodzki, 20-093 Lublin, Poland;
| | - Lukasz Krzowski
- Biomedical Engineering Centre, Institute of Optoeletronics. Military University of Technology, 2 Gen. Sylwestra Kaliskiego, 00-908 Warsaw, Poland;
| | - Lukasz Rabalski
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4, 24-100 Pulawy, Poland;
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Tomasz Lepionka
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4, 24-100 Pulawy, Poland;
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Fabbri A, Voza A, Riccardi A, Vanni S, De Iaco F; Study & Research Center of the Italian Society of Emergency Medicine (SIMEU). Unfavorable Outcome and Long-Term Sequelae in Cases with Severe COVID-19. Viruses 2023; 15. [PMID: 36851699 DOI: 10.3390/v15020485] [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] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
Emerging evidence shows that individuals with COVID-19 who survive the acute phase of illness may experience lingering symptoms in the following months. There is no clear indication as to whether these symptoms persist for a short time before resolving or if they persist for a long time. In this review, we will describe the symptoms that persist over time and possible predictors in the acute phase that indicate long-term persistence. Based on the literature available to date, fatigue/weakness, dyspnea, arthromyalgia, depression, anxiety, memory loss, slowing down, difficulty concentrating and insomnia are the most commonly reported persistent long-term symptoms. The extent and persistence of these in long-term follow-up is not clear as there are still no quality studies available. The evidence available today indicates that female subjects and those with a more severe initial disease are more likely to suffer permanent sequelae one year after the acute phase. To understand these complications, and to experiment with interventions and treatments for those at greater risk, we must first understand the physio-pathological mechanisms that sustain them.
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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Ferreira GM, Claro IM, Grosche VR, Cândido D, José DP, Rocha EC, de Moura Coletti T, Manuli ER, Gaburo N, Faria NR, Sabino EC, de Jesus JG, Jardim ACG. Molecular characterization and sequecing analysis of SARS-CoV-2 genome in Minas Gerais, Brazil. Biologicals 2022; 80:43-52. [PMID: 36175304 PMCID: PMC9436897 DOI: 10.1016/j.biologicals.2022.08.001] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/14/2022] [Accepted: 08/21/2022] [Indexed: 11/05/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in Wuhan, China, is the causative agent of the coronavirus disease 2019 (COVID-19). Since its first notification in São Paulo state (SP) on 26th February 2020, more than 22,300,000 cases and 619,000 deaths were reported in Brazil. In early pandemic, SARS-CoV-2 spread locally, however, over time, this virus was disseminated to other regions of the country. Herein, we performed genomic sequencing and phylogenetic analysis of SARS-CoV-2 using 20 clinical samples of COVID-19 confirmed cases from 9 cities of Minas Gerais state (MG), in order to evaluate the molecular properties of circulating viral strains in this locality from March to May 2020. Our analyses demonstrated the circulation of B.1 lineage isolates in the investigated locations and nucleotide substitutions were observed into the genomic regions related to important viral structures. Additionally, sequences generated in this study clustered with isolates from SP, suggesting a dissemination route between these two states. Alternatively, monophyletic groups of sequences from MG and other states or country were observed, indicating independent events of virus introduction. These results reinforce the need of genomic surveillance for understand the ongoing spread of emerging viral pathogens.
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Affiliation(s)
| | - Ingra Morales Claro
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Victória Riquena Grosche
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, MG, Brazil; Institute of Bioscience, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil
| | - Darlan Cândido
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Zoology, University of Oxford, Oxford, UK
| | | | - Esmenia Coelho Rocha
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Thaís de Moura Coletti
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Erika Regina Manuli
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | | | - Nuno Rodrigues Faria
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Zoology, University of Oxford, Oxford, UK; MCR Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Jaqueline Goes de Jesus
- Institute of Tropical Medicine, University of São Paulo Medical School, São Paulo, Brazil; Department of Infectious and Parasitic Diseases, University of São Paulo Medical School, São Paulo, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science, Federal University of Uberlândia, Uberlândia, MG, Brazil; Institute of Bioscience, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
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Afiahayati, Bernard S, Gunadi, Wibawa H, Hakim MS, Marcellus, Parikesit AA, Dewa CK, Sakakibara Y. A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains. Genes (Basel) 2022; 13:1330. [PMID: 35893066 DOI: 10.3390/genes13081330] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 02/04/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of the worldwide pandemic due to Coronavirus Disease 2019 (COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full-length SARS-CoV-2 genome on the 10 January 2020, with the hope of turning the table against the worsening pandemic situation. Previous studies in respiratory virus characterization require mapping of raw sequences to the human genome in the downstream bioinformatics pipeline as part of metagenomic principles. Illumina, as the major player in the NGS arena, took action by releasing guidelines for improved enrichment kits called the Respiratory Virus Oligo Panel (RVOP) based on a hybridization capture method capable of capturing targeted respiratory viruses, including SARS-CoV-2; therefore, allowing a direct map of raw sequences data to SARS-CoV-2 genome in downstream bioinformatics pipeline. Consequently, two bioinformatics pipelines emerged with no previous studies benchmarking the pipelines. This study focuses on gaining insight and understanding of target enrichment workflow by Illumina through the utilization of different bioinformatics pipelines named as 'Fast Pipeline' and 'Normal Pipeline' to SARS-CoV-2 strains isolated from Yogyakarta and Central Java, Indonesia. Overall, both pipelines work well in the characterization of SARS-CoV-2 samples, including in the identification of major studied nucleotide substitutions and amino acid mutations. A higher number of reads mapped to the SARS-CoV-2 genome in Fast Pipeline and merely were discovered as a contributing factor in a higher number of coverage depth and identified variations (SNPs, insertion, and deletion). Fast Pipeline ultimately works well in a situation where time is a critical factor. On the other hand, Normal Pipeline would require a longer time as it mapped reads to the human genome. Certain limitations were identified in terms of pipeline algorithm, whereas it is highly recommended in future studies to design a pipeline in an integrated framework, for instance, by using NextFlow, a workflow framework to combine all scripts into one fully integrated pipeline.
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Ritskes-hoitinga M, Barella Y, Kleinhout-vliek T. The Promises of Speeding Up: Changes in Requirements for Animal Studies and Alternatives during COVID-19 Vaccine Approval–A Case Study. Animals (Basel) 2022; 12:1735. [PMID: 35804634 PMCID: PMC9264994 DOI: 10.3390/ani12131735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary The COVID-19 pandemic led to intensive research into finding new vaccines for human protection. On 21 December 2020, the European Commission granted conditional marketing authorisation for the messenger RNA vaccine ‘Comirnaty’, produced by Pfizer (New York, NY, USA) and BioNTech (Mainz, Germany). This happened only twelve months after the first identification of the virus, whereas the development and approval of vaccines usually take ten years. Through document analysis and interviewing key expert stakeholders, we examined whether the role of animal studies and alternatives in this fast approval process had changed and, if so, whether this could lead to using fewer animal studies and more alternatives in the future. It turned out that in this case, for vaccine development and production, the number of animal studies performed and required had indeed declined, more alternatives had been used and accepted, human studies started earlier and ran in parallel with (rather than sequential to) animal studies, and regulators accepted historical data from earlier vaccine research. The Pfizer/BioNTech vaccine case illustrates the tremendous progress in quickly producing and authorising reliable, safe and effective vaccines, using fewer animal studies and more alternatives. It is time to study the broader implementation of these new procedures on a larger scale to benefit animals and humans. Abstract On 21 December 2020, the European Commission granted conditional marketing authorisation for the BNT162b2 COVID-19 vaccine ‘Comirnaty’, produced by Pfizer/BioNTech. This happened only twelve months after scientists first identified SARS-CoV-2. This stands in stark contrast with the usual ten years needed for vaccine development and approval. Many have suggested that the changes in required animal tests have sped up the development of Comirnaty and other vaccine candidates. However, few have provided an overview of the changes made and interviewed stakeholders on the potential of the pandemic’s pressure to achieve a lasting impact. Our research question is: how have stakeholders, including regulatory agencies and pharmaceutical companies, dealt with requirements concerning in vivo animal models in the expedited approval of vaccine candidates such as ‘Comirnaty’? We interviewed key stakeholders at the Dutch national and European levels (n = 11 individuals representing five stakeholder groups in eight interviews and two written statements) and analysed relevant publications, policy documents and other grey literature (n = 171 documents). Interviewees observed significant changes in regulatory procedures and requirements for the ‘Comirnaty’ vaccine compared to vaccine approval in non-pandemic circumstances. Specifically, the European Medicines Agency (EMA) actively promoted changes by using an accelerated assessment and rolling review procedure for fast conditional marketing authorisation, requiring a reduced number of animal studies and accepting more alternatives, allowing pre-clinical in vivo animal experiments to run in parallel with clinical trials and allowing re-use of historical data from earlier vaccine research. Pharmaceutical companies, in turn, actively anticipated these changes and contributed data from non-animal alternative sources for the development phase. After approval, they could also use in vitro methods only for all batch releases due to the thorough characterisation of the mRNA vaccine. Pharmaceutical companies were optimistic about future change because of societal concerns surrounding the use of animals, adding that, in their view, non-animal alternatives generally obtain faster, better, and cheaper results. Regulators we interviewed were more hesitant to permanently implement these changes as they feared backlash regarding safety issues and uncertainty surrounding adverse effects. Our analysis shows how the EMA shortened its approval timeline in times of crisis by reducing the number of requested animal studies and promoting alternative methods. It also highlights the readiness of pharmaceutical companies to contribute to these changes. More research is warranted to investigate these promising possibilities toward further replacement in science and regulations, contributing to faster vaccine development.
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Pondé RAA. Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern. Virology 2022; 572:44-54. [PMID: 35580380 PMCID: PMC9096574 DOI: 10.1016/j.virol.2022.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 01/17/2023]
Abstract
The spike protein comprises one of the main structural components of SARS-CoV-2 because it is directly involved in the infection process and viral transmission, and also because of its immunogenic properties, as an inducer of the protective antibodies production and as a vaccine component. The occurrence of mutations in this region or in other the virus genome regions, comprises a natural phenomenon in its evolution. However, they also occur due to the selective immune pressure, to which the agent is continuously subjected, especially in the spike protein immunodominant regions, such as the RBD. Mutations in the spike protein can change the virus' fitness, increasing its affinity for target cells, its transmissibility and its virulence. In addition, these mutations can giving it the potential ability to evade the protective antibodies action obtained from convalescent sera or vaccine origin, as well as those used in therapy, which may favor the virus expansion and compromise the infection control. Five mutations N501Y, E484K/Q, K417N/T, L452R and T478K, located in the spike protein RBD, have had a greater impact because they are associated with new attributes developed by the virus, which characterize the emerging variants of concern (VOCs) of SARS-Cov-2 identified so far. The occurrence of these mutations induces complex physicochemical effects that can alter the spike protein's structure and its function, which in turn, lead to changes in the agents' fitness. This manuscript discusses the attributes of VOCs associated with the physicochemical effects caused by the aforementioned mutations.
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Affiliation(s)
- R A A Pondé
- State Department of Health SES/Superintendence of Health Surveillance SUVISA/GO, Management of Epidemiological Surveillance-GVE/Coordination of Analysis and Research-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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Singanallur NB, van Vuren PJ, McAuley AJ, Bruce MP, Kuiper MJ, Gwini SM, Riddell S, Goldie S, Drew TW, Blasdell KR, Tachedjian M, Mangalaganesh S, Chahal S, Caly L, Druce JD, Juno JA, Kent SJ, Wheatley AK, Vasan SS. At Least Three Doses of Leading Vaccines Essential for Neutralisation of SARS-CoV-2 Omicron Variant. Front Immunol 2022; 13:883612. [PMID: 35655773 PMCID: PMC9152325 DOI: 10.3389/fimmu.2022.883612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Plasma samples taken at different time points from donors who received either AstraZeneca (Vaxzevria) or Pfizer (Comirnaty) or Moderna (Spikevax) coronavirus disease-19 (COVID-19) vaccine were assessed in virus neutralization assays against Delta and Omicron variants of concern and a reference isolate (VIC31). With the Pfizer vaccine there was 6-8-fold reduction in 50% neutralizing antibody titres (NT50) against Delta and VIC31 at 6 months compared to 2 weeks after the second dose; followed by 25-fold increase at 2 weeks after the third dose. Neutralisation of Omicron was only consistently observed 2 weeks after the third dose, with most samples having titres below the limit of detection at earlier timepoints. Moderna results were similar to Pfizer at 2 weeks after the second dose, while the titres for AstraZeneca samples derived from older donors were 7-fold lower against VIC31 and below the limit of detection against Delta and Omicron. Age and gender were not found to significantly impact our results. These findings indicate that vaccine matching may be needed, and that at least a third dose of these vaccines is necessary to generate sufficient neutralising antibodies against emerging variants of concern, especially Omicron, amidst the challenges of ensuring vaccine equity worldwide.
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Affiliation(s)
- Nagendrakumar B Singanallur
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Petrus Jansen van Vuren
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Alexander J McAuley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Matthew P Bruce
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Michael J Kuiper
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Docklands, VIC, Australia
| | - Stella M Gwini
- University Hospital Geelong, Barwon Health, Geelong, VIC, Australia
| | - Shane Riddell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Sarah Goldie
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Trevor W Drew
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Mary Tachedjian
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Shruthi Mangalaganesh
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia.,Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simran Chahal
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Julian D Druce
- Victorian Infectious Diseases Reference Laboratory (VIDRL), The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Seshadri S Vasan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
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11
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Shanbehzadeh M, Yazdani A, Shafiee M, Kazemi-Arpanahi H. Predictive modeling for COVID-19 readmission risk using machine learning algorithms. BMC Med Inform Decis Mak 2022; 22:139. [PMID: 35596167 PMCID: PMC9122247 DOI: 10.1186/s12911-022-01880-z] [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: 12/31/2021] [Accepted: 05/18/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction The COVID-19 pandemic overwhelmed healthcare systems with severe shortages in hospital resources such as ICU beds, specialized doctors, and respiratory ventilators. In this situation, reducing COVID-19 readmissions could potentially maintain hospital capacity. By employing machine learning (ML), we can predict the likelihood of COVID-19 readmission risk, which can assist in the optimal allocation of restricted resources to seriously ill patients. Methods In this retrospective single-center study, the data of 1225 COVID-19 patients discharged between January 9, 2020, and October 20, 2021 were analyzed. First, the most important predictors were selected using the horse herd optimization algorithms. Then, three classical ML algorithms, including decision tree, support vector machine, and k-nearest neighbors, and a hybrid algorithm, namely water wave optimization (WWO) as a precise metaheuristic evolutionary algorithm combined with a neural network were used to construct predictive models for COVID-19 readmission. Finally, the performance of prediction models was measured, and the best-performing one was identified. Results The ML algorithms were trained using 17 validated features. Among the four selected ML algorithms, the WWO had the best average performance in tenfold cross-validation (accuracy: 0.9705, precision: 0.9729, recall: 0.9869, specificity: 0.9259, F-measure: 0.9795). Conclusions Our findings show that the WWO algorithm predicts the risk of readmission of COVID-19 patients more accurately than other ML algorithms. The models developed herein can inform frontline clinicians and healthcare policymakers to manage and optimally allocate limited hospital resources to seriously ill COVID-19 patients.
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Affiliation(s)
- Mostafa Shanbehzadeh
- Department of Health Information Technology, School of Paramedical, Ilam University of Medical Sciences, Ilam, Iran
| | - Azita Yazdani
- Clinical Education Research Center, Health Human Resources Research Center, Department of Health Information Management, School of Health Management and Information Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Shafiee
- Department of Nursing, Abadan University of Medical Sciences, Abadan, Iran
| | - Hadi Kazemi-Arpanahi
- Department of Health Information Technology, Abadan University of Medical Sciences, Abadan, Iran. .,Department of Student Research Committee, Abadan University of Medical Sciences, Abadan, Iran.
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12
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Bai JPF, Guo EY. Combating Viral Diseases in the Era of Systems Medicine. Methods Mol Biol 2022; 2486:87-104. [PMID: 35437720 DOI: 10.1007/978-1-0716-2265-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Viruses can cause many diseases resulting in disabilities and death. Fortunately, advances in systems medicine enable the development of effective therapies for treating viral diseases, of vaccines to prevent viral infections, as well as of diagnostic tools to mitigate the risk and reduce the death toll. Characterizing the SARS-CoV-2 gene sequence and the role of its spike protein in infection informs development of small molecule drugs, antibodies, and vaccines to combat infection and complication, as well as to end the pandemic. Drug repurposing of small molecule drugs is a viable strategy to combat viral diseases; the key concepts include (1) linking a drug candidate's pharmacological network to its pharmacodynamic response in patients; (2) linking a drug candidate's physicochemical properties to its pharmacokinetic characteristics; and (3) optimizing the safe and effective dosing regimen within its therapeutic window. Computational integration of drug-induced signaling pathways with clinical outcomes is useful to inform selection of potential drug candidates with respect to safety and effectiveness. Key pharmacokinetic and pharmacodynamic principles for computational optimization of drug development include a drug candidate's Cminss/IC95 ratio, pharmacokinetic characteristics, and systemic exposure-response relationship, where Cminss is the trough concentration following multiple dosing. In summary, systems medicine approaches play a vital role in global success in combating viral diseases, including global real-time information sharing, development of test kits, drug repurposing, discovery and development of safe, effective therapies, detection of highly transmissible and deadly variants, and development of vaccines.
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13
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Jansen van Vuren P, McAuley AJ, Kuiper MJ, Singanallur NB, Bruce MP, Riddell S, Goldie S, Mangalaganesh S, Chahal S, Drew TW, Blasdell KR, Tachedjian M, Caly L, Druce JD, Ahmed S, Khan MS, Malladi SK, Singh R, Pandey S, Varadarajan R, Vasan SS. Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. Viruses 2022; 14:v14040800. [PMID: 35458530 PMCID: PMC9031315 DOI: 10.3390/v14040800] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We previously developed highly thermo-tolerant monomeric and trimeric receptor-binding domain derivatives that can withstand 100 °C for 90 min and 37 °C for four weeks and help eliminate cold-chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations and a 16.5-fold reduction for the three trimeric antigen-adjuvant combinations; the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for upcoming Phase I human clinical trials and that there is potential for increasing the efficacy with vaccine matching to improve the responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions, which show that, while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.
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Affiliation(s)
- Petrus Jansen van Vuren
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Alexander J. McAuley
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Michael J. Kuiper
- Data61, Commonwealth Scientific and Industrial Research Organisation, Docklands, VIC 3008, Australia;
| | - Nagendrakumar Balasubramanian Singanallur
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Matthew P. Bruce
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Shane Riddell
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Sarah Goldie
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Shruthi Mangalaganesh
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Simran Chahal
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Trevor W. Drew
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Kim R. Blasdell
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Mary Tachedjian
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital and The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (J.D.D.)
| | - Julian D. Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital and The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (J.D.D.)
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Mohammad Suhail Khan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Sameer Kumar Malladi
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Randhir Singh
- Mynvax Private Limited, ES-12, Incubation Centre, Society for Innovation and Development, Indian Institute of Science, Bengaluru 560012, India; (R.S.); (S.P.)
| | - Suman Pandey
- Mynvax Private Limited, ES-12, Incubation Centre, Society for Innovation and Development, Indian Institute of Science, Bengaluru 560012, India; (R.S.); (S.P.)
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Seshadri S. Vasan
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
- Department of Health Sciences, University of York, York YO10 5DD, UK
- Correspondence: ; Tel.: +61-352275346
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Prasetyoputri A, Dharmayanthi AB, Iryanto SB, Andriani A, Nuryana I, Wardiana A, Ridwanuloh AM, Swasthikawati S, Hariyatun H, Nugroho HA, Idris I, Indriawati I, Noviana Z, Oktavia L, Yuliawati Y, Masrukhin M, Hasrianda EF, Sukmarini L, Fahrurrozi F, Yanthi ND, Fathurahman AT, Wulandari AS, Setiawan R, Rizal S, Fathoni A, Kusharyoto W, Lisdiyanti P, Ningrum RA, Saputra S. The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. PeerJ 2022; 10:e13132. [PMID: 35341058 PMCID: PMC8953504 DOI: 10.7717/peerj.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/11/2021] [Accepted: 02/26/2022] [Indexed: 01/12/2023] Open
Abstract
Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.
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Affiliation(s)
- Anggia Prasetyoputri
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Anik B. Dharmayanthi
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Syam B. Iryanto
- Research Center for Informatics, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ade Andriani
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Isa Nuryana
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Andri Wardiana
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Asep M. Ridwanuloh
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Sri Swasthikawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Hariyatun Hariyatun
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Herjuno A. Nugroho
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Idris Idris
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Indriawati Indriawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Zahra Noviana
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Listiana Oktavia
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Yuliawati Yuliawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Masrukhin Masrukhin
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Erwin F. Hasrianda
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Linda Sukmarini
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Fahrurrozi Fahrurrozi
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Nova Dilla Yanthi
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Alfi T. Fathurahman
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ari S. Wulandari
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ruby Setiawan
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Syaiful Rizal
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ahmad Fathoni
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Wien Kusharyoto
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ratih A. Ningrum
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
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Banerjee S, Banerjee D, Singh A, Saharan VA. A Comprehensive Investigation Regarding the Differentiation of the Procurable COVID-19 Vaccines. AAPS PharmSciTech 2022; 23:95. [PMID: 35314902 PMCID: PMC8936379 DOI: 10.1208/s12249-022-02247-3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/06/2022] [Indexed: 11/30/2022] Open
Abstract
COVID-19 caused by coronavirus SARS-CoV-2 became a serious threat to humankind for the past couple of years. The development of vaccine and its immediate application might be the only to escape from the grasp of this demoniac pandemic. Approximately 343 clinical trials on COVID-19 vaccines are ongoing currently, and almost all countries are motivating ongoing researches at warp speed for the development of vaccines against COVID-19. This review explores the progress in the development of the vaccines, their current status of ongoing clinical research, mechanisms, and regulatory approvals. Many pharmaceutical companies are already in the endgame for manufacturing various vaccines of which some are already being marketed across the globe, while others are yet to get approval for marketing. The primary aim of this review is to compare regulatory accepted vaccines in terms of their composition, doses, regulatory status, and efficacy. The study is conducted by grouping into approved and unapproved vaccines for marketing. Different routes of administration of vaccines along with the efficacy of the routes are also presented in the review. A wide range of database and clinical trial data is reviewed for sorting out the information on different vaccines. Unfortunately, many mutations (alpha, beta, gamma, delta, kappa, omicron etc.) of SARS-CoV-2 have attacked people in very short time, which is the great challenge for investigational vaccines. Moreover, some vaccines like Pfizer's BNT162, Oxford's ChAdOx1, Moderna's mRNA-1273, and Bharat Biotech's Covaxin have got regulatory approval in some countries for its distribution which may prove to stand tall against the pandemic.
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Affiliation(s)
- Surojit Banerjee
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India.
| | - Debadri Banerjee
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India
| | - Anupama Singh
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India
| | - Vikas Anand Saharan
- School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Balawala, Dehradun, 248001, Uttarakhand, India
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Menasria T, Aguilera M. Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Microorganisms 2022; 10:microorganisms10020467. [PMID: 35208920 PMCID: PMC8877871 DOI: 10.3390/microorganisms10020467] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/26/2022] Open
Abstract
Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-Hu-1. Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). Lower prevalence was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the ORF3a coding protein NS3-G251V) (2.0%). Interestingly, 1.5% of total genomes were assigned as GRA (Omicron), the newly emerged clade. Across the North African countries, 108 SARS-CoV-2 lineages using the Pangolin assignment were identified, whereby most genomes fell within six major lineages and variants of concern (VOC) including B.1, the Delta variants (AY.X, B.1.617.2), C.36, B.1.1.7 and B.1.1. The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total sequences, respectively. In addition, mutations affecting other viral proteins appeared frequently including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. These findings highlight the importance of genomic surveillance for understanding the SARS-CoV-2 genetic diversity and its spread patterns, leading to a better guiding of public health intervention measures. The know-how analysis of the present work could be implemented worldwide in order to overcome this health crisis through harmonized approaches.
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Affiliation(s)
- Taha Menasria
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa 12002, Algeria
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
- Correspondence: or (T.M.); (M.A.)
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
- Correspondence: or (T.M.); (M.A.)
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Simões RSQ, Rodríguez-Lázaro D. Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Int J Environ Res Public Health 2022; 19:2392. [PMID: 35206580 DOI: 10.3390/ijerph19042392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Several coronaviruses (CoVs) have been identified as human pathogens, including the α-CoVs strains HCoV-229E and HCoV-NL63 and the β-CoVs strains HCoV-HKU1 and HCoV-OC43. SARS-CoV, MERS-CoV, and SARS-CoV-2 are also classified as β-coronavirus. New SARS-CoV-2 spike genomic variants are responsible for human-to-human and interspecies transmissibility, consequences of adaptations of strains from animals to humans. The receptor-binding domain (RBD) of SARS-CoV-2 binds to receptor ACE2 in humans and animal species with high affinity, suggesting there have been adaptive genomic variants. New genomic variants including the incorporation, replacement, or deletion of the amino acids at a variety of positions in the S protein have been documented and are associated with the emergence of new strains adapted to different hosts. Interactions between mutated residues and RBD have been demonstrated by structural modelling of variants including D614G, B.1.1.7, B1.351, P.1, P2; other genomic variants allow escape from antibodies generated by vaccines. Epidemiological and molecular tools are being used for real-time tracking of pathogen evolution and particularly new SARS-CoV-2 variants. COVID-19 vaccines obtained from classical and next-generation vaccine production platforms have entered clinicals trials. Biotechnology strategies of the first generation (attenuated and inactivated virus–CoronaVac, CoVaxin; BBIBP-CorV), second generation (replicating-incompetent vector vaccines–ChAdOx-1; Ad5-nCoV; Sputnik V; JNJ-78436735 vaccine-replicating-competent vector, protein subunits, virus-like particles–NVX-CoV2373 vaccine), and third generation (nucleic-acid vaccines–INO-4800 (DNA); mRNA-1273 and BNT 162b (RNA vaccines) have been used. Additionally, dendritic cells (LV-SMENP-DC) and artificial antigen-presenting (aAPC) cells modified with lentiviral vector have also been developed to inhibit viral activity. Recombinant vaccines against COVID-19 are continuously being applied, and new clinical trials have been tested by interchangeability studies of viral vaccines developed by classical and next-generation platforms.
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18
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Cable J, Rappuoli R, Klemm EJ, Kang G, Mutreja A, Wright GJ, Pizza M, Castro SA, Hoffmann JP, Alter G, Carfi A, Pollard AJ, Krammer F, Gupta RK, Wagner CE, Machado V, Modjarrad K, Corey L, B Gilbert P, Dougan G, Lurie N, Bjorkman PJ, Chiu C, Nemes E, Gordon SB, Steer AC, Rudel T, Blish CA, Sandberg JT, Brennan K, Klugman KP, Stuart LM, Madhi SA, Karp CL. Innovative vaccine approaches-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1511:59-86. [PMID: 35029310 DOI: 10.1111/nyas.14739] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022]
Abstract
The rapid development of COVID-19 vaccines was the result of decades of research to establish flexible vaccine platforms and understand pathogens with pandemic potential, as well as several novel changes to the vaccine discovery and development processes that partnered industry and governments. And while vaccines offer the potential to drastically improve global health, low-and-middle-income countries around the world often experience reduced access to vaccines and reduced vaccine efficacy. Addressing these issues will require novel vaccine approaches and platforms, deeper insight how vaccines mediate protection, and innovative trial designs and models. On June 28-30, 2021, experts in vaccine research, development, manufacturing, and deployment met virtually for the Keystone eSymposium "Innovative Vaccine Approaches" to discuss advances in vaccine research and development.
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Affiliation(s)
| | | | | | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK.,Department of Biology, Hull York Medical School, and York Biomedical Research Institute, University of York, York, UK
| | | | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joseph P Hoffmann
- Departments of Pediatrics and Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Florian Krammer
- The Tisch Cancer Institute and Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
| | - Caroline E Wagner
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Viviane Machado
- Measles and Respiratory Viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Lurie
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Harvard Medical School, Boston, Massachusetts
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Elisa Nemes
- Division of Immunology, Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Andrew C Steer
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Thomas Rudel
- Microbiology Biocenter, University of Würzburg, Würzburg, Germany
| | - Catherine A Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford Immunology Program, Stanford University School of Medicine, Stanford, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - John Tyler Sandberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kiva Brennan
- National Children's Research Centre, Crumlin and School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Lynda M Stuart
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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19
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Kuiper MJ, Wilson LOW, Mangalaganesh S, Lee C, Reti D, Vasan SS. "But Mouse, You Are Not Alone": On Some Severe Acute Respiratory Syndrome Coronavirus 2 Variants Infecting Mice. ILAR J 2021; 62:48-59. [PMID: 35022734 PMCID: PMC9236659 DOI: 10.1093/ilar/ilab031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 08/04/2021] [Revised: 10/31/2021] [Accepted: 11/21/2021] [Indexed: 12/20/2022] Open
Abstract
In silico predictions combined with in vitro, in vivo, and in situ observations collectively suggest that mouse adaptation of the severe acute respiratory syndrome 2 virus requires an aromatic substitution in position 501 or position 498 (but not both) of the spike protein's receptor binding domain. This effect could be enhanced by mutations in positions 417, 484, and 493 (especially K417N, E484K, Q493K, and Q493R), and to a lesser extent by mutations in positions 486 and 499 (such as F486L and P499T). Such enhancements, due to more favorable binding interactions with residues on the complementary angiotensin-converting enzyme 2 interface, are, however, unlikely to sustain mouse infectivity on their own based on theoretical and experimental evidence to date. Our current understanding thus points to the Alpha, Beta, Gamma, and Omicron variants of concern infecting mice, whereas Delta and "Delta Plus" lack a similar biomolecular basis to do so. This paper identifies 11 countries (Brazil, Chile, Djibouti, Haiti, Malawi, Mozambique, Reunion, Suriname, Trinidad and Tobago, Uruguay, and Venezuela) where targeted local field surveillance of mice is encouraged because they may have come in contact with humans who had the virus with adaptive mutation(s). It also provides a systematic methodology to analyze the potential for other animal reservoirs and their likely locations.
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Affiliation(s)
| | - Laurence O W Wilson
- CSIRO Transformational Bioinformatics Group, North Ryde, New South Wales, Australia
| | - Shruthi Mangalaganesh
- Monash University, Clayton, Victoria, Australia
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Carol Lee
- CSIRO Transformational Bioinformatics Group, North Ryde, New South Wales, Australia
| | - Daniel Reti
- CSIRO Transformational Bioinformatics Group, North Ryde, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Seshadri S Vasan
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
- Department of Health Sciences, University of York, York, UK
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20
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Abstract
The sudden rise in COVID-19 cases in 2020 and the incessant emergence of fast-spreading variants have created an alarming situation worldwide. Besides the continuous advancements in the design and development of vaccines to combat this deadly pandemic, new variants are frequently reported, possessing mutations that rapidly outcompeted an existing population of circulating variants. As concerns grow about the effects of mutations on the efficacy of vaccines, increased transmissibility, immune escape, and diagnostic failures are few other apprehensions liable for more deadly waves of COVID-19. Although the phenomenon of antigenic drift in new variants of SARS-CoV-2 is still not validated, it is conceived that the virus is acquiring new mutations as a fitness advantage for rapid transmission or to overcome immunological resistance of the host cell. Considerable evolution of SARS-CoV-2 has been observed since its first appearance in 2019, and despite the progress in sequencing efforts to characterize the mutations, their impacts in many variants have not been analyzed. The present article provides a substantial review of literature explaining the emerging variants of SARS-CoV-2 circulating globally, key mutations in viral genome, and the possible impacts of these new mutations on prevention and therapeutic strategies currently administered to combat this pandemic. Rising infections, mortalities, and hospitalizations can possibly be tackled through mass vaccination, social distancing, better management of available healthcare infrastructure, and by prioritizing genome sequencing for better serosurveillance studies and community tracking.
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Affiliation(s)
- Aakriti Dubey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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21
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Al-Jaf SMA, Niranji SS, Mahmood ZH. Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Meta Gene 2021; 30:100950. [PMID: 34307051 PMCID: PMC8286243 DOI: 10.1016/j.mgene.2021.100950] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/19/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in the impact of this mutation on the virus's infectivity. Also, the whole genome sequencings are expensive and time-consuming. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples. Both rRT and ARMS data showed G614 mutants indicated by the presence of HEX probe and 176 bp, respectively. Additionally, the results of the RFLP data and DNA sequencings confirmed the prevalence of the G614 mutants. These methods will be important, in epidemiological, reinfections and zoonotic aspects, through detecting the G614 mutant in retro-perspective samples to track its origins and future re-emergence of D614 wild type.
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Affiliation(s)
- Sirwan M A Al-Jaf
- Department of Biology, College of Education, University of Garmian, Kurdistan Region, Iraq
- Coronavirus Research and Identification Lab., University of Garmian, Kurdistan Region, Iraq
| | - Sherko S Niranji
- Department of Biology, College of Education, University of Garmian, Kurdistan Region, Iraq
- Coronavirus Research and Identification Lab., University of Garmian, Kurdistan Region, Iraq
| | - Zana H Mahmood
- Molecular Diagnostic Laboratory, Sulaimani Veterinary Directorate, Sulaimani, Kurdistan, Iraq
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
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22
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Wong LP, Lin Y, Alias H, Bakar SA, Zhao Q, Hu Z. COVID-19 Anti-Vaccine Sentiments: Analyses of Comments from Social Media. Healthcare (Basel) 2021; 9:1530. [PMID: 34828576 PMCID: PMC8622531 DOI: 10.3390/healthcare9111530] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/14/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
PURPOSE This study analyzed the insights and sentiments of COVID-19 anti-vaccine comments from Instagram feeds and Facebook postings. The sentiments related to the acceptance and effectiveness of the vaccines that were on the verge of being made available to the public. PATIENTS AND METHODS The qualitative software QSR-NVivo 10 was used to manage, code, and analyse the data. RESULTS The analyses uncovered several major issues concerning COVID-19 vaccine hesitancy. The production of the COVID-19 vaccine at an unprecedented speed evoked the fear of skipping steps that would compromise vaccine safety. The unknown long-term effects and duration of protection erode confidence in taking the vaccines. There were also persistent concerns with regard to vaccine compositions that could be harmful or contain aborted foetal cells. The rate of COVID-19 death was viewed as low. Many interpreted the 95% effectiveness of the COVID-19 vaccine as insufficient. Preference for immunity gains from having an infection was viewed as more effective. Peer-reviewed publication-based data were favoured as a source of trust in vaccination decision-making. CONCLUSIONS The anti-COVID-19 vaccine sentiments found in this study provide important insights for the formulation of public health messages to instill confidence in the vaccines.
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Affiliation(s)
- Li Ping Wong
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia;
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China;
| | - Yulan Lin
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China;
| | - Haridah Alias
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Sazaly Abu Bakar
- Tropical Infectious Diseases Research and Educational Centre (TIDREC), University of Malaya, Kuala Lumpur 50603, Malaysia;
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen 361005, China;
| | - Zhijian Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou 350122, China;
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23
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Chen HY, Huang C, Tian L, Huang X, Zhang C, Llewellyn GN, Rogers GL, Andresen K, O’Gorman MRG, Chen YW, Cannon PM. Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. J Virol 2021; 95:e0096621. [PMID: 34495700 PMCID: PMC8549521 DOI: 10.1128/jvi.00966-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 06/18/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022] Open
Abstract
The high pathogenicity of SARS-CoV-2 requires it to be handled under biosafety level 3 conditions. Consequently, Spike protein-pseudotyped vectors are a useful tool to study viral entry and its inhibition, with retroviral, lentiviral (LV), and vesicular stomatitis virus (VSV) vectors the most commonly used systems. Methods to increase the titer of such vectors commonly include concentration by ultracentrifugation and truncation of the Spike protein cytoplasmic tail. However, limited studies have examined whether such a modification also impacts the protein's function. Here, we optimized concentration methods for SARS-CoV-2 Spike-pseudotyped VSV vectors, finding that tangential flow filtration produced vectors with more consistent titers than ultracentrifugation. We also examined the impact of Spike tail truncation on transduction of various cell types and sensitivity to convalescent serum neutralization. We found that tail truncation increased Spike incorporation into both LV and VSV vectors and resulted in enhanced titers but had no impact on sensitivity to convalescent serum. In addition, we analyzed the effect of the D614G mutation, which became a dominant SARS-CoV-2 variant early in the pandemic. Our studies revealed that, similar to the tail truncation, D614G independently increases Spike incorporation and vector titers, but this effect is masked by also including the cytoplasmic tail truncation. Therefore, the use of full-length Spike protein, combined with tangential flow filtration, is recommended as a method to generate high titer pseudotyped vectors that retain native Spike protein functions. IMPORTANCE Pseudotyped viral vectors are useful tools to study the properties of viral fusion proteins, especially those from highly pathogenic viruses. The Spike protein of SARS-CoV-2 has been investigated using pseudotyped lentiviral and VSV vector systems, where truncation of its cytoplasmic tail is commonly used to enhance Spike incorporation into vectors and to increase the titers of the resulting vectors. However, our studies have shown that such effects can also mask the phenotype of the D614G mutation in the ectodomain of the protein, which was a dominant variant arising early in the COVID-19 pandemic. To better ensure the authenticity of Spike protein phenotypes when using pseudotyped vectors, we recommend using full-length Spike proteins, combined with tangential flow filtration methods of concentration if higher-titer vectors are required.
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Affiliation(s)
- Hsu-Yu Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Chun Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Lu Tian
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Hastings Center for Pulmonary Research, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Xiaoli Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Chennan Zhang
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Hastings Center for Pulmonary Research, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - George N. Llewellyn
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Geoffrey L. Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Kevin Andresen
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles/Keck School of Medicine of USC, Los Angeles, California, USA
| | - Maurice R. G. O’Gorman
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles/Keck School of Medicine of USC, Los Angeles, California, USA
| | - Ya-Wen Chen
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Hastings Center for Pulmonary Research, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Paula M. Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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24
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Xi H, Jiang H, Juhas M, Zhang Y. Multiplex Biosensing for Simultaneous Detection of Mutations in SARS-CoV-2. ACS Omega 2021; 6:25846-25859. [PMID: 34632242 PMCID: PMC8491437 DOI: 10.1021/acsomega.1c04024] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/10/2021] [Indexed: 05/02/2023]
Abstract
COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become the world's largest public health emergency of the past few decades. Thousands of mutations were identified in the SARS-CoV-2 genome. Some mutants are more infectious and may replace the original strains. Recently, B.1.1.7(Alpha), B1.351(Beta), and B.1.617.2(Delta) strains, which appear to have increased transmissibility, were detected. These strains accounting for the high proportion of newly diagnosed cases spread rapidly over the world. Particularly, the Delta variant has been reported to account for a vast majority of the infections in several countries over the last few weeks. The application of biosensors in the detection of SARS-CoV-2 is important for the control of the COVID-19 pandemic. Due to high demand for SARS-CoV-2 genotyping, it is urgent to develop reliable and efficient systems based on integrated multiple biosensor technology for rapid detection of multiple SARS-CoV-2 mutations simultaneously. This is important not only for the detection and analysis of the current but also for future mutations. Novel biosensors combined with other technologies can be used for the reliable and effective detection of SARS-CoV-2 mutants.
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Affiliation(s)
- Hui Xi
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| | - Hanlin Jiang
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
| | - Mario Juhas
- Medical
and Molecular Microbiology Unit, Department of Medicine, Faculty of
Science and Medicine, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Yang Zhang
- College
of Science, Harbin Institute of Technology
(Shenzhen), Shenzhen, Guangdong 518055, China
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25
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Wong LP, Alias H, Danaee M, Ahmed J, Lachyan A, Cai CZ, Lin Y, Hu Z, Tan SY, Lu Y, Cai G, Nguyen DK, Seheli FN, Alhammadi F, Madhale MD, Atapattu M, Quazi-Bodhanya T, Mohajer S, Zimet GD, Zhao Q. COVID-19 vaccination intention and vaccine characteristics influencing vaccination acceptance: a global survey of 17 countries. Infect Dis Poverty 2021; 10:122. [PMID: 34620243 PMCID: PMC8496428 DOI: 10.1186/s40249-021-00900-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The availability of various types of COVID-19 vaccines and diverse characteristics of the vaccines present a dilemma in vaccination choices, which may result in individuals refusing a particular COVID-19 vaccine offered, hence presenting a threat to immunisation coverage and reaching herd immunity. The study aimed to assess global COVID-19 vaccination intention, vaccine characteristics influencing vaccination acceptance and desirable vaccine characteristics influencing the choice of vaccines. METHODS An anonymous cross-sectional survey was conducted between 4 January and 5 March 2021 in 17 countries worldwide. Proportions and the corresponding 95% confidence intervals (CI) of COVID-19 vaccine acceptance and vaccine characteristics influencing vaccination acceptance were generated and compared across countries and regions. Multivariable logistic regression analysis was used to determine the factors associated with COVID-19 vaccine hesitancy. RESULTS Of the 19,714 responses received, 90.4% (95% CI 81.8-95.3) reported likely or extremely likely to receive COVID-19 vaccine. A high proportion of likely or extremely likely to receive the COVID-19 vaccine was reported in Australia (96.4%), China (95.3%) and Norway (95.3%), while a high proportion reported being unlikely or extremely unlikely to receive the vaccine in Japan (34.6%), the U.S. (29.4%) and Iran (27.9%). Males, those with a lower educational level and those of older age expressed a higher level of COVID-19 vaccine hesitancy. Less than two-thirds (59.7%; 95% CI 58.4-61.0) reported only being willing to accept a vaccine with an effectiveness of more than 90%, and 74.5% (95% CI 73.4-75.5) said they would accept a COVID-19 vaccine with minor adverse reactions. A total of 21.0% (95% CI 20.0-22.0) reported not accepting an mRNA vaccine and 51.8% (95% CI 50.3-53.1) reported that they would only accept a COVID-19 vaccine from a specific country-of-origin. Countries from the Southeast Asia region reported the highest proportion of not accepting mRNA technology. The highest proportion from Europe and the Americas would only accept a vaccine produced by certain countries. The foremost important vaccine characteristic influencing vaccine choice is adverse reactions (40.6%; 95% CI 39.3-41.9) of a vaccine and effectiveness threshold (35.1%; 95% CI 33.9-36.4). CONCLUSIONS The inter-regional and individual country disparities in COVID-19 vaccine hesitancy highlight the importance of designing an efficient plan for the delivery of interventions dynamically tailored to the local population.
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Affiliation(s)
- Li Ping Wong
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, China.
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Haridah Alias
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mahmoud Danaee
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jamil Ahmed
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Community Health Science, Muhammad Medical College, Mirpurkhas, Sindh, 69000, Pakistan
| | - Abhishek Lachyan
- Centre for Epidemiology and Evidence-Based Practice, Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
- World Health Organization National Polio Surveillance Project (NPSP) Unit Belgaum World Customs Organization, Hindu Nagar, Tilakwadi, Belgaum, Karnataka, 590006, India
| | - Carla Zi Cai
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Yulan Lin
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, China.
| | - Zhijian Hu
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, 350122, Fujian, China.
| | - Si Ying Tan
- Leadership Institute for Global Health Transformation, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore, 117549, Singapore
| | - Yixiao Lu
- Department of Public Health, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Guoxi Cai
- Department of Public Health, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Di Khanh Nguyen
- Department of Academic Affairs and Testing, Dong Nai Technology University, Dong Nai, Vietnam
| | - Farhana Nishat Seheli
- Institute of Epidemiology, Disease Control & Research (IEDCR), Mohakhali, Dhaka, 1212, Bangladesh
| | - Fatma Alhammadi
- Ministry of Health and Prevention (MOHAP), Sharjah, United Arab Emirates
| | - Milkar D Madhale
- Vijaya College of Nursing, Belgaum, Ayodhya Nagar, Belgaum, Karnataka, 590001, India
| | - Muditha Atapattu
- Department of Nursing, Faculty of Allied Health Sciences, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - Samira Mohajer
- Nursing and Midwifery Care Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gregory D Zimet
- Department of Pediatrics, School of Medicine, Indiana University, 410 W, 10th St., HS 1001, Indianapolis, IN, 46202, USA
| | - Qinjian Zhao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China
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26
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Sharma S, Dash PK, Sharma SK, Srivastava A, Kumar JS, Karothia BS, Chelvam KT, Singh S, Gupta A, Yadav RG, Yadav R, Greeshma TS, Kushwaha PK, Kumar RB, Nagar DP, Nandan M, Kumar S, Thavaselvam D, Dubey DK. Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Sci Rep 2021; 11:18126. [PMID: 34518554 PMCID: PMC8437943 DOI: 10.1038/s41598-021-95822-w] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/23/2021] [Indexed: 11/09/2022] Open
Abstract
COVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating SARS-CoV-2 strains in India will enable the scientific community to understand the emergence of new variants and their impact on human health. The first case of COVID-19 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of cases within next three months. More than 5000 COVID-19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh were analyzed during the nation -wide lockdown and unlock period. A total of 136 cases were found positive over a span of three months that included virus introduction to the region and its further spread. Whole genome sequences employing Oxford nanopore technology were generated for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh state of India. This period witnessed index cases with multiple travel histories responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were identified. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades including A2a, A4 and B. The cluster-wise segregation was observed, suggesting multiple introduction links and subsequent evolution of virus in the region. This is the first comprehensive whole genome sequence analysis from central India, which revealed the emergence and evolution of SARS-CoV-2 during thenation-wide lockdown and unlock.
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Affiliation(s)
- Shashi Sharma
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Paban Kumar Dash
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
| | - Sushil Kumar Sharma
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Ambuj Srivastava
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Jyoti S Kumar
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - B S Karothia
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - K T Chelvam
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Sandeep Singh
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Abhaydeep Gupta
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Ram Govind Yadav
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Ruchi Yadav
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - T S Greeshma
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Pramod Kumar Kushwaha
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Ravi Bhushan Kumar
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - D P Nagar
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Manvendra Nandan
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Subodh Kumar
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
| | - Duraipandian Thavaselvam
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Devendra Kumar Dubey
- COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
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27
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Sotoodeh Ghorbani S, Taherpour N, Bayat S, Ghajari H, Mohseni P, Hashemi Nazari SS. Epidemiologic characteristics of cases with reinfection, recurrence, and hospital readmission due to COVID-19: A systematic review and meta-analysis. J Med Virol 2021; 94:44-53. [PMID: 34411311 PMCID: PMC8427032 DOI: 10.1002/jmv.27281] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 01/05/2023]
Abstract
Recent studies reported that some recovered COVID‐19 patients have tested positive for virus nucleic acid again. A systematic search was performed in Web of Science, PubMed, Scopus, and Google Scholar up to March 6, 2021. The pooled estimation of reinfection, recurrence, and hospital readmission among recovered COVID‐19 patients was 3, 133, and 75 per 1000 patients, respectively. The overall estimation of reinfection among males compared to females was greater. The prevalence of recurrence in females compared to males was more common. Also, hospital readmission between sex groups was the same. There is uncertainty about long‐term immunity after SARS‐Cov‐2 infection. Thus, the possibility of reinfection and recurrence after recovery is not unexpected. In addition, there is a probability of hospital readmission due to adverse events of COVID‐19 after discharge. However, with mass vaccination of people and using the principles of prevention and appropriate management of the disease, frequent occurrence of the disease can be controlled. The pooled estimation of re‐infection rate among recovered COVID‐19 patients was 3 per 1000 patients. The pooled estimation of recurrence rate among recovered COVID‐19 patients was 133 per 1000 patients. Hospital readmission among recovered COVID‐19 patients was 75 per 1000 patients. The possibility of re‐infection, recurrence and hospital readmission after recovery is not unexpected. Thus, adherence to principles of prevention besides vaccination is essential.
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Affiliation(s)
- Sahar Sotoodeh Ghorbani
- Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Niloufar Taherpour
- Prevention of Cardiovascular Disease Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sahar Bayat
- Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadis Ghajari
- Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parisa Mohseni
- Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Saeed Hashemi Nazari
- Department of Epidemiology, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Prevention of Cardiovascular Disease Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Zimmerman PA, King CL, Ghannoum M, Bonomo RA, Procop GW. Molecular Diagnosis of SARS-CoV-2: Assessing and Interpreting Nucleic Acid and Antigen Tests. Pathog Immun 2021; 6:135-156. [PMID: 34405126 PMCID: PMC8360705 DOI: 10.20411/pai.v6i1.422] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
In this review, we summarize the current status of nucleic acid and antigen testing required for diagnosing SARS-CoV-2 infection and COVID-19 disease. Nucleic acid amplification (NAAT) and antigen-detection (Ag) tests occupy a critically important frontline of defense against SARS-CoV-2 in clinical and public health settings. In early stages of this outbreak, we observed that identifying the causative agent of a new illness of unknown origin was greatly accelerated by characterizing the nucleic acid signature of the novel coronavirus. Results from nucleic acid sequencing led to the development of highly sensitive RT-PCR testing for use in clinical settings and to informing best practices for patient care, and in public health settings to the development of strategies for protecting populations. As the current COVID-19 pandemic has evolved, we have seen how NAAT performance has been used to guide and optimize specimen collection, inform patient triage decisions, reveal unexpected clinical symptoms, clarify risks of transmission within patient care facilities, and guide appropriate treatment strategies. For public health settings during the earliest stages of the pandemic, NAATs served as the only tool available for studying the epidemiology of this new disease by identifying infected individuals, studying transmission patterns, modeling population impacts, and enabling disease control organizations and governments to make challenging disease mitigation recommendations to protect the expanding breadth of populations at risk. With time, the nucleic acid signature has provided the information necessary to understand SARS-CoV-2 protein expression for further development of antigen-based point-of-care (POC) diagnostic tests. The advent of massive parallel sequencing (ie, next generation sequencing) has afforded the characterization of this novel pathogen, informed the sequences best adapted for RT-PCR assays, guided vaccine production, and is currently used for tracking and monitoring SARS-CoV-2 variants.
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Affiliation(s)
- Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Christopher L King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Mahmoud Ghannoum
- Center for Medical Mycology and Integrated Microbiome Core, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio; Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio; and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, Ohio
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29
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Malladi S, Patel UR, Rajmani RS, Singh R, Pandey S, Kumar S, Khaleeq S, van Vuren PJ, Riddell S, Goldie S, Gayathri S, Chakraborty D, Kalita P, Pramanick I, Agarwal N, Reddy P, Girish N, Upadhyaya A, Khan MS, Kanjo K, Bhat M, Mani S, Bhattacharyya S, Siddiqui S, Tyagi A, Jha S, Pandey R, Tripathi S, Dutta S, McAuley AJ, Singanallur N, Vasan SS, Ringe RP, Varadarajan R. Immunogenicity and Protective Efficacy of a Highly Thermotolerant, Trimeric SARS-CoV-2 Receptor Binding Domain Derivative. ACS Infect Dis 2021; 7:2546-2564. [PMID: 34260218 PMCID: PMC8996237 DOI: 10.1021/acsinfecdis.1c00276] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 05/20/2021] [Indexed: 02/07/2023]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of ∼80-100 mg/L in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of up to 100 °C and were stable to long-term storage of over 4 weeks at 37 °C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were ∼3-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1, and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.
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Affiliation(s)
- Sameer
Kumar Malladi
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Unnatiben Rajeshbhai Patel
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Raju S. Rajmani
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Randhir Singh
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Suman Pandey
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Sahil Kumar
- Virology
Unit, Institute of Microbial Technology,
Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India
| | - Sara Khaleeq
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Petrus Jansen van Vuren
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Shane Riddell
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Sarah Goldie
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Savitha Gayathri
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Debajyoti Chakraborty
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Parismita Kalita
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Ishika Pramanick
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Nupur Agarwal
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Poorvi Reddy
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Nidhi Girish
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Aditya Upadhyaya
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Mohammad Suhail Khan
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Kawkab Kanjo
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Madhuraj Bhat
- Mynvax
Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India
| | - Shailendra Mani
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Gurugram-Faridabad
Expressway, Faridabad 121001, India
| | - Sankar Bhattacharyya
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Gurugram-Faridabad
Expressway, Faridabad 121001, India
| | - Samreen Siddiqui
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Akansha Tyagi
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Sujeet Jha
- Max Super
Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 1100017, India
| | - Rajesh Pandey
- Integrative
Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Shashank Tripathi
- Department
of Microbiology & Cell Biology, Indian
Institute of Science, Bengaluru 560012, India
- Centre
for Infectious Disease Research, Indian
Institute of Science, Bengaluru 560012, India
| | - Somnath Dutta
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
| | - Alexander J. McAuley
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Nagendrakumar
Balasubramanian Singanallur
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
| | - Seshadri S. Vasan
- Australian
Centre for Disease Preparedness (ACDP), Commonwealth Scientific and Industrial Research Organisation (CSIRO), 5 Portarlington Road, Geelong 3220, Victoria, Australia
- Department
of Health Sciences, University of York, York YO10 5DD, United Kingdom
| | - Rajesh P. Ringe
- Virology
Unit, Institute of Microbial Technology,
Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India
| | - Raghavan Varadarajan
- Molecular
Biophysics Unit (MBU), Indian Institute
of Science, Bengaluru 560012, India
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30
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Wang C, Zheng Y, Niu Z, Jiang X, Sun Q. The virological impacts of SARS-CoV-2 D614G mutation. J Mol Cell Biol 2021; 13:712-720. [PMID: 34289053 PMCID: PMC8344946 DOI: 10.1093/jmcb/mjab045] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/25/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/12/2022] Open
Abstract
The coronavirus diseases 2019 (COVID-19) caused by the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 has caused more than 140 million infections worldwide by the end of April 2021. As an enveloped single-stranded positive-sense RNA virus, SARS-CoV-2 underwent constant evolution that produced novel variants carrying mutation conferring fitness advantages. The current prevalent D614G variant, with glycine substituted for aspartic acid at position 614 in the spike glycoprotein, is one of such variants that became the main circulating strain worldwide in a short period of time. Over the past year, intensive studies from all over the world had defined the epidemiological characteristics of this highly contagious variant and revealed the underlying mechanisms. This review aims at presenting an overall picture of the impacts of D614G mutation on virus transmission, elucidating the underlying mechanisms of D614G in virus pathogenicity, and providing insights into the development of effective therapeutics.
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Affiliation(s)
- Chenxi Wang
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - You Zheng
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Zubiao Niu
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Xiaoyi Jiang
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
| | - Qiang Sun
- Laboratory of Cell Engineering, Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Science, 2020RU009, Beijing 100071, China
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31
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Jacob JJ, Vasudevan K, Pragasam AK, Gunasekaran K, Veeraraghavan B, Mutreja A. Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. mBio 2021; 12:e0118821. [PMID: 34281387 DOI: 10.1128/mBio.01188-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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] [Indexed: 01/17/2023] Open
Abstract
The currently ongoing COVID-19 pandemic caused by SARS-CoV-2 has accounted for millions of infections and deaths across the globe. Genome sequences of SARS-CoV-2 are being published daily in public databases and the availability of these genome data sets has allowed unprecedented access to the mutational patterns of SARS-CoV-2 evolution. We made use of the same genomic information for conducting phylogenetic analysis and identifying lineage-specific mutations. The catalogued lineage-defining mutations were analyzed for their stabilizing or destabilizing impact on viral proteins. We recorded persistence of D614G, S477N, A222V, and V1176F variants and a global expansion of the PANGOLIN variant B.1. In addition, a retention of Q57H (B.1.X), R203K/G204R (B.1.1.X), T85I (B.1.2-B.1.3), G15S+T428I (C.X), and I120F (D.X) variations was observed. Overall, we recorded a striking balance between stabilizing and destabilizing mutations, therefore leading to well-maintained protein structures. With selection pressures in the form of newly developed vaccines and therapeutics to mount in the coming months, the task of mapping viral mutations and recording their impact on key viral proteins should be crucial to preemptively catch any escape mechanism for which SARS-CoV-2 may evolve.
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32
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Riddell S, Goldie S, McAuley AJ, Kuiper MJ, Durr PA, Blasdell KR, Tachedjian M, Druce JD, Smith TRF, Broderick KE, Vasan SS. Live Virus Neutralisation of the 501Y.V1 and 501Y.V2 SARS-CoV-2 Variants following INO-4800 Vaccination of Ferrets. Front Immunol 2021; 12:694857. [PMID: 34248993 PMCID: PMC8269317 DOI: 10.3389/fimmu.2021.694857] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/08/2021] [Indexed: 11/13/2022] Open
Abstract
The ongoing COVID-19 pandemic has resulted in significant global morbidity and mortality on a scale similar to the influenza pandemic of 1918. Over the course of the last few months, a number of SARS-CoV-2 variants have been identified against which vaccine-induced immune responses may be less effective. These "variants-of-concern" have garnered significant attention in the media, with discussion around their impact on the future of the pandemic and the ability of leading COVID-19 vaccines to protect against them effectively. To address concerns about emerging SARS-CoV-2 variants affecting vaccine-induced immunity, we investigated the neutralisation of representative 'G614', '501Y.V1' and '501Y.V2' virus isolates using sera from ferrets that had received prime-boost doses of the DNA vaccine, INO-4800. Neutralisation titres against G614 and 501Y.V1 were comparable, but titres against the 501Y.V2 variant were approximately 4-fold lower, similar to results reported with other nucleic acid vaccines and supported by in silico biomolecular modelling. The results confirm that the vaccine-induced neutralising antibodies generated by INO-4800 remain effective against current variants-of-concern, albeit with lower neutralisation titres against 501Y.V2 similar to other leading nucleic acid-based vaccines.
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Affiliation(s)
- Shane Riddell
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Sarah Goldie
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Alexander J. McAuley
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Michael J. Kuiper
- Commonwealth Scientific and Industrial Research Organisation, Data61, Docklands, VIC, Australia
| | - Peter A. Durr
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kim R. Blasdell
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Mary Tachedjian
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Julian D. Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital and The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Trevor R. F. Smith
- Research & Development Centre, Inovio Pharmaceuticals, San Diego, CA, United States
| | - Kate E. Broderick
- Research & Development Centre, Inovio Pharmaceuticals, San Diego, CA, United States
| | - Seshadri S. Vasan
- Commonwealth Scientific and Industrial Research Organisation, Australian Centre for Disease Preparedness, Geelong, VIC, Australia
- Department of Health Sciences, University of York, York, United Kingdom
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33
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Dao MH, Phan LT, Cao TM, Luong QC, Pham HTT, Vu NHP, Khuu NV, Nguyen TV, Nguyen LT, Nguyen HT, Nguyen AH, Huynh LKT, Huynh TP, Nguyen QH, Truong HC, Nguyen HM, Trinh TX, Nguyen DT, Nguyen TB, Do HT, Pham QD, Nguyen TV. Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. J Med Virol 2021; 93:5660-5665. [PMID: 34042186 PMCID: PMC8242548 DOI: 10.1002/jmv.27103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 11/18/2022]
Abstract
Genome‐wide analysis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) strains is essential to better understand infectivity and virulence and to track coronavirus disease 2019 (COVID‐19) cases and outbreaks. We performed whole‐genome sequencing of 27 SARS‐CoV‐2 strains isolated between January 2020 and April 2020. A total of 54 mutations in different genomic regions was found. The D614G mutation, first detected in March 2020, was identified in 18 strains and was more likely associated with a lower cycle threshold (<25) in real‐time reverse‐transcription polymerase chain reaction diagnostic tests than the original D614 (prevalence ratio = 2.75; 95% confidence interval, 1.19–6.38). The integration of sequencing and epidemiological data suggests that SARS‐CoV‐2 transmission in both quarantine areas and in the community in Vietnam occur at the beginning of the epidemic although the country implemented strict quarantine quite early, with strict contact tracing, and testing. These findings provide insights into the nature of the epidemic, as well as shape strategies for COVID‐19 prevention and control in Vietnam.
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Affiliation(s)
- Manh H Dao
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Lan T Phan
- Directorial Board, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thang M Cao
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Quang C Luong
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hang T T Pham
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nhung H P Vu
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nghia V Khuu
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thinh V Nguyen
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Long T Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hieu T Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Anh H Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Loan Kim Thi Huynh
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thao P Huynh
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Quan H Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hieu C Truong
- Department for Disease Control and Prevention, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Dung T Nguyen
- Ho Chi Minh City Center for Diseases Control, Ho Chi Minh City, Vietnam
| | | | - Hung T Do
- Pasteur Institute of Nha Trang, Nha Trang, Vietnam
| | - Quang D Pham
- Planning Division, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam.,Training Center, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thuong V Nguyen
- Microbiology and Immunology Department, Pasteur Institute of Ho Chi Minh City, Ho Chi Minh City, Vietnam
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34
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Remington JM, McKay KT, Ferrell JB, Schneebeli ST, Li J. Enhanced sampling protocol to elucidate fusion peptide opening of SARS-CoV-2 spike protein. Biophys J 2021; 120:2848-2858. [PMID: 34087207 PMCID: PMC8169235 DOI: 10.1016/j.bpj.2021.05.022] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/14/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Large-scale conformational transitions in the spike protein S2 domain are required during host-cell infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although conventional molecular dynamics simulations have been extensively used to study therapeutic targets of SARS-CoV-2, it is still challenging to gain molecular insight into the key conformational changes because of the size of the spike protein and the long timescale required to capture these transitions. In this work, we have developed an efficient simulation protocol that leverages many short simulations, a dynamic selection algorithm, and Markov state models to interrogate the structural changes of the S2 domain. We discovered that the conformational flexibility of the dynamic region upstream of the fusion peptide in S2 is coupled to the proteolytic cleavage state of the spike protein. These results suggest that opening of the fusion peptide likely occurs on a submicrosecond timescale after cleavage at the S2' site. Building on the structural and dynamical information gained to date about S2 domain dynamics, we provide proof of principle that a small molecule bound to a seam neighboring the fusion peptide can slow the opening of the fusion peptide, leading to a new inhibition strategy for experiments to confirm. In aggregate, these results will aid the development of drug cocktails to inhibit infections caused by SARS-CoV-2 and other coronaviruses.
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Affiliation(s)
| | - Kyle T McKay
- Department of Chemistry, University of Vermont, Burlington, Vermont
| | | | | | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, Vermont.
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35
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Marsh GA, McAuley AJ, Au GG, Riddell S, Layton D, Singanallur NB, Layton R, Payne J, Durr PA, Bender H, Barr JA, Bingham J, Boyd V, Brown S, Bruce MP, Burkett K, Eastwood T, Edwards S, Gough T, Halpin K, Harper J, Holmes C, Horman WSJ, van Vuren PJ, Lowther S, Maynard K, McAuley KD, Neave MJ, Poole T, Rootes C, Rowe B, Soldani E, Stevens V, Stewart CR, Suen WW, Tachedjian M, Todd S, Trinidad L, Walter D, Watson N, Drew TW, Gilbert SC, Lambe T, Vasan SS. ChAdOx1 nCoV-19 (AZD1222) vaccine candidate significantly reduces SARS-CoV-2 shedding in ferrets. NPJ Vaccines 2021; 6:67. [PMID: 33972565 PMCID: PMC8110954 DOI: 10.1038/s41541-021-00315-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 01/12/2021] [Accepted: 03/12/2021] [Indexed: 01/05/2023] Open
Abstract
Vaccines against SARS-CoV-2 are likely to be critical in the management of the ongoing pandemic. A number of candidates are in Phase III human clinical trials, including ChAdOx1 nCoV-19 (AZD1222), a replication-deficient chimpanzee adenovirus-vectored vaccine candidate. In preclinical trials, the efficacy of ChAdOx1 nCoV-19 against SARS-CoV-2 challenge was evaluated in a ferret model of infection. Groups of ferrets received either prime-only or prime-boost administration of ChAdOx1 nCoV-19 via the intramuscular or intranasal route. All ChAdOx1 nCoV-19 administration combinations resulted in significant reductions in viral loads in nasal-wash and oral swab samples. No vaccine-associated adverse events were observed associated with the ChAdOx1 nCoV-19 candidate, with the data from this study suggesting it could be an effective and safe vaccine against COVID-19. Our study also indicates the potential for intranasal administration as a way to further improve the efficacy of this leading vaccine candidate.
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Affiliation(s)
- Glenn A Marsh
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Gough G Au
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Sarah Riddell
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Daniel Layton
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Rachel Layton
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jean Payne
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Peter A Durr
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Hannah Bender
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jennifer A Barr
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - John Bingham
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Victoria Boyd
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Sheree Brown
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Matthew P Bruce
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kathie Burkett
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Teresa Eastwood
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Sarah Edwards
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Tamara Gough
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kim Halpin
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Jenni Harper
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Clare Holmes
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - William S J Horman
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Suzanne Lowther
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kate Maynard
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Kristen D McAuley
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Matthew J Neave
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Timothy Poole
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Christina Rootes
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Brenton Rowe
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Elisha Soldani
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Vittoria Stevens
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Cameron R Stewart
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Willy W Suen
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Mary Tachedjian
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Shawn Todd
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Lee Trinidad
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Duane Walter
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Naomi Watson
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Trevor W Drew
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Sarah C Gilbert
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - S S Vasan
- CSIRO Australian Centre for Disease Preparedness, Geelong, VIC, Australia.
- Department of Health Sciences, University of York, York, UK.
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36
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Winkler MS, Skirecki T, Brunkhorst FM, Cajander S, Cavaillon JM, Ferrer R, Flohé SB, García-Salido A, Giamarellos-Bourboulis EJ, Girardis M, Kox M, Lachmann G, Martin-Loeches I, Netea MG, Spinetti T, Schefold JC, Torres A, Uhle F, Venet F, Weis S, Scherag A, Rubio I, Osuchowski MF. Bridging animal and clinical research during SARS-CoV-2 pandemic: A new-old challenge. EBioMedicine 2021; 66:103291. [PMID: 33813139 PMCID: PMC8016444 DOI: 10.1016/j.ebiom.2021.103291] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 12/19/2020] [Revised: 02/22/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
Many milestones in medical history rest on animal modeling of human diseases. The SARS-CoV-2 pandemic has evoked a tremendous investigative effort primarily centered on clinical studies. However, several animal SARS-CoV-2/COVID-19 models have been developed and pre-clinical findings aimed at supporting clinical evidence rapidly emerge. In this review, we characterize the existing animal models exposing their relevance and limitations as well as outline their utility in COVID-19 drug and vaccine development. Concurrently, we summarize the status of clinical trial research and discuss the novel tactics utilized in the largest multi-center trials aiming to accelerate generation of reliable results that may subsequently shape COVID-19 clinical treatment practices. We also highlight areas of improvement for animal studies in order to elevate their translational utility. In pandemics, to optimize the use of strained resources in a short time-frame, optimizing and strengthening the synergy between the preclinical and clinical domains is pivotal.
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Affiliation(s)
- Martin S Winkler
- Department of Anesthesiology, Emergency and Intensive Care Medicine, University of Göttingen, Göttingen, Robert-Koch-Str. 40, 37085 Göttingen, Germany
| | - Tomasz Skirecki
- Laboratory of Flow Cytometry, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Frank M Brunkhorst
- Dept. of Anesthesiology and Intensive Care Medicine & Center for Sepsis Control and Care (CSCC), Jena University Hospital-Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany; Center for Clinical Studies, Jena University Hospital, 07747 Jena, Germany
| | - Sara Cajander
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, Sweden
| | | | - Ricard Ferrer
- Intensive Care Department and Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron University Hospital, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, Barcelona, 08035, Spain; Centro de Investigación Biomedica En Red-Enfermedades Respiratorias (CibeRes, CB06/06/0028), Instituto de salud Carlos III (ISCIII), Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Stefanie B Flohé
- Department of Trauma, Hand, and Reconstructive Surgery, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Alberto García-Salido
- Pediatric Critical Care Unit, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | | | - Massimo Girardis
- Department of Anesthesia and Intensive Care, University Hospital of Modena, Italy
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Gunnar Lachmann
- Department of Anesthesiology and Operative Intensive Care Medicine (CCM, CVK), Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Ignacio Martin-Loeches
- Multidisciplinary Intensive Care Research Organization (MICRO), St. James's Hospital, James's St N, Ushers, Dublin, D03 VX82, Ireland
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thibaud Spinetti
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland
| | - Joerg C Schefold
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland
| | - Antoni Torres
- Pneumology Department, Respiratory Institute (ICR), Hospital Clinic of Barcelona - Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - University of Barcelona (UB), Spain
| | - Florian Uhle
- Department of Anesthesiology, Heidelberg University Hospital, Im Neuenheimer Feld 110, 69120 Heidelberg, Germany
| | - Fabienne Venet
- Hospices Civils de Lyon, Immunology Laboratory, Edouard Herriot Hospital, 5 Place d'Arsonval, 69003 Lyon, France; EA 7426 "Pathophysiology of Injury-Induced Immunosuppression - PI3", Université Claude Bernard Lyon 1/bioMérieux/Hospices Civils de Lyon, Edouard Herriot Hospital, 5 Place d'Arsonval, 69003 Lyon, France
| | - Sebastian Weis
- Dept. of Anesthesiology and Intensive Care Medicine & Center for Sepsis Control and Care (CSCC), Jena University Hospital-Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany; Institute for Infectious Disease and Infection Control, Jena University Hospital-Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany
| | - André Scherag
- Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital-Friedrich Schiller University, Bachstrasse 18, 07743 Jena, Germany
| | - Ignacio Rubio
- Dept. of Anesthesiology and Intensive Care Medicine & Center for Sepsis Control and Care (CSCC), Jena University Hospital-Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany
| | - Marcin F Osuchowski
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in the AUVA Research Center, Donaueschingenstrasse 13, 1200, Vienna, Austria.
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37
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Jakhmola S, Indari O, Kashyap D, Varshney N, Das A, Manivannan E, Jha HC. Mutational analysis of structural proteins of SARS-CoV-2. Heliyon 2021; 7:e06572. [PMID: 33778179 PMCID: PMC7980187 DOI: 10.1016/j.heliyon.2021.e06572] [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: 10/21/2020] [Revised: 01/16/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 transmissibility is higher than that of other human coronaviruses; therefore, it poses a threat to the populated communities. We investigated mutations among envelope (E), membrane (M), and spike (S) proteins from different isolates of SARS-CoV-2 and plausible signaling influenced by mutated virus in a host. We procured updated protein sequences from the NCBI virus database. Mutations were analyzed in the retrieved sequences of the viral proteins through multiple sequence alignment. Additionally, the data was subjected to ScanPROSITE to analyse if the mutations generated a relevant sequence for host signaling. Unique mutations in E, M, and S proteins resulted in modification sites like PKC phosphorylation and N-myristoylation sites. Based on structural analysis, our study revealed that the D614G mutation in the S protein diminished the interaction with T859 and K854 of adjacent chains. Moreover, the S protein of SARS-CoV-2 consists of an Arg-Gly-Asp (RGD) tripeptide sequence, which could potentially interact with various members of integrin family receptors. RGD sequence in S protein might aid in the initial virus attachment. We speculated crucial host pathways which the mutated isolates of SARS-CoV-2 may alter like PKC, Src, and integrin mediated signaling pathways. PKC signaling is known to influence the caveosome/raft pathway which is critical for virus entry. Additionally, the myristoylated proteins might activate NF-κB, a master molecule of inflammation. Thus the mutations may contribute to the disease pathogenesis and distinct lung pathophysiological changes. Further the frequently occurring mutations in the protein can be studied for possible therapeutic interventions.
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Affiliation(s)
- Shweta Jakhmola
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Omkar Indari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Ayan Das
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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38
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Jackson CB, Zhang L, Farzan M, Choe H. Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Biochem Biophys Res Commun 2021; 538:108-115. [PMID: 33220921 PMCID: PMC7664360 DOI: 10.1016/j.bbrc.2020.11.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus which binds its cellular receptor angiotensin-converting enzyme 2 (ACE2) and enters hosts cells through the action of its spike (S) glycoprotein displayed on the surface of the virion. Compared to the reference strain of SARS-CoV-2, the majority of currently circulating isolates possess an S protein variant characterized by an aspartic acid-to-glycine substitution at amino acid position 614 (D614G). Residue 614 lies outside the receptor binding domain (RBD) and the mutation does not alter the affinity of monomeric S protein for ACE2. However, S(G614), compared to S(D614), mediates more efficient ACE2-mediated transduction of cells by S-pseudotyped vectors and more efficient infection of cells and animals by live SARS-CoV-2. This review summarizes and synthesizes the epidemiological and functional observations of the D614G spike mutation, with focus on the biochemical and cell-biological impact of this mutation and its consequences for S protein function. We further discuss the significance of these recent findings in the context of the current global pandemic.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
| | - Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
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39
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Bauer DC, Metke-Jimenez A, Maurer-Stroh S, Tiruvayipati S, Wilson LOW, Jain Y, Perrin A, Ebrill K, Hansen DP, Vasan SS. Interoperable medical data: The missing link for understanding COVID-19. Transbound Emerg Dis 2021; 68:1753-1760. [PMID: 33095970 PMCID: PMC8359419 DOI: 10.1111/tbed.13892] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/11/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
Being able to link clinical outcomes to SARS‐CoV‐2 virus strains is a critical component of understanding COVID‐19. Here, we discuss how current processes hamper sustainable data collection to enable meaningful analysis and insights. Following the ‘Fast Healthcare Interoperable Resource’ (FHIR) implementation guide, we introduce an ontology‐based standard questionnaire to overcome these shortcomings and describe patient 'journeys' in coordination with the World Health Organization's recommendations. We identify steps in the clinical health data acquisition cycle and workflows that likely have the biggest impact in the data‐driven understanding of this virus. Specifically, we recommend detailed symptoms and medical history using the FHIR standards. We have taken the first steps towards this by making patient status mandatory in GISAID (‘Global Initiative on Sharing All Influenza Data’), immediately resulting in a measurable increase in the fraction of cases with useful patient information. The main remaining limitation is the lack of controlled vocabulary or a medical ontology.
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Affiliation(s)
- Denis C Bauer
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia, Australia.,Department of Biomedical Sciences, Macquarie University, Macquarie Park, NSW, Australia
| | - Alejandro Metke-Jimenez
- Commonwealth Scientific and Industrial Research Organisation, Australian e-Health Research Centre, Herston, QLD, Australia
| | - Sebastian Maurer-Stroh
- Agency for Science Technology and Research, Bioinformatics Institute, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore, Singapore.,Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany
| | - Suma Tiruvayipati
- Global Initiative on Sharing All Influenza Data (GISAID), Munich, Germany.,Infectious Diseases Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Bacterial Genomics Laboratory, Genome Institute of Singapore, Singapore, Singapore
| | - Laurence O W Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia, Australia
| | - Yatish Jain
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia, Australia
| | - Amandine Perrin
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France.,Microbial Evolutionary Genomics, Institut Pasteur, UMR 3525 CNRS, Paris, France.,Collège doctoral, Sorbonne Université, Paris, France
| | - Kate Ebrill
- Commonwealth Scientific and Industrial Research Organisation, Australian e-Health Research Centre, Herston, QLD, Australia
| | - David P Hansen
- Commonwealth Scientific and Industrial Research Organisation, Australian e-Health Research Centre, Herston, QLD, Australia
| | - Seshadri S Vasan
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia.,Department of Health Sciences, University of York, York, UK
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40
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Everett HE, Lean FZX, Byrne AMP, van Diemen PM, Rhodes S, James J, Mollett B, Coward VJ, Skinner P, Warren CJ, Bewley KR, Watson S, Hurley S, Ryan KA, Hall Y, Simmons H, Núñez A, Carroll MW, Brown IH, Brookes SM. Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Viruses 2021; 13:113. [PMID: 33467732 PMCID: PMC7830262 DOI: 10.3390/v13010113] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [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: 12/16/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 02/07/2023] Open
Abstract
Ferrets were experimentally inoculated with SARS-CoV-2 (severe acute respiratory syndrome (SARS)-related coronavirus 2) to assess infection dynamics and host response. During the resulting subclinical infection, viral RNA was monitored between 2 and 21 days post-inoculation (dpi), and reached a peak in the upper respiratory cavity between 4 and 6 dpi. Viral genomic sequence analysis in samples from three animals identified the Y453F nucleotide substitution relative to the inoculum. Viral RNA was also detected in environmental samples, specifically in swabs of ferret fur. Microscopy analysis revealed viral protein and RNA in upper respiratory tract tissues, notably in cells of the respiratory and olfactory mucosae of the nasal turbinates, including olfactory neuronal cells. Antibody responses to the spike and nucleoprotein were detected from 21 dpi, but virus-neutralizing activity was low. A second intranasal inoculation (re-exposure) of two ferrets after a 17-day interval did not produce re-initiation of viral RNA shedding, but did amplify the humoral response in one animal. Therefore, ferrets can be experimentally infected with SARS-CoV-2 to model human asymptomatic infection.
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Affiliation(s)
- Helen E. Everett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Fabian Z. X. Lean
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alexander M. P. Byrne
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Pauline M. van Diemen
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Shelley Rhodes
- Bacteriology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK;
| | - Joe James
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Benjamin Mollett
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Vivien J. Coward
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Paul Skinner
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Caroline J. Warren
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Kevin R. Bewley
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Samantha Watson
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Shellene Hurley
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Kathryn A. Ryan
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Yper Hall
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
| | - Hugh Simmons
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Alejandro Núñez
- Pathology and Animal Sciences Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (F.Z.X.L.); (S.W.); (S.H.); (H.S.); (A.N.)
| | - Miles W. Carroll
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, Wiltshire SP4 0JG, UK; (K.R.B.); (K.A.R.); (Y.H.); (M.W.C.)
- Nuffield Department of Medicine, Oxford University, Oxford OX1 3SY, UK
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
| | - Sharon M. Brookes
- Virology Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (P.M.v.D.); (J.J.); (B.M.); (V.J.C.); (P.S.); (C.J.W.); (I.H.B.); (S.M.B.)
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