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Tolksdorf B, Heinze J, Niemeyer D, Röhrs V, Berg J, Drosten C, Kurreck J. Development of a highly stable, active small interfering RNA with broad activity against SARS-CoV viruses. Antiviral Res 2024; 226:105879. [PMID: 38599550 DOI: 10.1016/j.antiviral.2024.105879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Treatment options for COVID-19 remain limited. Here, we report the optimization of an siRNA targeting the highly conserved leader region of SARS-CoV-2. The siRNA was rendered nuclease resistant by the introduction of modified nucleotides without loss of activity. Importantly, the siRNA also retained its inhibitory activity against the emerged omicron sublineage variant BA.2, which occurred after the siRNA was designed and is resistant to other antiviral agents such as antibodies. In addition, we show that a second highly active siRNA designed against the viral 5'-UTR can be applied as a rescue molecule, to minimize the spread of escape mutations. We therefore consider our siRNA-based molecules to be promising broadly active candidates for the treatment of current and future SARS-CoV-2 variants.
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Affiliation(s)
- Beatrice Tolksdorf
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Julian Heinze
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Daniela Niemeyer
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Viola Röhrs
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Johanna Berg
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany
| | - Christian Drosten
- German Center for Infection Research (DZIF), Charitéplatz 1, 10117, Berlin, Germany; Institute of Virology, Charité-Universitätsmedizin Berlin, 10117, Germany
| | - Jens Kurreck
- Chair of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Berlin, 10623, Germany.
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Barbosa AN, Chebabo A, Starling C, Pérez C, Cunha CA, de Luna D, Nunes EP, Zambrano G, Ferreira JC, Croda J, Falavigna M, Gomes-da-Silva MM, Thormann M, Cimerman S, Parahiba SM, Tanni S, Bernardo WM, Rodriguez-Morales AJ. Pan-American Guidelines for the treatment of SARS-CoV-2/COVID-19: a joint evidence-based guideline of the Brazilian Society of Infectious Diseases (SBI) and the Pan-American Association of Infectious Diseases (API). Ann Clin Microbiol Antimicrob 2023; 22:67. [PMID: 37550690 PMCID: PMC10408214 DOI: 10.1186/s12941-023-00623-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/19/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Since the beginning of the COVID-19 pandemic, therapeutic options for treating COVID-19 have been investigated at different stages of clinical manifestations. Considering the particular impact of COVID-19 in the Americas, this document aims to present recommendations for the pharmacological treatment of COVID-19 specific to this population. METHODS Fifteen experts, members of the Brazilian Society of Infectious Diseases (SBI) and the Pan-American Association of Infectious Diseases (API) make up the panel responsible for developing this guideline. Questions were formulated regarding prophylaxis and treatment of COVID-19 in outpatient and inpatient settings. The outcomes considered in decision-making were mortality, hospitalisation, need for mechanical ventilation, symptomatic COVID-19 episodes, and adverse events. In addition, a systematic review of randomised controlled trials was conducted. The quality of evidence assessment and guideline development process followed the GRADE system. RESULTS Nine technologies were evaluated, and ten recommendations were made, including the use of tixagevimab + cilgavimab in the prophylaxis of COVID-19, tixagevimab + cilgavimab, molnupiravir, nirmatrelvir + ritonavir, and remdesivir in the treatment of outpatients, and remdesivir, baricitinib, and tocilizumab in the treatment of hospitalised patients with severe COVID-19. The use of hydroxychloroquine or chloroquine and ivermectin was discouraged. CONCLUSION This guideline provides recommendations for treating patients in the Americas following the principles of evidence-based medicine. The recommendations present a set of drugs that have proven effective in the prophylaxis and treatment of COVID-19, emphasising the strong recommendation for the use of nirmatrelvir/ritonavir in outpatients as the lack of benefit from the use of hydroxychloroquine and ivermectin.
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Affiliation(s)
- Alexandre Naime Barbosa
- Infectious Diseases Department - Botucatu School of Medicine - UNESP, Av. Prof. Mário R. G. Montenegro, s/n, Botucatu, SP, CEP 18.618-687, Brazil.
- Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubiao Jr, s/n, Botucatu, SP, CEP 18618-970, Brazil.
| | - Alberto Chebabo
- Universidade Federal do Rio de Janeiro, Avenida Professor Rodolpho Paulo Rocco, 255, 50. Andar, Rio de Janeiro, RJ, CEP 21941-913, Brazil
- Brazilian Society for Infectious Diseases, Rua Teixeira da Silva, 660, São Paulo, SP, CEP 04002-033, Brazil
| | - Carlos Starling
- Sociedade Mineira de Infectologia - SMI, Avenida João Pinheiro, 161, Belo Horizonte, MG, CEP 30130-180, Brazil
| | - Clevy Pérez
- Universidad Autónoma de Santo Domingo (UASD), Avenida Simón Bolívar, 902, Santo Domingo, 10108, República Dominicana
| | - Clóvis Arns Cunha
- Brazilian Society for Infectious Diseases, Rua Teixeira da Silva, 660, São Paulo, SP, CEP 04002-033, Brazil
- Universidade Federal do Paraná, Rua XV de Novembro, 1299, Curitiba, PR, CEP 80060-000, Brazil
| | - David de Luna
- Comisión Nacional de Arbitraje Médico, C Mitla, 250, Ciudad de México, 03020, México
| | - Estevão Portela Nunes
- Instituto Nacional de Infectologia (INI), Fiocruz, Avenida Brasil, 4365, Rio de Janeiro, RJ, CEP 21040-360, Brazil
| | - Gabriela Zambrano
- Faculty of Medicine, Department of Infectious Diseases, Universidad Central del Ecuador, Quito, Ecuador
- Pontificia Universidad Católica del Ecuador, Facultad de Medicina, Posgrado de Medicina Interna, Quito, Ecuador
| | - Juliana Carvalho Ferreira
- Divisão de Pneumologia, Instituto do Coração, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Universidade de São Paulo, Avenida Dr. Enéas Carvalho de Aguiar, 44, São Paulo, SP, CEP 05403-900, Brazil
- Intensive Care Unit, AC Camargo Cancer Center, Rua Prof. Antônio Prudente, 211, São Paulo, SP, CEP 01509-001, Brazil
| | - Julio Croda
- Oswaldo Cruz Foundation, Avenida Costa e Silva, s/n, Cidade Universitária, Campo Grande, MS, CEP 79070-900, Brazil
| | - Maicon Falavigna
- HTAnalyze Consulting and Training, Rua João Abbott, 109, Porto Alegre, RS, CEP 90460-150, Brazil
| | - Monica Maria Gomes-da-Silva
- Infectious Disease Control Service, Clinical Hospital, Universidade Federal Do Paraná, Rua General Carneiro, 181, Curitiba, PR, CEP 80060-900, Brazil
| | - Monica Thormann
- Hospital Salvador Bienvenido Gautier, Calle Alexander Fleming, 177, Santo Domingo, 10514, Dominican Republic
| | - Sergio Cimerman
- Brazilian Society for Infectious Diseases, Rua Teixeira da Silva, 660, São Paulo, SP, CEP 04002-033, Brazil
- Institute of Infectious Diseases Emilio Ribas, Avenida Dr. Arnaldo, 165, São Paulo, SP, CEP 05402-000, Brazil
| | - Suena Medeiros Parahiba
- HTAnalyze Consulting and Training, Rua João Abbott, 109, Porto Alegre, RS, CEP 90460-150, Brazil
| | - Suzana Tanni
- Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubiao Jr, s/n, Botucatu, SP, CEP 18618-970, Brazil
| | - Wanderley Marques Bernardo
- Medical Education Development Center (CEDEM) of Medical Faculty of São Paulo University (FMUSP), São Paulo, SP, Brazil
| | - Alfonso J Rodriguez-Morales
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de Las Américas-Institución Universitaria Visión de Las Américas, 660003, Pereira, Risaralda, Colombia.
- Clinical Epidemiology and Biostatistics, Faculty of Health Sciences, Universidad Científica del Sur, Lima, 4861, Peru.
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, P.O. Box 36, Beirut, Lebanon.
- Latin American Network of Coronavirus Disease 2019 - COVID-19 Research (LANCOVID-19), Pereira, Risaralda, Colombia.
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Silva LM, Riani LR, Leite JB, de Assis Chagas JM, Fernandes LS, Fochat RC, Perches CGP, Nascimento TC, Jaeger LH, Silvério MS, dos Santos Pereira-Júnior O, Pittella F. The Influence of the Omicron Variant on RNA Extraction and RT-qPCR Detection of SARS-CoV-2 in a Laboratory in Brazil. Viruses 2023; 15:1690. [PMID: 37632032 PMCID: PMC10458054 DOI: 10.3390/v15081690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This characteristic increases the viscosity of clinical samples collected for diagnosis. Coinciding with the arrival of the Omicron variant, we observed a failure in control gene expression in our laboratory. In this report, we have optimized a rapid nucleic acid extraction step to restore gene expression and detect the presence of the SARS-CoV-2 virus. We reevaluated 3000 samples, compared variant types occurring in different time periods, and confirmed that the presence of the Omicron variant was responsible for changes observed in the characteristics of these clinical samples. For samples with large amounts of mucus, such as those containing the Omicron variant, a modification to the nucleic acid extraction step was sufficient to restore the quality of RT-qPCR results.
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Affiliation(s)
- Lívia Mara Silva
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Lorena Rodrigues Riani
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Juliana Brovini Leite
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Jessica Mara de Assis Chagas
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Laura Silva Fernandes
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Romário Costa Fochat
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Carmen Gomide Pinto Perches
- Hospital Universitário, Universidade Federal de Juiz de Fora, Av. Eugênio do Nascimento, s/n, Juiz de Fora 36038-330, MG, Brazil;
| | - Thiago César Nascimento
- Faculdade de Enfermagem, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil;
| | - Lauren Hubert Jaeger
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Marcelo Silva Silvério
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Olavo dos Santos Pereira-Júnior
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Frederico Pittella
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
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Anand U, Pal T, Zanoletti A, Sundaramurthy S, Varjani S, Rajapaksha AU, Barceló D, Bontempi E. The spread of the omicron variant: Identification of knowledge gaps, virus diffusion modelling, and future research needs. Environ Res 2023; 225:115612. [PMID: 36871942 PMCID: PMC9985523 DOI: 10.1016/j.envres.2023.115612] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/11/2023]
Abstract
The World Health Organization (WHO) recognised variant B.1.1.529 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a variant of concern, termed "Omicron", on November 26, 2021. Its diffusion was attributed to its several mutations, which allow promoting its ability to diffuse worldwide and its capability in immune evasion. As a consequence, some additional serious threats to public health posed the risk to undermine the global efforts made in the last two years to control the pandemic. In the past, several works were devoted to discussing a possible contribution of air pollution to the SARS-CoV-2 spread. However, to the best of the authors' knowledge, there are still no works dealing with the Omicron variant diffusion mechanisms. This work represents a snapshot of what we know right now, in the frame of an analysis of the Omicron variant spread. The paper proposes the use of a single indicator, commercial trade data, to model the virus spread. It is proposed as a surrogate of the interactions occurring between humans (the virus transmission mechanism due to human-to-human contacts) and could be considered for other diseases. It allows also to explain the unexpected increase in infection cases in China, detected at beginning of 2023. The air quality data are also analyzed to evaluate for the first time the role of air particulate matter (PM) as a carrier of the Omicron variant diffusion. Due to emerging concerns associated with other viruses (such as smallpox-like virus diffusion in Europe and America), the proposed approach seems to be promising to model the virus spreading.
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Affiliation(s)
- Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Tarun Pal
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Alessandra Zanoletti
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123, Brescia, Italy
| | - Suresh Sundaramurthy
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, 462003, Madhya Pradesh, India
| | - Sunita Varjani
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248007, Uttarakhand, India
| | - Anushka Upamali Rajapaksha
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO, 10250, Sri Lanka; Instrument Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA-CERCA), H2O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, Girona, 17003, Spain; Water and Soil Quality Research Group, Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), JordiGirona, 1826, Barcelona, 08034, Spain
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123, Brescia, Italy.
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J. Rodriguez-Morales A, Katterine Bonilla-Aldana D. Introductory Chapter: Lessons from SARS-CoV-2/COVID-19 after Two Years of Pandemic. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.108769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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Hillary VE, Ceasar SA. An update on COVID-19: SARS-CoV-2 variants, antiviral drugs, and vaccines. Heliyon 2023; 9:e13952. [PMID: 36855648 PMCID: PMC9946785 DOI: 10.1016/j.heliyon.2023.e13952] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious and pathogenic virus that first appeared in late December 2019. This SARS-CoV-2 causes an infection of an acute respiratory disease called "coronavirus infectious disease-2019 (COVID-19). The World Health Organization (WHO) declared this SARS-CoV-2 outbreak a great pandemic on March 11, 2020. As of January 31, 2023, SARS-CoV-2 recorded more than 67 million cases and over 6 million deaths. Recently, novel mutated variants of SARS-CoV are also creating a serious health concern worldwide, and the future novel variant is still mysterious. As infection cases of SARS-CoV-2 are increasing daily, scientists are trying to combat the disease using numerous antiviral drugs and vaccines against SARS-CoV-2. To our knowledge, this is the first comprehensive review that summarized the dynamic nature of SARS-CoV-2 transmission, SARS-CoV-2 variants (a variant of concern and variant of interest), antiviral drugs and vaccines utilized against SARS-CoV-2 at a glance. Hopefully, this review will enable the researcher to gain knowledge on SARS-CoV-2 variants and vaccines, which will also pave the way to identify efficient novel vaccines against forthcoming SARS-CoV-2 strains.
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Key Words
- ACE2, Angiotensin-converting enzyme 2
- Antiviral drugs
- COVID-19
- COVID-19, Coronavirus infectious disease-2019
- EUA, Emergency Use Authorization
- FDA, Food and Drug Administration
- NIH, National Institutes of Health
- RBD, Receptor-binding domain
- SARS-CoV-2
- SARS-CoV-2 variants
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- VOC, Variants of Concern
- VOI, Variants of Interests
- Vaccines
- WHO, World Health Organization
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Affiliation(s)
- Varghese Edwin Hillary
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683 104, Kerala, India
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Mohseni Afshar Z, Tavakoli Pirzaman A, Karim B, Rahimipour Anaraki S, Hosseinzadeh R, Sanjari Pireivatlou E, Babazadeh A, Hosseinzadeh D, Miri SR, Sio TT, Sullman MJM, Barary M, Ebrahimpour S. SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13. [PMID: 36766664 DOI: 10.3390/diagnostics13030559] [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: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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Palasio RGS, Lorenz C, Lucas PCDC, Nielsen L, Masuda ET, Trevisan CM, Cortez AL, Monteiro PDCM, Simões CS, Ferreira PM, Pellini ACG, Yu ALF, Carvalhanas TRM. Spatial, spatio-temporal, and origin-destination flow analyses of patients with severe acute respiratory syndrome hospitalized for COVID-19 in Southeastern Brazil, 2020-2021. Rev Inst Med Trop Sao Paulo 2023; 65:e6. [PMID: 36651467 PMCID: PMC9870244 DOI: 10.1590/s1678-9946202365006] [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: 09/20/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023] Open
Abstract
Brazil experienced one of the fastest increasing numbers of coronavirus disease (COVID-19) cases worldwide. The Sao Paulo State (SPS) reported a high incidence, particularly in Sao Paulo municipality. This study aimed to identify clusters of incidence and mortality of hospitalized patients with severe acute respiratory syndrome for COVID-19 in the SPS, in 2020-2021, and describe the origin flow pattern of the cases. Cases and mortality risk area clusters were identified through different analyses (spatial clusters, spatio-temporal clusters, and spatial variation in temporal trends) by weighting areas. Ripley's K12-function verified the spatial dependence between the cases and infrastructure. There were 517,935 reported cases, with 152,128 cases resulting in death. Of the 470,441 patients hospitalized and residing in the SPS, 357,526 remained in the original municipality, while 112,915 did not. Cases and death clusters were identified in the Sao Paulo metropolitan region (SPMR) and Baixada Santista region in the first study period, and in the SPMR and the Campinas, Sao Jose do Rio Preto, Barretos, and Sorocaba municipalities during the second period. We highlight the priority areas for control and surveillance actions for COVID-19, which could lead to better outcomes in future outbreaks.
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Affiliation(s)
- Raquel Gardini Sanches Palasio
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Camila Lorenz
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Pamella Cristina de Carvalho Lucas
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Lucca Nielsen
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Eliana Tiemi Masuda
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Camila Martins Trevisan
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - André Lazzeri Cortez
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Pedro de Campos Mello Monteiro
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Caroline Salomão Simões
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Patrícia Marques Ferreira
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Alessandra Cristina Guedes Pellini
- Universidade Nove de Julho, Faculdade de Medicina, Programa de Pós-Graduação em Cidades Inteligentes e Sustentáveis. São Paulo, São Paulo, Brazil
| | - Ana Lucia Frugis Yu
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
| | - Telma Regina Marques Carvalhanas
- Secretaria de Saúde do Estado de São Paulo, Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica “Prof. Alexandre Vranjac”, Divisão de Doenças de Transmissão Respiratória, São Paulo, São Paulo, Brazil
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9
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Samanta A, Alam SSM, Ali S, Hoque M. Evaluating the transmission feasibility of SARS-CoV-2 Omicron (B.1.1.529) variant to 143 mammalian hosts: insights from S protein RBD and host ACE2 interaction studies. Funct Integr Genomics 2023; 23:36. [PMID: 36631570 DOI: 10.1007/s10142-023-00962-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023]
Abstract
In comparison to previously known severe respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, the newly emerged Omicron (B.1.1.529) variant shows higher infectivity in humans. Exceptionally high infectivity of this variant raises concern of its possible transmission via other intermediate hosts. The SARS-CoV-2 infectivity is established via the association of spike (S) protein receptor binding domain (RBD) with host angiotensin I converting enzyme 2 (hACE2) receptor. In the course of this study, we investigated the interaction between Omicron S protein RBD with the ACE2 receptor of 143 mammalian hosts including human by protein-protein interaction analysis. The goal of this study was to forecast the likelihood that the virus may infect other mammalian species that coexist with or are close to humans in the household, rural, agricultural, or zoological environments. The Omicron RBD was found to interact with higher binding affinity with the ACE2 receptor of 122 mammalian hosts via different amino acid residues from the human ACE2 (hACE2). The rat (Rattus rattus) ACE2 was found to show the strongest interaction with Omicron RBD with a binding affinity of -1393.6 kcal/mol. These distinct strong binding affinity of RBD of Omicron with host ACE2 indicates a greater potential of new host transmissibility and infection via intermediate hosts. Though expected but the phylogenetic position of the mammalian species may not dictate the Omicron RBD binding to the host ACE2 receptor suggesting an involvement of multiple factors in guiding host divergence of the variant.
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10
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Ning B, Chandra S, Rosen J, Multala E, Argrave M, Pierson L, Trinh I, Simone B, Escarra MD, Drury S, Zwezdaryk KJ, Norton E, Lyon CJ, Hu T. Evaluation of SARS-CoV-2-Specific T-Cell Activation with a Rapid On-Chip IGRA. ACS Nano 2023; 17:1206-1216. [PMID: 36595218 PMCID: PMC9878992 DOI: 10.1021/acsnano.2c09018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Interferon-gamma release assays (IGRAs) that measure pathogen-specific T-cell response rates can provide a more reliable estimate of protection than specific antibody levels but have limited potential for widespread use due to their workflow, personnel, and instrumentation demands. The major vaccines for SARS-CoV-2 have demonstrated substantial efficacy against all of its current variants, but approaches are needed to determine how these vaccines will perform against future variants, as they arise, to inform vaccine and public health policies. Here we describe a rapid, sensitive, nanolayer polylysine-integrated microfluidic chip IGRA read by a fluorescent microscope that has a 5 h sample-to-answer time and uses ∼25 μL of a fingerstick whole blood sample. Results from this assay correlated with those of a comparable clinical IGRA when used to evaluate the T-cell response to SARS-CoV-2 peptides in a population of vaccinated and/or infected individuals. Notably, this streamlined and inexpensive assay is suitable for high-throughput analyses in resource-limited settings for other infectious diseases.
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Affiliation(s)
- Bo Ning
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Sutapa Chandra
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Juniper Rosen
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Evan Multala
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Melvin Argrave
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Lane Pierson
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Ivy Trinh
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Brittany Simone
- Department
of Physics and Engineering Physics, Tulane
University, New Orleans, Louisiana 70118, United States
| | - Matthew David Escarra
- Department
of Physics and Engineering Physics, Tulane
University, New Orleans, Louisiana 70118, United States
| | - Stacy Drury
- Department
of Psychiatry, Tulane University, New Orleans, Louisiana 70112, United States
- Tulane
Brain
Institute, Tulane University, New Orleans, Louisiana 70112, United States
| | - Kevin J. Zwezdaryk
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Elizabeth Norton
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Christopher J. Lyon
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Tony Hu
- Center
for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
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11
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Puenpa J, Rattanakomol P, Saengdao N, Chansaenroj J, Yorsaeng R, Suwannakarn K, Thanasitthichai S, Vongpunsawad S, Poovorawan Y. Molecular characterisation and tracking of severe acute respiratory syndrome coronavirus 2 in Thailand, 2020-2022. Arch Virol 2023; 168:26. [PMID: 36593392 PMCID: PMC9807426 DOI: 10.1007/s00705-022-05666-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/30/2022] [Indexed: 01/04/2023]
Abstract
The global COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in China in December 2019. To date, there have been approximately 3.4 million reported cases of COVID-19 and over 24,000 deaths in Thailand. In this study, we investigated the molecular characteristics and evolution of SARS-CoV-2 in Thailand from 2020 to 2022. Two hundred sixty-eight SARS-CoV-2 isolates, collected mostly in Bangkok from COVID-19 patients, were characterised by partial genome sequencing. Moreover, the viruses in 5,627 positive SARS-CoV-2 samples were identified as viral variants - B.1.1.7 (Alpha), B.1.617.2 (Delta), B.1.1.529 (Omicron/BA.1), or B.1.1.529 (Omicron/BA.2) - by multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. The results revealed that B.1.36.16 caused the predominant outbreak in the second wave (December 2020-January 2021), B.1.1.7 (Alpha) in the third wave (April-June 2021), B.1.617.2 (Delta) in the fourth wave (July-December 2021), and B.1.1.529 (Omicron) in the fifth wave (January-March 2022). The evolutionary rate of the viral genome was 2.60 × 10-3 (95% highest posterior density [HPD], 1.72 × 10-3 to 3.62 × 10-3) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants with the potential to cause new COVID-19 outbreaks.
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Affiliation(s)
- Jiratchaya Puenpa
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patthaya Rattanakomol
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nutsada Saengdao
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.416009.aDepartment of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jira Chansaenroj
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ritthideach Yorsaeng
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kamol Suwannakarn
- grid.416009.aDepartment of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Somchai Thanasitthichai
- grid.415836.d0000 0004 0576 2573Institute of Medical Research and Technology Assessment, Ministry of Public Health, Bangkok, Thailand
| | - Sompong Vongpunsawad
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.512985.2FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok, Thailand
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Samanta A, Ahamed A, Alam SSM, Ali S, Shahnawaz Khan M, Al-Amri AM, Tabrez S, Hoque M. Non-synonymous Single Nucleotide Polymorphisms in Human ACE2 Gene May Affect the Infectivity of SARS-CoV-2 Omicron Subvariants. Curr Pharm Des 2023; 29:2891-2901. [PMID: 38018194 DOI: 10.2174/0113816128275739231106055502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), which first appeared in December 2019. Angiotensin I converting enzyme 2 (ACE2) receptor, present on the host cells, interacts with the receptor binding domain (RBD) of spike (S) protein of SARS-CoV-2 and facilitates the viral entry into host cells. METHODS Non-synonymous single nucleotide polymorphisms (nsSNPs) in the ACE2 gene may have an impact on the protein's stability and its function. The deleterious or harmful nsSNPs of the ACE2 gene that can change the strength as well as the pattern of interaction with the RBD of S protein were selected for this study. RESULTS The ACE2:RBD interactions were analyzed by protein-protein docking study. The missense mutations A242V, R708W, G405E, D292N, Y633C, F308L, and G405E in ACE2 receptor were found to interact with RBD of Omicron subvariants with stronger binding affinity. Among the other selected nsSNPs of human ACE2 (hACE2), R768W, Y654S, F588S, R710C, R710C, A191P, and R710C were found to have lower binding affinity for RBD of Omicron subvariants. CONCLUSION The findings of this study suggest that the nsSNPs present in the human ACE2 gene alter the structure and function of the protein and, consequently, the susceptibility to Omicron subvariants.
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Affiliation(s)
- Arijit Samanta
- Applied Biochemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
| | - Ashif Ahamed
- Department of Zoology, Netaji Subhas Open University, Kolkata, West Bengal, India
| | | | - Safdar Ali
- Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdulaziz M Al-Amri
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mehboob Hoque
- Applied Biochemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
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Krishnakumar HN, Momtaz DA, Sherwani A, Mhapankar A, Gonuguntla RK, Maleki A, Abbas A, Ghali AN, Al Afif A. Pathogenesis and progression of anosmia and dysgeusia during the COVID-19 pandemic. Eur Arch Otorhinolaryngol 2023; 280:505-9. [PMID: 36209486 DOI: 10.1007/s00405-022-07689-w] [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: 09/09/2022] [Accepted: 10/04/2022] [Indexed: 01/21/2023]
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is the causative agent of COVID-19 which was detected in late 2019 in Wuhan, China. As of September 2022, there have been over 612 million confirmed cases of COVID-19 with over 6.5 million associated deaths. In many cases, anosmia and dysgeusia have been identified as primary symptoms of COVID-19 infection in patients. While the loss of smell (anosmia) and loss of taste (dysgeusia) due to COVID-19 infection is transient in most patients, many report that these symptoms persist following recovery. Understanding the pathogenesis of these symptoms is paramount to early treatment of the infection. We conducted a literature review of Google Scholar and PubMed to find and analyze studies discussing anosmia and dysgeusia in the context of COVID-19 to understand the progression and management of these symptoms. The mechanism for dysgeusia is largely unknown; however, pathogenesis of anosmia includes inflammation and cytokine release resulting from the infection that alters neuronal signaling, thus inducing the loss of smell that patients experience. Anosmia may be managed and potentially resolved sooner with a combination therapy of olfactory training and budesonide irrigation of the nasal cavity. It is important to note that the variants of SARS-CoV-2 are genetically distinguished from the original virion due to a mutation in their spike proteins, giving them a different symptom profile regarding anosmia and dysgeusia. This variability in symptomatology is an area of study that needs to be further explored.
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14
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Elssaig EH, Alnour TM, Ullah MF, Ahmed-Abakur EH. Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern. Pol J Microbiol 2022; 71:577-587. [PMID: 36537060 PMCID: PMC9944972 DOI: 10.33073/pjm-2022-053] [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: 09/19/2022] [Accepted: 11/12/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).
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Affiliation(s)
- Elmutuz H. Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
| | - Tarig M.S. Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan, T.M.S. Alnour, Department of Medical Laboratory Technology (FAMS), University of Tabuk, Saudi Arabia; Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia; Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan;
| | - Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Eltayib H. Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
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15
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Lu X, Lin H, Feng X, Lui GC, Hsing IM. Disposable and low-cost pen-like sensor incorporating nucleic-acid amplification based lateral-flow assay for at-home tests of communicable pathogens. Biosens Bioelectron X 2022; 12:100248. [PMID: 36092541 PMCID: PMC9443926 DOI: 10.1016/j.biosx.2022.100248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/12/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
Rapid at-home test is a good alternative to the gold standard quantitative polymerase chain reaction (qPCR) for early identification and management of infected individuals in pandemic. However, the currently available at-home rapid antigen kits and nucleic acid tests (NATs) are prone to false results. Although some CRISPR-mediated NATs enhanced accuracy, long turnaround time (ca. 1 h) and aerosol contamination due to additional open-lid reaction hinder its applicability for self-tests. Moreover, the accuracy of at-home NATs is also impacted by interference of sample matrix due to lack of sample purification. Here we report a Fast, Low-cost, Aerosol contamination-free and Sensitive molecular assay for at-Home tests of communicable pathogens (FLASH) incorporating oLAMP, a recently reported isothermal and target-specific NATs by our group, and a visible lateral-flow readout. The integrated platform enabled sample-to-result SARS-CoV-2 RNA detection in 20-30 min achieving a sensitivity of 0.5 copies/μL in a blinded experiment with a high accuracy comparable with the qPCR. Its prototype consists of two disposable pen-like instruments for single-step sample preparation and contamination-free NATs, respectively. The simplified workflow of the FLASH enabled detection to be readily conducted by untrained users for at-home tests. All in all, the FLASH prototype demonstrates itself to be a promising home-use assay platform for effective mitigation of the pandemic.
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Affiliation(s)
- Xiao Lu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Haosi Lin
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xianzhen Feng
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Grace Cy Lui
- Department of Medicine & Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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16
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Dobrynin D, Polischuk I, Pokroy B. A Comparison Study of the Detection Limit of Omicron SARS-CoV-2 Nucleocapsid by Various Rapid Antigen Tests. Biosensors (Basel) 2022; 12:1083. [PMID: 36551050 PMCID: PMC9775131 DOI: 10.3390/bios12121083] [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] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Rapid antigen tests (RATs) are widely used worldwide to detect SARS-CoV-2 since they are an easy-to-use kit and offer rapid results. The RAT detects the presence of the nucleocapsid protein, which is located inside the virus. However, the sensitivity of the different RATs varies between commercially available kits. The test result might change due to various factors, such as the variant type, infection date, swab's surface, the manner in which one performs the testing and the mucus components. Here, we compare the detection limit of seven commercially available RATs by introducing them to known SARS-CoV-2 nucleocapsid protein amounts from the Omicron variant. It allows us to determine the detection limit, disregarding the influences of other factors. A lower detection limit of the RAT is necessary since earlier detection will help reduce the spread of the virus and allow faster treatment, which might be crucial for the population at risk.
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Affiliation(s)
- Daniela Dobrynin
- Department of Materials Science and Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Iryna Polischuk
- Department of Materials Science and Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Boaz Pokroy
- Department of Materials Science and Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
- The Russel Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
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17
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Caputo E, Mandrich L. SARS-CoV-2: Searching for the Missing Variants. Viruses 2022; 14:v14112364. [PMID: 36366461 PMCID: PMC9697249 DOI: 10.3390/v14112364] [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: 10/05/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 01/31/2023] Open
Abstract
Structural and phylogenetic analysis of the spike glycoprotein highlighted that the last variants, annotated as omicron, have about 30 mutations compared to the initial version reported in China, while the delta variant, supposed to be the omicron ancestor, shows only 7 mutations. Moreover, the five omicron variants were isolated between November 2021 and January 2022, and the last variant BA.2.75, unofficially named centaurus, was isolated in May 2022. It appears that, since the isolation of the delta variant (October 2020) to the omicron BA.1 (November 2021), there was an interval of one year, whereas the five omicron variants were isolated in three months, and after a successive four months period, the BA.2.75 variant was isolated. So, what is the temporal and phylogenetic correlation among all these variants? The analysis of common mutations among delta and the omicron variants revealed: (i) a phylogenetic correlation among these variants; (ii) the existence of BA.1 and BA.2 omicron variants a few months before being isolated; (iii) at least three possible intermediate variants during the evolution of omicron; (iv) the evolution of the BA.2.12.1, BA.4 and BA.5 variants from omicron BA.2; (v) the centaurus variant evolution from omicron BA.2.12.1.
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Affiliation(s)
- Emilia Caputo
- Institute of Genetics and Biophysics-IGB-CNR, “A. Buzzati-Traverso”, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems-IRET-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
- Correspondence:
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18
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Pandey AK, Verma S. In-silico structural inhibition of ACE-2 binding site of SARS-CoV-2 and SARS-CoV-2 Omicron spike protein by lectin antiviral dyad system to treat COVID-19. Drug Dev Ind Pharm 2022; 48:539-551. [PMID: 36250723 DOI: 10.1080/03639045.2022.2137196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Spike glycoprotein of SARS-CoV-2 binds ACE-2 receptors via its receptor-binding-domain (RBD) and mediates virus-to-host cell fusion. Recently emerged omicron variant of SARS-CoV-2 possess around 30 mutations in spike protein where N501Y tremendously increases viral infectivity and transmission. Lectins interact with glycoproteins and mediate innate immunity displaying antiviral, antibacterial and anticarcinogenic properties. In this study, we analysed the potential of lectin, and lectin-antibody (spike-specific) complex to inhibit the ACE-2 binding site of wild and N501Y mutated spike protein by utilizing in-silico molecular docking and simulation approach. Docking of lectin at reported ACE-2 binding spike-RBD residues displayed the ZDock scores of 1907 for wild and 1750 for N501Y mutated spike-RBD. Binding of lectin with antibody to form proposed dyad complex gave ZDock score of 1174 revealing stable binding. Docking of dyad complex with wild and N501Y mutated spike-RBD, at lectin and antibody individually, showed high efficiency binding hence, effective structural inhibition of spike-RBD. MD simulation of 100ns of each complex proved high stability of complexes with RMSD values ranging from 0.2 -1.5nm. Consistent interactions of lead ACE-2 binding spike residues with lectin during simulation disclosed efficient structural inhibition by lectin against formation of spike RBD-ACE-2 complex.Hence, lectins along with their ability to induce innate immunity against spike glycoprotein can structurally inhibit the spike-RBD when given as lectin-antibody dyad system and thus can be developed into a dual effect treatment against COVID-19. Moreover, the high binding specificity of this system with spike-RBD can be exploited for development of diagnostic and drug-delivery systems.
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Affiliation(s)
- Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi Uttar Pradesh-284128, India
| | - Shalja Verma
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi Uttar Pradesh-284128, India.,Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand-247667, India
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19
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Rabaan AA, Mutair AA, Hajissa K, Alfaraj AH, Al-Jishi JM, Alhajri M, Alwarthan S, Alsuliman SA, Al-Najjar AH, Al Zaydani IA, Al-Absi GH, Alshaikh SA, Alkathlan MS, Almuthree SA, Alawfi A, Alshengeti A, Almubarak FZ, Qashgari MS, Abdalla ANK, Alhumaid S. A Comprehensive Review on the Current Vaccines and Their Efficacies to Combat SARS-CoV-2 Variants. Vaccines (Basel) 2022; 10. [PMID: 36298520 DOI: 10.3390/vaccines10101655] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Since the first case of Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, SARS-CoV-2 infection has affected many individuals worldwide. Eventually, some highly infectious mutants-caused by frequent genetic recombination-have been reported for SARS-CoV-2 that can potentially escape from the immune responses and induce long-term immunity, linked with a high mortality rate. In addition, several reports stated that vaccines designed for the SARS-CoV-2 wild-type variant have mixed responses against the variants of concern (VOCs) and variants of interest (VOIs) in the human population. These results advocate the designing and development of a panvaccine with the potential to neutralize all the possible emerging variants of SARS-CoV-2. In this context, recent discoveries suggest the design of SARS-CoV-2 panvaccines using nanotechnology, siRNA, antibodies or CRISPR-Cas platforms. Thereof, the present comprehensive review summarizes the current vaccine design approaches against SARS-CoV-2 infection, the role of genetic mutations in the emergence of new viral variants, the efficacy of existing vaccines in limiting the infection of emerging SARS-CoV-2 variants, and efforts or challenges in designing SARS panvaccines.
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20
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Agrawal S, Pathak E, Mishra R, Mishra V, Parveen A, Mishra SK, Byadgi PS, Dubey SK, Chaudhary AK, Singh V, Chaurasia RN, Atri N. Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host. Comput Biol Med 2022; 149:106049. [PMID: 36103744 PMCID: PMC9452420 DOI: 10.1016/j.compbiomed.2022.106049] [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: 01/11/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections generate approximately one million virions per day, and the majority of available antivirals are ineffective against it due to the virus's inherent genetic mutability. This necessitates the investigation of concurrent inhibition of multiple SARS-CoV-2 targets. We show that fortunellin (acacetin 7-O-neohesperidoside), a phytochemical, is a promising candidate for preventing and treating coronavirus disease (COVID-19) by targeting multiple key viral target proteins. Fortunellin supports protective immunity while inhibiting pro-inflammatory cytokines and apoptosis pathways and protecting against tissue damage. Fortunellin is a phytochemical found in Gojihwadi kwath, an Indian traditional Ayurvedic formulation with an antiviral activity that is effective in COVID-19 patients. The mechanistic action of its antiviral activity, however, is unknown. The current study comprehensively evaluates the potential therapeutic mechanisms of fortunellin in preventing and treating COVID-19. We have used molecular docking, molecular dynamics simulations, free-energy calculations, host target mining of fortunellin, gene ontology enrichment, pathway analyses, and protein-protein interaction analysis. We discovered that fortunellin reliably binds to key targets that are necessary for viral replication, growth, invasion, and infectivity including Nucleocapsid (N-CTD) (-54.62 kcal/mol), Replicase-monomer at NSP-8 binding site (-34.48 kcal/mol), Replicase-dimer interface (-31.29 kcal/mol), Helicase (-30.02 kcal/mol), Papain-like-protease (-28.12 kcal/mol), 2'-O-methyltransferase (-23.17 kcal/mol), Main-protease (-21.63 kcal/mol), Replicase-monomer at dimer interface (-22.04 kcal/mol), RNA-dependent-RNA-polymerase (-19.98 kcal/mol), Nucleocapsid-NTD (-16.92 kcal/mol), and Endoribonuclease (-16.81 kcal/mol). Furthermore, we identify and evaluate the potential human targets of fortunellin and its effect on the SARS-CoV-2 infected tissues, including normal-human-bronchial-epithelium (NHBE) and lung cells and organoids such as pancreatic, colon, liver, and cornea using a network pharmacology approach. Thus, our findings indicate that fortunellin has a dual role; multi-target antiviral activities against SARS-CoV-2 and immunomodulatory capabilities against the host.
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Affiliation(s)
- Shivangi Agrawal
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Ekta Pathak
- Institute of Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Rajeev Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India.
| | - Vibha Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Afifa Parveen
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | | | | | - Sushil Kumar Dubey
- Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, India
| | | | | | | | - Neelam Atri
- Department of Botany, MMV, Banaras Hindu University, India
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21
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de Freitas Bueno R, Claro ICM, Augusto MR, Duran AFA, Camillo LDMB, Cabral AD, Sodré FF, Brandão CCS, Vizzotto CS, Silveira R, de Melo Mendes G, Arruda AF, de Brito NN, Machado BAS, Duarte GRM, de Lourdes Aguiar-Oliveira M. Wastewater-based epidemiology: A Brazilian SARS-COV-2 surveillance experience. J Environ Chem Eng 2022; 10:108298. [PMID: 35873721 PMCID: PMC9295330 DOI: 10.1016/j.jece.2022.108298] [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] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 05/11/2023]
Abstract
Since 2020, developed countries have rapidly shared both publicly and academically relevant wastewater surveillance information. Data on SARS-CoV-2 circulation is pivotal for guiding public health policies and improving the COVID-19 pandemic response. Conversely, low- and middle-income countries, such as Latin America and the Caribbean, showed timid activities in the Wastewater-Based Epidemiology (WBE) context. In these countries, isolated groups perform viral wastewater monitoring, and the data are unevenly shared or accessible to health agencies and the scientific community. This manuscript aims to highlight the relevance of a multiparty effort involving research, public health, and governmental agencies to support usage of WBE methodology to its full potential during the COVID-19 pandemic as part of a joint One Health surveillance approach. Thus, in this study, we explored the results obtained from wastewater surveillance in different regions of Brazil as a part of the COVID-19 Wastewater Monitoring Network ANA (National Water Agency), MCTI (Ministry of Science, Technology, and Innovations) and MS (Ministry of Health). Over the epidemiological weeks of 2021 and early 2022, viral RNA concentrations in wastewater followed epidemiological trends and variations. The highest viral loads in wastewater samples were detected during the second Brazilian wave of COVID-19. Corroborating international reports, our experience demonstrated usefulness of the WBE approach in viral surveillance. Wastewater surveillance allows hotspot identification, and therefore, early public health interventions. In addition, this methodology allows tracking of asymptomatic and oligosymptomatic individuals, who are generally underreported, especially in emerging countries with limited clinical testing capacity. Therefore, WBE undoubtedly contributes to improving public health responses in the context of this pandemic, as well as other sanitary emergencies.
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Affiliation(s)
- Rodrigo de Freitas Bueno
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | - Ieda Carolina Mantovani Claro
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | - Matheus Ribeiro Augusto
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | - Adriana Feliciano Alves Duran
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | | | - Aline Diniz Cabral
- Federal University of ABC. Center of Engineering, Modelling and Applied Social Sciences (CECS), Santo Andre, São Paulo, Brazil
| | | | | | - Carla Simone Vizzotto
- University of Brasilia, Department of Civil and Environmental Engineering, Brasília, Federal District, Brazil
| | - Rafaella Silveira
- University of Brasilia. Institute of Chemistry, Brasília, Federal District, Brazil
- University of Brasilia, Department of Civil and Environmental Engineering, Brasília, Federal District, Brazil
| | | | | | | | - Bruna Aparecida Souza Machado
- University Center SENAI/CIMATEC. SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), Salvador, Bahia, Brazil
| | | | - Maria de Lourdes Aguiar-Oliveira
- Laboratory of Respiratory Viruses and Measles, National/MoH and International/WHO Reference Laboratory in COVID-19, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
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22
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Zoran MA, Savastru RS, Savastru DM, Tautan MN. Cumulative effects of air pollution and climate drivers on COVID-19 multiwaves in Bucharest, Romania. Process Saf Environ Prot 2022; 166:368-383. [PMID: 36034108 PMCID: PMC9391082 DOI: 10.1016/j.psep.2022.08.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Over more than two years of global health crisis due to ongoing COVID-19 pandemic, Romania experienced a five-wave pattern. This study aims to assess the potential impact of environmental drivers on COVID-19 transmission in Bucharest, capital of Romania during the analyzed epidemic period. Through descriptive statistics and cross-correlation tests applied to time series of daily observational and geospatial data of major outdoor inhalable particulate matter with aerodynamic diameter ≤ 2.5 µm (PM2.5) or ≤ 10 µm (PM10), nitrogen dioxide (NO2), ozone (O3), sulfur dioxide (SO2), carbon monoxide (CO), Aerosol Optical Depth at 550 nm (AOD) and radon (222Rn), we investigated the COVID-19 waves patterns under different meteorological conditions. This study examined the contribution of individual climate variables on the ground level air pollutants concentrations and COVID-19 disease severity. As compared to the long-term average AOD over Bucharest from 2015 to 2019, for the same year periods, this study revealed major AOD level reduction by ~28 % during the spring lockdown of the first COVID-19 wave (15 March 2020-15 May 2020), and ~16 % during the third COVID-19 wave (1 February 2021-1 June 2021). This study found positive correlations between exposure to air pollutants PM2.5, PM10, NO2, SO2, CO and 222Rn, and significant negative correlations, especially for spring-summer periods between ground O3 levels, air temperature, Planetary Boundary Layer height, and surface solar irradiance with COVID-19 incidence and deaths. For the analyzed time period 1 January 2020-1 April 2022, before and during each COVID-19 wave were recorded stagnant synoptic anticyclonic conditions favorable for SARS-CoV-2 virus spreading, with positive Omega surface charts composite average (Pa/s) at 850 mb during fall- winter seasons, clearly evidenced for the second, the fourth and the fifth waves. These findings are relevant for viral infections controls and health safety strategies design in highly polluted urban environments.
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Key Words
- 222Rn
- 222Rn, Radon
- AOD, Total Aerosol Optical Depth at 550 nm
- Aerosol Optical Depth (AOD)
- CAMS, Copernicus Atmosphere Monitoring Service
- CO, Carbon monoxide
- COVID, 19 Coronavirus Disease 2019
- COVID-19 disease
- Climate variables
- DNC, Daily New COVID-19 positive cases
- DND, Daily New COVID-19 Deaths
- MERS, CoV Middle East respiratory syndrome coronavirus
- NO2, Nitrogen dioxide
- NOAA, National Oceanic and Atmospheric Administration U.S.A.
- O3, Ozone
- Outdoor air pollutants
- PBL, Planetary Boundary Layer height
- PM, Particulate Matter: PM1(1 µm), PM2.5 (2.5 µm) and PM10(10.0 µm) diameter
- RH, Air relative humidity
- SARS, CoV Severe Outdoor Respiratory Syndrome Coronavirus
- SARS, CoV-2 Severe Outdoor Respiratory Syndrome Coronavirus 2
- SI, Surface solar global irradiance
- SO2, Sulfur dioxide
- Synoptic meteorological circulation
- T, Air temperature at 2 m height
- p, Air pressure
- w, Wind speed intensity
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Affiliation(s)
- Maria A Zoran
- IT Department, National Institute of R&D for Optoelectronics, Atomistilor Street 409, MG5, Magurele, Bucharest 077125, Romania
| | - Roxana S Savastru
- IT Department, National Institute of R&D for Optoelectronics, Atomistilor Street 409, MG5, Magurele, Bucharest 077125, Romania
| | - Dan M Savastru
- IT Department, National Institute of R&D for Optoelectronics, Atomistilor Street 409, MG5, Magurele, Bucharest 077125, Romania
| | - Marina N Tautan
- IT Department, National Institute of R&D for Optoelectronics, Atomistilor Street 409, MG5, Magurele, Bucharest 077125, Romania
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23
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Staessen JA, Wendt R, Yu YL, Kalbitz S, Thijs L, Siwy J, Raad J, Metzger J, Neuhaus B, Papkalla A, von der Leyen H, Mebazaa A, Dudoignon E, Spasovski G, Milenkova M, Canevska-Taneska A, Salgueira Lazo M, Psichogiou M, Rajzer MW, Fuławka Ł, Dzitkowska-Zabielska M, Weiss G, Feldt T, Stegemann M, Normark J, Zoufaly A, Schmiedel S, Seilmaier M, Rumpf B, Banasik M, Krajewska M, Catanese L, Rupprecht HD, Czerwieńska B, Peters B, Nilsson Å, Rothfuss K, Lübbert C, Mischak H, Beige J. Predictive performance and clinical application of COV50, a urinary proteomic biomarker in early COVID-19 infection: a prospective multicentre cohort study. Lancet Digit Health 2022; 4:e727-e737. [PMID: 36057526 PMCID: PMC9432869 DOI: 10.1016/s2589-7500(22)00150-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
Background The SARS-CoV-2 pandemic is a worldwide challenge. The CRIT-CoV-U pilot study generated a urinary proteomic biomarker consisting of 50 peptides (COV50), which predicted death and disease progression from SARS-CoV-2. After the interim analysis presented for the German Government, here, we aimed to analyse the full dataset to consolidate the findings and propose potential clinical applications of this biomarker. Methods CRIT-CoV-U was a prospective multicentre cohort study. In eight European countries (Austria, France, Germany, Greece, North Macedonia, Poland, Spain, and Sweden), 1012 adults with PCR-confirmed COVID-19 were followed up for death and progression along the 8-point WHO scale. Capillary electrophoresis coupled with mass spectrometry was used for urinary proteomic profiling. Statistical methods included logistic regression and receiver operating characteristic curve analysis with a comparison of the area under curve (AUC) between nested models. Hospitalisation costs were derived from the care facility corresponding with the Markov chain probability of reaching WHO scores ranging from 3 to 8 and flat-rate hospitalisation costs adjusted for the gross per capita domestic product of each country. Findings From June 30 to Nov 19, 2020, 228 participants were recruited, and from April 30, 2020, to April 14, 2021, 784 participants were recruited, resulting in a total of 1012 participants. The entry WHO scores were 1–3 in 445 (44%) participants, 4–5 in 529 (52%) participants, and 6 in 38 (4%) participants; and of all participants, 119 died and 271 had disease progression. The odds ratio (OR) associated with COV50 in all 1012 participants for death was 2·44 (95% CI 2·05–2·92) unadjusted and 1·67 (1·34–2·07) when adjusted for sex, age, BMI, comorbidities, and baseline WHO score; and for disease progression, the OR was 1·79 (1·60–2·01) when unadjusted and 1·63 (1·41–1·91) when adjusted (p<0·0001 for all). The predictive accuracy of the optimised COV50 thresholds was 74·4% (71·6–77·1%) for mortality (threshold 0·47) and 67·4% (64·4–70·3%) for disease progression (threshold 0·04). When adjusted for covariables and the baseline WHO score, these thresholds improved AUCs from 0·835 to 0·853 (p=0·033) for death and from 0·697 to 0·730 (p=0·0008) for progression. Of 196 participants who received ambulatory care, 194 (99%) did not reach the 0·04 threshold. The cost reductions associated with 1 day less hospitalisation per 1000 participants were million Euro (M€) 0·887 (5–95% percentile interval 0·730–1·039) in participants at a low risk (COV50 <0·04) and M€2·098 (1·839-2·365) in participants at a high risk (COV50 ≥0·04). Interpretation The urinary proteomic COV50 marker might be predictive of adverse COVID-19 outcomes. Even in people with mild-to-moderate PCR-confirmed infections (WHO scores 1–4), the 0·04 COV50 threshold justifies earlier drug treatment, thereby potentially reducing the number of days in hospital and associated costs. Funding German Federal Ministry of Health.
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Affiliation(s)
- Jan A Staessen
- Non-Profit Research Institute Alliance for the Promotion of Preventive Medicine, Mechelen, Belgium; Biomedical Sciences Group, Faculty of Medicine, University of Leuven, Leuven, Belgium
| | - Ralph Wendt
- Department of Infectious Diseases and Tropical Medicine, Nephrology and Kuratorium für Dialyse und Nierentransplantation Renal Unit and Rheumatology, St Georg Hospital, Leipzig, Germany
| | - Yu-Ling Yu
- Research Unit Environment and Health, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Sven Kalbitz
- Department of Infectious Diseases and Tropical Medicine, Nephrology and Kuratorium für Dialyse und Nierentransplantation Renal Unit and Rheumatology, St Georg Hospital, Leipzig, Germany
| | - Lutgarde Thijs
- Research Unit Hypertension and Cardiovascular Epidemiology, Department of Cardiovascular Diseases, University of Leuven, Leuven, Belgium
| | | | - Julia Raad
- Mosaiques-Diagnostics, Hannover, Germany
| | | | - Barbara Neuhaus
- Centre for Clinical Trials, Medizinische Hochschule, Hannover, Germany
| | - Armin Papkalla
- Centre for Clinical Trials, Medizinische Hochschule, Hannover, Germany
| | | | - Alexandre Mebazaa
- Department of Anaesthesiology and Intensive Care, Hospital Saint Louis-Lariboisière, Paris, France
| | - Emmanuel Dudoignon
- Department of Anaesthesiology and Intensive Care, Hospital Saint Louis-Lariboisière, Paris, France
| | | | | | | | | | - Mina Psichogiou
- First Department of Internal Medicine, Laiko General Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Marek W Rajzer
- First Department of Cardiology, Interventional Electrocardiology and Arterial Hypertension, Jagiellonian University Medical College, Kraków, Poland
| | | | - Magdalena Dzitkowska-Zabielska
- Faculty of Physical Education, Gdańsk University of Physical Education and Sport and Centre of Translational Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Guenter Weiss
- Department of Internal Medicine II, Medical University Innsbruck, Innsbruck, Austria
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty of Heinrich Heine University, Düsseldorf, Germany
| | - Miriam Stegemann
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, Corporate Member of the Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johan Normark
- Wallenberg Centre for Molecular Medicine, Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Alexander Zoufaly
- Department of Medicine IV, Clinic Favoriten and Faculty of Medicine, Sigmund Freud University, Vienna, Austria
| | - Stefan Schmiedel
- Medical Department I and Bernhard-Nocht-Clinic for Tropical Medicine, University Medical Centre Hamburg Eppendorf, Hamburg, Germany
| | - Michael Seilmaier
- Department of Haematology, Oncology, Immunology, Palliative Care, Infectious Disease and Tropical Medicine, München Klinik Schwabing, München, Germany
| | - Benedikt Rumpf
- Nephrology and Dialysis, Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mirosław Banasik
- Department of Nephrology and Transplantation Medicine, Wrocław Medical University, Wrocław, Poland
| | - Magdalena Krajewska
- Department of Nephrology and Transplantation Medicine, Wrocław Medical University, Wrocław, Poland
| | - Lorenzo Catanese
- Department of Nephrology, Angiology and Rheumatology, Hospital Bayreuth, Bayreuth, Germany
| | - Harald D Rupprecht
- Department of Nephrology, Angiology and Rheumatology, Hospital Bayreuth, Bayreuth, Germany
| | | | - Björn Peters
- Department of Nephrology, Skaraborg Hospital, Skövde and Department of Molecular and Clinical Medicine, Institute of Medicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Research and Development Centre, Skaraborg Hospital, Skövde, Sweden
| | - Åsa Nilsson
- Research and Development Centre, Skaraborg Hospital, Skövde, Sweden
| | - Katja Rothfuss
- Department of Gastroenterology, Hepatology and Endocrinology, Robert Bosch Hospital, Stuttgart, Germany
| | - Christoph Lübbert
- Department of Infectious Diseases and Tropical Medicine, Nephrology and Kuratorium für Dialyse und Nierentransplantation Renal Unit and Rheumatology, St Georg Hospital, Leipzig, Germany; Division of Infectious Diseases and Tropical Medicine, Leipzig University Medical Centre, Leipzig, Germany
| | - Harald Mischak
- Mosaiques-Diagnostics, Hannover, Germany; Institute of Cardiovascular and Medical Sciences, Glasgow, UK
| | - Joachim Beige
- Department of Infectious Diseases and Tropical Medicine, Nephrology and Kuratorium für Dialyse und Nierentransplantation Renal Unit and Rheumatology, St Georg Hospital, Leipzig, Germany; Martin-Luther-University Halle-Wittenberg, Halle an der Saale, Halle, Germany.
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24
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Margiana R, Sharma SK, Khan BI, Alameri AA, Opulencia MJC, Hammid AT, Hamza TA, Babakulov SK, Abdelbasset WK, Jawhar ZH. RETRACTED: The pathogenicity of COVID-19 and the role of pentraxin-3: An updated review study. Pathol Res Pract 2022; 238:154128. [PMID: 36137396 PMCID: PMC9476367 DOI: 10.1016/j.prp.2022.154128] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/03/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/policies/article-withdrawal). This article has been retracted at the request of the Editor-in-Chief. In investigating concerns regarding the contributions of the authors to this article, the editors reached out to the authors for an explanation. In addition to the concerns regarding the contribution of each author, the editors discovered suspicious changes in authorship between the original submission and the revised version of this paper. The names of the authors Ameer A Alameri and Zanko Hassan Jawhar were added to the revised version of the article without explanation and without the exceptional approval by the handling Editor, which is contrary to the journal policy on changes to authorship. The authors were unable to provide a reasonable explanation for either of the issues raised. The editor therefore feels that the findings of the manuscript cannot be relied upon and that the article needs to be retracted.
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Affiliation(s)
- Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Andrology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia; Dr. Soetomo General Academic Hospital, Surabaya, Indonesia.
| | - Satish Kumar Sharma
- Department of Pharmacology, Glocal School of Pharmacy, The Glocal University, Saharanpur, India.
| | | | | | | | - Ali Thaeer Hammid
- Computer Engineering Techniques Department, Faculty of Information Technology, Imam Ja'afar Al-Sadiq University, Baghdad, Iraq
| | - Thulfeqar Ahmed Hamza
- Medical laboratory techniques department, Al-Mustaqbal University College, Babylon, Iraq
| | - Sharaf Khamrakulovich Babakulov
- Tashkent State Dental Institute, Makhtumkuli Street 103, Tashkent, 100047, Uzbekistan; Research scholar, Department of Scientific affairs, Samarkand State Medical Institute, Amir Temur Street 18, Samarkand, Uzbekistan
| | - Walid Kamal Abdelbasset
- Department of Health and Rehabilitation Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia; Department of Physical Therapy, Kasr Al-Aini Hospital, Cairo University, Giza, Egypt
| | - Zanko Hassan Jawhar
- Department of Medical Laboratory Science, College of Health Science, Lebanese French University, Kurdistan Region, Iraq
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25
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Zhang Y, Li H, Xiang B, Du J, Huang Y, Lin G, Wu D. Dynamic characteristics of COVID-19 infection in Chinese children. Am J Transl Res 2022; 14:6375-6381. [PMID: 36247253 PMCID: PMC9556448] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/20/2022] [Indexed: 06/16/2023]
Abstract
From the start of the coronavirus disease 2019 (COVID-19) pandemic in 2020, COVID-19 infection in the pediatric population has aroused great attention. This article presents dynamic epidemiological characteristics of COVID-19 infection in pediatric patients from January 2020 to March 2022 in China. These data contributed essential insights and shared experience on the management of COVID-19 in children. To date, the unvaccinated population and events with children need more attention.
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Affiliation(s)
- Yunhua Zhang
- Hainan Hospital of Hainan Medical University, Hainan General HospitalHaikou 570311, Hainan, P.R. China
- Hubei Provincial Hospital of Traditional Chinese MedicineWuhan 430061, P.R. China
- Clinical Medical College of Hubei University of Chinese MedicineWuhan 430061, P.R. China
- Hubei Province Academy of Traditional Chinese MedicineWuhan 430061, P.R. China
| | - Hui Li
- The Office of Nosocomial, Public Health Office, Maternal and Child Health Hospital of Hubei ProvinceWuhan 430070, P.R. China
| | - Boqi Xiang
- School of Public Health, Rutgers UniversityNew Brunswick, NJ, United States
| | - Jing Du
- Hainan Hospital of Hainan Medical University, Hainan General HospitalHaikou 570311, Hainan, P.R. China
| | - Yan Huang
- Department of Interventional Therapy, The First Affiliated Hospital of Dalian Medical UniversityDalian 116000, Liaoning, P.R. China
| | - Guanwen Lin
- Hainan Hospital of Hainan Medical University, Hainan General HospitalHaikou 570311, Hainan, P.R. China
| | - Duozhi Wu
- Hainan Hospital of Hainan Medical University, Hainan General HospitalHaikou 570311, Hainan, P.R. China
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Kamble P, Daulatabad V, Patil R, John NA, John J. Omicron variant in COVID-19 current pandemic: a reason for apprehension. Horm Mol Biol Clin Investig 2022; 44:89-96. [PMID: 36064193 DOI: 10.1515/hmbci-2022-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/22/2022] [Indexed: 11/15/2022]
Abstract
COVID-19 emerged in Wuhan, China, but was caused by the original coronavirus, severe acute respiratory syndrome associated coronavirus-2 (SARS-CoV2). In early 2020, there was a widespread breakout of cases well over world, resulting in an epidemic that rapidly escalated to become a pandemic. This abruptly shook the global healthcare system. The emergence of the alpha, beta, and delta SARS-CoV-2 were associated with new waves of infections, sometimes across the entire world but until this month i.e., between Nov-Dec, 2021, Delta variant reigned supreme until the emergence of a newer variant i.e., Omicron (B.1.1.529) of SARS-CoV-2. Delta had 13 mutations. Of these, nine are in the spike protein, the protrusion on the surface of the virus that helps it latch onto human cells. Specifically, two are in a molecular hook, called the "receptor-binding domain". Omicron, a creation caused by monstrous mutations. At least 32 mutations are in the spike protein and 10 in the receptor-binding domain. was designated a COVID-19 variant of concern (VoC) by the World Health Organization (WHO) on 26th November 2021. Structurally, the omicron variant has shown too mutated at antibody binding sites which would leverage them for escaping the possible immune response by the body. We don't yet know much about the other alterations and how they might affect the virus's behavior. Omicron COVID-19 strain after identifying individuals with symptoms that were not the same as those seen in the Delta form. People with night sweats have also been reported. The new omicron variant has more mutations than the prevailing rampant delta virus. This makes the newer variant more transmissible, better able to evade itself from various vaccines readily available in the current scenario. These overall increases in the percentage changes in a single day cases of COVID-19 reported cases can be attributed to the beginning of third wave or can be speculated as newer surge of omicron variant cases. Yet another new variant has been detected in France with 46 mutations and 37 deletions in its genetic code, many affecting the spike protein. 'B.1.640.2' is the current nomenclature for this variation.
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Affiliation(s)
- Prafull Kamble
- Department of Physiology, All India Institute of Medical Sciences, Bibinagar, Telangana, India
| | - Vandana Daulatabad
- RVM Institute of Medical Sciences, Siddipet, Hyderabad, Telangana, India
| | - Ramesh Patil
- Ashwini Rural Medical College, Hospital and Research Centre, Solapur, India
| | - Nitin Ashok John
- Department of Physiology, All India Institute of Medical Sciences, Bibinagar, Telangana, India
| | - Jyoti John
- Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, Maharashtra, India
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Konyak BM, Sharma M, Kharia S, Pandey RP, Chang C. A Systematic Review on the Emergence of Omicron Variant and Recent Advancement in Therapies. Vaccines (Basel) 2022; 10:1468. [PMID: 36146546 PMCID: PMC9503441 DOI: 10.3390/vaccines10091468] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 01/18/2023] Open
Abstract
With the ongoing COVID-19 pandemic, the emergence of the novel Omicron variant in November 2021 has created chaos around the world. Despite mass vaccination, Omicron has spread rapidly, raising concerns around the globe. The Omicron variant has a vast array of mutations, as compared to another variant of concern, with a total of 50 mutations, 30 of which are present on its spike protein alone. These mutations have led to immune escape and more transmissibility compared to other variants, including the Delta variant. A cluster of mutations (H655Y, N679K, and P681H) present in the Omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of the anti-viral and mAbs drugs. However, two monoclonal antibody drugs, Sotrovimab and Evusheld, are authorized for emergency use in COVID-19 patients. This virus is not fading away soon. The easiest solution and least expensive measure to fight against this pandemic are to follow the appropriate COVID-19 protocols. There is a need to strengthen the level of research for the development of potential vaccines and anti-viral drugs. It is also important to monitor and expand the genomic surveillance to keep track of the emergence of new variants, thus avoiding the spread of new diseases worldwide. This article highlights the emergence of the new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), and the vast number of mutations in its protein. In addition, recent advancements in drugs approved by FDA to treat COVID patients have been listed and focused in this paper.
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Xu A, Hong B, Lou F, Wang S, Li W, Shafqat A, An X, Zhao Y, Song L, Tong Y, Fan H. Sub-lineages of the SARS-CoV-2 Omicron variants: Characteristics and prevention. MedComm (Beijing) 2022; 3:e172. [PMID: 35992968 PMCID: PMC9380698 DOI: 10.1002/mco2.172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/07/2022] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, new variants of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) have emerged, accelerating the spread of the virus. Omicron was defined by the World Health Organization in November 2021 as the fifth "variant of concern" after Alpha, Beta, Gamma, and Delta. In recent months, Omicron has become the main epidemic strain. Studies have shown that Omicron carries more mutations than Alpha, Beta, Gamma, Delta, and wild-type, facilitating immune escape and accelerating its transmission. This review focuses on the Omicron variant's origin, transmission, main biological features, subvariants, mutations, immune escape, vaccination, and detection methods. We also discuss the appropriate preventive and therapeutic measures that should be taken to address the new challenges posed by the Omicron variant. This review is valuable to guide the surveillance, prevention, and development of vaccines and other therapies for Omicron variants. It is desirable to develop a more efficient vaccine against the Omicron variant and take more effective measures to constrain the spread of the epidemic and promote public health.
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Affiliation(s)
- Ailan Xu
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
- The First Affiliated Hospital of Jiamusi UniversityJiamusiChina
| | - Bixia Hong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Fuxing Lou
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Shuqi Wang
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Wenye Li
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Amna Shafqat
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Xiaoping An
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yunwei Zhao
- The First Affiliated Hospital of Jiamusi UniversityJiamusiChina
| | - Lihua Song
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yigang Tong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Huahao Fan
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
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29
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Zoran MA, Savastru RS, Savastru DM, Tautan MN. Impacts of exposure to air pollution, radon and climate drivers on the COVID-19 pandemic in Bucharest, Romania: A time series study. Environ Res 2022; 212:113437. [PMID: 35594963 PMCID: PMC9113773 DOI: 10.1016/j.envres.2022.113437] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
During the ongoing global COVID-19 pandemic disease, like several countries, Romania experienced a multiwaves pattern over more than two years. The spreading pattern of SARS-CoV-2 pathogens in the Bucharest, capital of Romania is a multi-factorial process involving among other factors outdoor environmental variables and viral inactivation. Through descriptive statistics and cross-correlation analysis applied to daily time series of observational and geospatial data, this study aims to evaluate the synergy of COVID-19 incidence and lethality with air pollution and radon under different climate conditions, which may exacerbate the coronavirus' effect on human health. During the entire analyzed period 1 January 2020-21 December 2021, for each of the four COVID-19 waves were recorded different anomalous anticyclonic synoptic meteorological patterns in the mid-troposphere, and favorable stability conditions during fall-early winter seasons for COVID-19 disease fast-spreading, mostly during the second, and the fourth waves. As the temporal pattern of airborne SARS-CoV-2 and its mutagen variants is affected by seasonal variability of the main air pollutants and climate parameters, this paper found: 1) the daily outdoor exposures to air pollutants (particulate matter PM2.5 and PM10, nitrogen dioxide-NO2, sulfur dioxide-SO2, carbon monoxide-CO) and radon - 222Rn, are directly correlated with the daily COVID-19 incidence and mortality, and may contribute to the spread and the severity of the pandemic; 2) the daily ground ozone-O3 levels, air temperature, Planetary Boundary Layer height, and surface solar irradiance are anticorrelated with the daily new COVID-19 incidence and deaths, averageingful for spring-summer periods. Outdoor exposure to ambient air pollution associated with radon is a non-negligible driver of COVID-19 transmission in large metropolitan areas, and climate variables are risk factors in spreading the viral infection. The findings of this study provide useful information for public health authorities and decision-makers to develop future pandemic diseases strategies in high polluted metropolitan environments.
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Affiliation(s)
- Maria A Zoran
- National Institute of R&D for Optoelectronics, Bucharest, Magurele, Romania.
| | - Roxana S Savastru
- National Institute of R&D for Optoelectronics, Bucharest, Magurele, Romania
| | - Dan M Savastru
- National Institute of R&D for Optoelectronics, Bucharest, Magurele, Romania
| | - Marina N Tautan
- National Institute of R&D for Optoelectronics, Bucharest, Magurele, Romania
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Jalal K, Khan K, Basharat Z, Abbas MN, Uddin R, Ali F, Khan SA, Hassan SSU. Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2. Environ Sci Pollut Res Int 2022; 29:60035-60053. [PMID: 35414157 PMCID: PMC9005162 DOI: 10.1007/s11356-022-19979-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 01/07/2022] [Accepted: 03/25/2022] [Indexed: 06/01/2023]
Abstract
The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.
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Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Sciences, HEJ Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, Karachi, Pakistan
| | | | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
| | - Fawad Ali
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Saeed Ahmad Khan
- Department of Pharmacy, KUST, Khyber Pakhtunkhwa, Kohat, 26000, Pakistan
| | - Syed Shams Ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
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31
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Ma H, Zhang X, Zheng P, Dube PH, Zeng W, Chen S, Cheng Q, Yang Y, Wu Y, Zhou J, Hu X, Xiang Y, Zhang H, Chiu S, Jin T. Hetero-bivalent nanobodies provide broad-spectrum protection against SARS-CoV-2 variants of concern including Omicron. Cell Res 2022. [PMID: 35906408 DOI: 10.1038/s41422-022-00700-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/06/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 variants with adaptive mutations have continued to emerge, causing fresh waves of infection even amongst vaccinated population. The development of broad-spectrum antivirals is thus urgently needed. We previously developed two hetero-bivalent nanobodies (Nbs), aRBD-2-5 and aRBD-2-7, with potent neutralization activity against the wild-type (WT) Wuhan isolated SARS-CoV-2, by fusing aRBD-2 with aRBD-5 and aRBD-7, respectively. Here, we resolved the crystal structures of these Nbs in complex with the receptor-binding domain (RBD) of the spike protein, and found that aRBD-2 contacts with highly-conserved RBD residues and retains binding to the RBD of the Alpha, Beta, Gamma, Delta, Delta plus, Kappa, Lambda, Omicron BA.1, and BA.2 variants. In contrast, aRBD-5 and aRBD-7 bind to less-conserved RBD epitopes non-overlapping with the epitope of aRBD-2, and do not show apparent binding to the RBD of some variants. However, when fused with aRBD-2, they effectively enhance the overall binding affinity. Consistently, aRBD-2-5-Fc and aRBD-2-7-Fc potently neutralized all of the tested authentic or pseudotyped viruses, including WT, Alpha, Beta, Gamma, Delta, and Omicron BA.1, BA.1.1 and BA.2. Furthermore, aRBD-2-5-Fc provided prophylactic protection against the WT and mouse-adapted SARS-CoV-2 in mice, and conferred protection against the Omicron BA.1 variant in hamsters prophylactically and therapeutically, indicating that aRBD-2-5-Fc could potentially benefit the prevention and treatment of COVID-19 caused by the emerging variants of concern. Our strategy provides new solutions in the development of broad-spectrum therapeutic antibodies for COVID-19.
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32
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Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission. Rev Med Virol 2022; 32:e2381. [PMID: 35856385 PMCID: PMC9349777 DOI: 10.1002/rmv.2381] [Citation(s) in RCA: 211] [Impact Index Per Article: 105.5] [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: 05/11/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022]
Abstract
The first dominant SARS‐CoV‐2 Omicron variant BA.1 harbours 35 mutations in its Spike protein from the original SARS‐CoV‐2 variant that emerged late 2019. Soon after its discovery, BA.1 rapidly emerged to become the dominant variant worldwide and has since evolved into several variants. Omicron is of major public health concern owing to its high infectivity and antibody evasion. This review article examines the theories that have been proposed on the evolution of Omicron including zoonotic spillage, infection in immunocompromised individuals and cryptic spread in the community without being diagnosed. Added to the complexity of Omicron's evolution are the multiple reports of recombination events occurring between co‐circulating variants of Omicron with Delta and other variants such as XE. Current literature suggests that the combination of the novel mutations in Omicron has resulted in the variant having higher infectivity than the original Wuhan‐Hu‐1 and Delta variant. However, severity is believed to be less owing to the reduced syncytia formation and lower multiplication in the human lung tissue. Perhaps most challenging is that several studies indicate that the efficacy of the available vaccines have been reduced against Omicron variant (8–127 times reduction) as compared to the Wuhan‐Hu‐1 variant. The administration of booster vaccine, however, compensates with the reduction and improves the efficacy by 12–35 fold. Concerningly though, the broadly neutralising monoclonal antibodies, including those approved by FDA for therapeutic use against previous SARS‐CoV‐2 variants, are mostly ineffective against Omicron with the exception of Sotrovimab and recent reports suggest that the Omicron BA.2 is also resistant to Sotrovimab. Currently two new Omicron variants BA.4 and BA.5 are emerging and are reported to be more transmissible and resistant to immunity generated by previous variants including Omicron BA.1 and most monoclonal antibodies. As new variants of SARS‐CoV‐2 will likely continue to emerge it is important that the evolution, and biological consequences of new mutations, in existing variants be well understood.
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Affiliation(s)
- Lok Bahadur Shrestha
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Charles Foster
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - William Rawlinson
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Nicodemus Tedla
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,The Kirby Institute, UNSW, Sydney, New South Wales, Australia
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33
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Khan K, Khan SA, Jalal K, Ul-haq Z, Uddin R. Immunoinformatic approach for the construction of multi-epitopes vaccine against omicron COVID-19 variant. Virology 2022; 572:28-43. [PMID: 35576833 PMCID: PMC9087879 DOI: 10.1016/j.virol.2022.05.001] [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: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/22/2022]
Abstract
The newly discovered SARS-CoV-2 Omicron variant B.1.1.529 is a Variant of Concern (VOC) announced by the World Health Organization (WHO). It's becoming increasingly difficult to keep these variants from spreading over the planet. The fifth wave has begun in several countries because of Omicron variant, and it is posing a threat to human civilization. As a result, we need effective vaccination that can tackle Omicron SARS-CoV-2 variants that are bound to emerge. Therefore, the current study is an initiative to design a peptide-based chimeric vaccine that may potentially battle SARS-CoV-2 Omicron variant. As a result, the most relevant epitopes present in the mutagenic areas of Omicron spike protein were identified using a set of computational tools and immunoinformatic techniques to uncover common MHC-1, MHC-II, and B cell epitopes that may have the ability to influence the host immune mechanism. A final of three epitopes from CD8+ T-cell, CD4+ T-cell epitopes, and B-cell were shortlisted from spike protein, and that are highly antigenic, IFN-γ inducer, as well as overlapping for the construction of twelve vaccine models. As a result, the antigenic epitopes were coupled with a flexible and stable peptide linker, and the adjuvant was added at the N-terminal end to create a unique vaccine candidate. The structure of a 3D vaccine candidate was refined, and its quality was assessed by using web servers. However, the applied immunoinformatic study along with the molecular docking and simulation of 12 modeled vaccines constructs against six distinct HLAs, and TLRs (TLR2, and TLR4) complexes revealed that the V1 construct was non-allergenic, non-toxic, highly immunogenic, antigenic, and most stable. The vaccine candidate's stability was confirmed by molecular dynamics investigations. Finally, we studied the expression of the suggested vaccination using codon optimization and in-silico cloning. The current study proposed V1 Multi-Epitope Vaccine (MEV) as a significant vaccine candidate that may help the scientific community to treat SARS-CoV-2 infections.
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34
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Liu Y, Yu Y, Zhao Y, He D. Reduction in the infection fatality rate of Omicron variant compared with previous variants in South Africa. Int J Infect Dis 2022; 120:146-149. [PMID: 35462038 PMCID: PMC9022446 DOI: 10.1016/j.ijid.2022.04.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 01/18/2022] [Revised: 04/04/2022] [Accepted: 04/17/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE The SARS-CoV-2 Omicron (B.1.1.529) variant has caused global concern. Previous studies have shown that the variant has enhanced immune evasion ability and transmissibility and reduced severity. METHODS In this study, we developed a mathematical model with time-varying transmission rate, vaccination, and immune evasion. We fit the model to reported case and death data up to February 6, 2022 to estimate the transmissibility and infection fatality ratio of the Omicron variant in South Africa. RESULTS We found that the high relative transmissibility of the Omicron variant was mainly due to its immune evasion ability, whereas its infection fatality rate substantially decreased by approximately 78.7% (95% confidence interval: 66.9%, 85.0%) with respect to previous variants. CONCLUSION On the basis of data from South Africa and mathematical modeling, we found that the Omicron variant is highly transmissible but with significantly lower infection fatality rates than those of previous variants of SARS-CoV-2.
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Affiliation(s)
- Yuan Liu
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Yangyang Yu
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong SAR, China,State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yanji Zhao
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong SAR, China,Research Institute for Future Food, The Hong Kong Polytechnic University, Hong Kong SAR, China,Correspondence author: Daihai He, Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong, China
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35
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Parvez MSA, Saha MK, Ibrahim M, Araf Y, Islam MT, Ohtsuki G, Hosen MJ. Insights from a computational analysis of the SARS‐CoV‐2 Omicron variant: Host–pathogen interaction, pathogenicity, and possible drug therapeutics. Immun Inflamm Dis 2022; 10:e639. [PMID: 35759231 PMCID: PMC9210926 DOI: 10.1002/iid3.639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Md Sorwer Alam Parvez
- Department of Drug Discovery Medicine Kyoto University Graduate School of Medicine Kyoto Japan
- Department of Genetic Engineering & Biotechnology Shahjalal University of Science & Technology Sylhet Bangladesh
| | - Manash Kumar Saha
- Department of Genetic Engineering & Biotechnology Shahjalal University of Science & Technology Sylhet Bangladesh
| | - Md. Ibrahim
- Department of Genetic Engineering & Biotechnology Shahjalal University of Science & Technology Sylhet Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering & Biotechnology Shahjalal University of Science & Technology Sylhet Bangladesh
| | - Md. Taufiqul Islam
- Department of Genetic Engineering & Biotechnology Shahjalal University of Science & Technology Sylhet Bangladesh
| | - Gen Ohtsuki
- Department of Drug Discovery Medicine Kyoto University Graduate School of Medicine Kyoto Japan
| | - Mohammad Jakir Hosen
- Department of Genetic Engineering & Biotechnology Shahjalal University of Science & Technology Sylhet Bangladesh
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36
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Khan A, Khan SA, Zia K, Altowyan MS, Barakat A, Ul-Haq Z. Deciphering the Impact of Mutations on the Binding Efficacy of SARS-CoV-2 Omicron and Delta Variants With Human ACE2 Receptor. Front Chem 2022; 10:892093. [PMID: 35755247 PMCID: PMC9213841 DOI: 10.3389/fchem.2022.892093] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
The pandemic of COVID-19, caused by SARS-CoV-2, has globally affected the human health and economy. Since the emergence of the novel coronavirus SARS-CoV-2, the life-threatening virus continues to mutate and evolve. Irrespective of acquired natural immunity and vaccine-induced immunity, the emerging multiple variants are growing exponentially, crossing the territorial barriers of the modern world. The rapid emergence of SARS-CoV-2 multiple variants challenges global researchers regarding the efficacy of available vaccines and variant transmissibility. SARS-CoV-2 surface-anchored S-protein recognizes and interacts with the host-cell ACE2, facilitating viral adherence and entrance into the cell. Understanding the interfacial interactions between the spike protein of SARS-CoV-2 variants and human ACE2 receptor is important for the design and development of antiviral therapeutics against SARS-CoV-2 emerging variants. Despite extensive research, the crucial determinants related to the molecular interactions between the spike protein of SARS-CoV-2 variants and host receptors are poorly understood. Thus, in this study, we explore the comparative interfacial binding pattern of SARS-CoV-2 spike RBD of wild type, Delta, and Omicron with the human ACE2 receptor to determine the crucial determinants at the atomistic level, using MD simulation and MM/GBSA energy calculations. Based on our findings, the substitution of Q493R, G496S, Q498R, and Y505H induced internal conformational changes in Omicron spike RBD, which leads to higher binding affinity than Delta spike RBD with the human ACE2 receptor, eventually contributing to higher transmission and infectivity. Taken together, these results could be used for the structure-based design of effective antiviral therapeutics against SARS-CoV-2 variants.
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Affiliation(s)
- Alamgir Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Salman Ali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Mezna Saleh Altowyan
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Chemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Zaheer Ul-Haq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.,Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Lekagul A, Chattong A, Rueangsom P, Waleewong O, Tangcharoensathien V. Multi-dimensional impacts of Coronavirus disease 2019 pandemic on Sustainable Development Goal achievement. Global Health 2022; 18:65. [PMID: 35761400 PMCID: PMC9235167 DOI: 10.1186/s12992-022-00861-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Health, social and economic crises triggered by the Coronavirus disease pandemic (COVID-19) can derail progress and achievement of the Sustainable Development Goals. This commentary analyses the complex nexus of multi-dimensional impacts of the pandemic on people, prosperity, planet, partnership and peace. From our analysis, we generate a causal loop diagram explaining these complex pathways and proposed policy recommendations. MAIN TEXT Health systems, health and wellbeing of people are directly affected by the pandemic, while impacts on prosperity, education, food security and environment are indirect consequences from pandemic containment, notably social measures, business and school closures and international travel restrictions. The magnitude of impacts is determined by the level of prior vulnerability and inequity in the society, and the effectiveness and timeliness of comprehensive pandemic responses. CONCLUSIONS To exit the acute phase of the pandemic, equitable access to COVID-19 vaccines by all countries and continued high coverage of face masks and hand hygiene are critical entry points. During recovery, governments should strengthen preparedness based on the One Health approach, rebuild resilient health systems and an equitable society, ensure universal health coverage and social protection mechanisms for all. Governments should review progress and challenges from the pandemic and sustain a commitment to implementing the Sustainable Development Goals.
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Affiliation(s)
- Angkana Lekagul
- International Health Policy Program, Ministry of Public Health, Nonthaburi, 11000, Thailand.
| | - Anamika Chattong
- International Health Policy Program, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Putthipanya Rueangsom
- International Health Policy Program, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Orratai Waleewong
- International Health Policy Program, Ministry of Public Health, Nonthaburi, 11000, Thailand
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Armando F, Beythien G, Kaiser FK, Allnoch L, Heydemann L, Rosiak M, Becker S, Gonzalez-Hernandez M, Lamers MM, Haagmans BL, Guilfoyle K, van Amerongen G, Ciurkiewicz M, Osterhaus ADME, Baumgärtner W. SARS-CoV-2 Omicron variant causes mild pathology in the upper and lower respiratory tract of hamsters. Nat Commun 2022; 13:3519. [PMID: 35725735 DOI: 10.1038/s41467-022-31200-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
Abstract
Since its discovery in 2019, multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have been identified. This study investigates virus spread and associated pathology in the upper and lower respiratory tracts of Syrian golden hamsters at 4 days post intranasal SARS-CoV-2 Omicron infection, in comparison to infection with variants of concern (VOCs) Gamma and Delta as well as ancestral strain 614 G. Pathological changes in the upper and lower respiratory tract of VOC Omicron infected hamsters are milder than those caused by other investigated strains. VOC Omicron infection causes a mild rhinitis with little involvement of the olfactory epithelium and minimal lesions in the lung, with frequent sparing of the alveolar compartment. Similarly, viral antigen, RNA and infectious virus titers are lower in respiratory tissues of VOC Omicron infected hamsters. These findings demonstrate that the variant has a decreased pathogenicity for the upper and lower respiratory tract of hamsters. Since the emergence of SARS-CoV-2 several variants of concerns have been identified, with altered disease progression and transmission dynamics. Here, Armando et al. compare virus spread and pathology in the upper and lower respiratory tracts of Syrian golden hamster after 4 days post infection for VOCs Gamma, Delta and Omicron and find milder pathology for Omicron.
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Satta S, Shahabipour F, Gao W, Lentz SR, Perlman S, Ashammakhi N, Hsiai T. Engineering viral genomics and nano-liposomes in microfluidic platforms for patient-specific analysis of SARS-CoV-2 variants. Theranostics 2022; 12:4779-4790. [PMID: 35832078 PMCID: PMC9254234 DOI: 10.7150/thno.72339] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuing to spread globally, contributing to the persistence of the COVID-19 pandemic. Increasing resources have been focused on developing vaccines and therapeutics that target the Spike glycoprotein of SARS-CoV-2. Recent advances in microfluidics have the potential to recapitulate viral infection in the organ-specific platforms, known as organ-on-a-chip (OoC), in which binding of SARS-CoV-2 Spike protein to the angiotensin-converting enzyme 2 (ACE2) of the host cells occurs. As the COVID-19 pandemic lingers, there remains an unmet need to screen emerging mutations, to predict viral transmissibility and pathogenicity, and to assess the strength of neutralizing antibodies following vaccination or reinfection. Conventional detection of SARS-CoV-2 variants relies on two-dimensional (2-D) cell culture methods, whereas simulating the micro-environment requires three-dimensional (3-D) systems. To this end, analyzing SARS-CoV-2-mediated pathogenicity via microfluidic platforms minimizes the experimental cost, duration, and optimization needed for animal studies, and obviates the ethical concerns associated with the use of primates. In this context, this review highlights the state-of-the-art strategy to engineer the nano-liposomes that can be conjugated with SARS-CoV-2 Spike mutations or genomic sequences in the microfluidic platforms; thereby, allowing for screening the rising SARS-CoV-2 variants and predicting COVID-19-associated coagulation. Furthermore, introducing viral genomics to the patient-specific blood accelerates the discovery of therapeutic targets in the face of evolving viral variants, including B1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), c.37 (Lambda), and B.1.1.529 (Omicron). Thus, engineering nano-liposomes to encapsulate SARS-CoV-2 viral genomic sequences enables rapid detection of SARS-CoV-2 variants in the long COVID-19 era.
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Affiliation(s)
- Sandro Satta
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, Los Angeles, California, USA
- Division of Cardiology, Department of Medicine, School of Medicine, University of California, Los Angeles, California, USA
| | - Fahimeh Shahabipour
- Skin Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Wei Gao
- Medical Engineering, California Institute of Technology, California, Pasadena, USA
| | - Steven R. Lentz
- Section of Hematology, Oncology, and Blood & Marrow Transplantation, Department of Medicine, College of Medicine, University of Iowa, Iowa, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, College of Medicine, University of Iowa, USA
| | - Nureddin Ashammakhi
- Department of Bioengineering, Henry Samueli School of Engineering & Applied Science, University of California, CA, USA
- Institute for Quantitative Health Science & Engineering and Department of Biomedical Engineering, College of Engineering, Michigan State University, MI, USA
| | - Tzung Hsiai
- Department of Bioengineering, School of Engineering, University of California, Los Angeles, California, USA
- Department of Medicine, Greater Los Angeles VA Healthcare System, Los Angeles, California, USA
- Division of Cardiology, Department of Medicine, School of Medicine, University of California, Los Angeles, California, USA
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Peng KL, Lin PM, Xu J, Wang X. Realtime online courses mutated amid the COVID-19 pandemic: Empirical study in hospitality program. Journal of Hospitality, Leisure, Sport & Tourism Education 2022; 30:100379. [PMID: 35313467 PMCID: PMC8926878 DOI: 10.1016/j.jhlste.2022.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 12/02/2022]
Abstract
Real-time online courses (RTOCs), a new online learning mode, have been developed because of a longitudinal suspension of classes amid the COVID-19 pandemic worldwide. We explore an information model to review the learning process and outcomes of RTOCs, which conducted educational activities via social media. Results show that social media can be a potent mediation factor with the moderation of structural differentiation to facilitate online learning outcomes. Conclusions imply that the life-changing impact of COVID-19 has caused an evolutionary online education mode that can be hybridized with face-to-face education and massive open online courses to flourish education approaches and pedagogies.
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Khandia R, Singhal S, Alqahtani T, Kamal MA, El-Shall NA, Nainu F, Desingu PA, Dhama K. Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic. Environ Res 2022; 209:112816. [PMID: 35093310 PMCID: PMC8798788 DOI: 10.1016/j.envres.2022.112816] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 02/05/2023]
Abstract
Since the appearance in the late of December 2019, SARS-CoV-2 is rapidly evolving and mutating continuously, giving rise to various variants with variable degrees of infectivity and lethality. The virus that initially appeared in China later mutated several times, wreaking havoc and claiming many lives worldwide amid the ongoing COVID-19 pandemic. After Alpha, Beta, Gamma, and Delta variants, the most recently emerged variant of concern (VOC) is the Omicron (B.1.1.529) that has evolved due to the accumulation of high numbers of mutations especially in the spike protein, raising concerns for its ability to evade from pre-existing immunity acquired through vaccination or natural infection as well as overpowering antibodies-based therapies. Several theories are on the surface to explain how the Omicron has gathered such a high number of mutations within less time. Few of them are higher mutation rates within a subgroup of population and then its introduction to a larger population, long term persistence and evolution of the virus in immune-compromised patients, and epizootic infection in animals from humans, where under different immune pressures the virus mutated and then got reintroduced to humans. Multifaceted approach including rapid diagnosis, genome analysis of emerging variants, ramping up of vaccination drives and receiving booster doses, efficacy testing of vaccines and immunotherapies against newly emerged variants, updating the available vaccines, designing of multivalent vaccines able to generate hybrid immunity, up-gradation of medical facilities and strict implementation of adequate prevention and control measures need to be given high priority to handle the on-going SARS-CoV-2 pandemic successfully.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, MP, India.
| | - Shailja Singhal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, 462026, MP, India
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, 62529, Abha, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Bangladesh; Enzymoics, 7 Peterlee place, Hebersham, NSW, 2770, Novel Global Community Educational Foundation, Australia
| | - Nahed A El-Shall
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Alexandria University, Edfina, El-Beheira, 22758, Egypt
| | - Firzan Nainu
- Department of Pharmacy, Faculty of Pharmacy, Hasanuddin University, Makassar, 90245, Indonesia
| | - Perumal Arumugam Desingu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
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Poudel S, Nepali P, Baniya S, Shah S, Bogati S, Nepal G, Ojha R, Edaki O, Lazovic G, Kara S. Bell's palsy as a possible complication of mRNA-1273 (Moderna) vaccine against COVID-19. Ann Med Surg (Lond) 2022; 78:103897. [PMID: 35663122 PMCID: PMC9151463 DOI: 10.1016/j.amsu.2022.103897] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/20/2022] Open
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Herrera-calderon O, Saleh AM, Yepes-perez AF, Aljarba NH, Alkahtani S, Batiha GE, Hañari-quispe RD, Chavez H, Pari-olarte JB, Loyola-gonzales E, Almeida-galindo JS, Kong-chirinos JF, Benali T, Eldehna W. Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein. J CHEM-NY 2022; 2022:1-19. [DOI: 10.1155/2022/8539918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The SARS-CoV-2 Omicron variant has spread rapidly and is considered the predominant variant in the world, and its main characteristic is related to evade immunity from natural infection or vaccines, due to its multiple mutations in the spike protein. On the other hand, medicinal plants have been used as alternatives therapies to ameliorate some signs and symptoms in COVID-19, and in our previous work, the cat’s claw (Uncaria tomentosa) stem bark has been studied in vitro and showed antiviral activity on SARS-CoV-2 as well as in silico studies on the 3CLpro protein and as disruptor between the ACE-2 human receptor and the spike protein. The aim in this computational study was to determine the main phytochemical constituents from U. tomentosa stem bark against the SARS-CoV-2 Omicron spike protein based on molecular modeling. A molecular docking was carried out on the isolated phytochemicals in a previous work against the SARS-CoV-2 Omicron spike protein-binding domain (PDB ID: 7T9K). Next, a molecular dynamic study was carried out to monitor the stability during the MD simulations. As results proanthocyanidin-C1 (-10.76 kcal/mol), quinovic acid-type 2 (-9.86 kcal/mol), and proanthocyanidin-B2 (-9.82 kcal/mol) were the constituents with the best binding free energy on the SARS-CoV-2 Omicron spike protein, and the best compound was stable during the dynamic simulation under physiological conditions. It is concluded that the anthocyanidin-based compounds determined in the stem bark ethanol extract could be responsible for the potential antiviral activity on SARS-CoV-2 Omicron variant, and the proanthocyanidin-C1 emerged as a powerful candidate to combat new variants.
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Javadinia SA, Alizadeh K, Mojadadi MS, Nikbakht F, Dashti F, Joudi M, Harati H, Welsh JS, Farahmand SA, Attarian F. COVID-19 Vaccination in Patients With Malignancy; A Systematic Review and Meta-Analysis of the Efficacy and Safety. Front Endocrinol (Lausanne) 2022; 13:860238. [PMID: 35586627 PMCID: PMC9108702 DOI: 10.3389/fendo.2022.860238] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/25/2022] [Indexed: 12/20/2022] Open
Abstract
Background Data on the efficacy and safety of COVID-19 vaccines in patients with malignancy are immature. In this paper, we assessed the literature involving the use of COVID-19 vaccines in cancer patients and reported the seroconversion rates as the main outcome and severity of COVID-19 infection and side effects following COVID-19 vaccination as the secondary outcomes. Methods A systematic review with meta-analysis was performed. Searches were conducted in electronic websites, databases, and journals, including Scopus, PubMed, Embase, and Web of Science from January 01, 2019, to November 30, 2021. Studies reporting data on the safety and efficacy of COVID vaccine in cancer patients using any human samples were included. The risk of bias was assessed using the NEWCASTLE-OTTAWA scale in the included studies. Results A total of 724 articles were identified from databases, out of which 201 articles were duplicates and were discarded. Subsequently, 454 articles were excluded through initial screening of the titles and abstracts. Moreover, 41 studies did not report the precise seroconversion rate either based on the type of cancer or after injection of a second dose of COVID vaccine. Finally, 28 articles met all the inclusion criteria and were included in this systematic review. The overall seroconversion rates after receiving a second dose of COVID-19 vaccine, based on type of cancer were 88% (95% CI, 81%-92%) and 70% (95% CI, 60%-79%) in patients with solid tumors and hematologic malignancies, respectively. Conclusion Overall, we conclude that vaccination against COVID-19 in patients with active malignancies using activated and inactivated vaccines is a safe and tolerable procedure that is also accompanied by a high efficacy.
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Affiliation(s)
- Seyed Alireza Javadinia
- Non-Communicable Diseases Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Kimia Alizadeh
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | | | - Fateme Nikbakht
- Department of Epidemiology, School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzaneh Dashti
- Faculty of Medicine, Birjand University of Medical Science, Birjand, Iran
| | - Maryam Joudi
- Department of Pediatrics, School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Hadi Harati
- Pediatric Gastroenterology and Hepatology Research Center, Zabol University of Medical Sciences, Zabol, Iran
| | - James S. Welsh
- Department of Radiation Oncology, Edward Hines Jr Veterans Administration (VA) Hospital and Loyola University Chicago Stritch School of Medicine, Chicago, IL, United States
| | - Seyed Amir Farahmand
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Fahimeh Attarian
- Department of Public Health, School of Health, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
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Zandi M, Soltani S, Tabibzadeh A, Nasimzadeh S, Behboudi E, Zakeri A, Erfani Y, Salmanzadeh S, Abbasi S. Partial sequence conservation of SARS-CoV-2 NSP-2, NSP-12, and Spike in stool samples from Abadan, Iran. Biotechnol Appl Biochem 2022; 70:201-209. [PMID: 35396867 PMCID: PMC9082511 DOI: 10.1002/bab.2343] [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: 11/01/2021] [Accepted: 02/28/2022] [Indexed: 11/09/2022]
Abstract
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, the clinical manifestations of the virus have undergone many changes. Recently, there have been many reports on gastrointestinal symptoms in COVID-19 patients. This study is aimed to perform a detailed phylogenetic study and assessment of different SNVs in the RNA genome of viruses isolated from fecal samples of patients with COVID-19 who have gastrointestinal symptoms, which can help better understand viral pathogenesis. In the present study, 20 fecal samples were collected by written consent from COVID-19 patients. According to the manufacturer's protocol, virus nucleic acid was extracted from stool samples and the SARS-CoV-2 genome presence in stool samples was confirmed by RT-PCR assay. Three viral genes, S, nsp12, and nsp2, were amplified using the reverse transcription polymerase chain reaction (RT-PCR) method and specific primers. Multiple sequencing alignment (MSA) was performed in the CLC word bench, and a phylogenetic tree was generated by MEGA X based on the neighbor-joining method. Of all cases, 11 (55%) were males. The mean age of the patients was 33.6 years. Diabetes (70%) and blood pressure (55%) were the most prevalent comorbidities. All 20 patients were positive for SARS-CoV-2 infection in respiratory samples. Molecular analysis investigation among 20 stool samples revealed that the SARS-CoV-2 genome was found among 10 stool samples; only three samples were used for sequencing. The polymorphism and phylogenetic analysis in SARS-CoV-2 showed great similarity among all of the evaluated genes with the Wuhan reference sequence and all of the current variants of concern (VOCs). The current study represents a great similarity in polymorphism and phylogenetic analysis of the SARS-CoV-2 isolates with the Wuhan reference sequence and all of the current VOC in the particular evaluated partial sequences of S, nsp12, and nsp2.
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Affiliation(s)
- Milad Zandi
- Department of VirologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Saber Soltani
- Department of VirologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | | | - Sepideh Nasimzadeh
- Department of Medical VirologySchool of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Emad Behboudi
- Department of MicrobiologyGolestan University of Medical SciencesGorganIran
| | - Armin Zakeri
- Department of HematologyFaculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | - Yousef Erfani
- Department of Medical Laboratory SciencesSchool of Allied Medical SciencesTehran University Medical SciencesTehranIran
| | - Shokrollah Salmanzadeh
- Health Research InstituteInfectious and Tropical Diseases Research CenterAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Samaneh Abbasi
- Department of MicrobiologySchool of MedicineAbadan University of Medical SciencesAbadanIran
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Abstract
![]()
Simple
and effective molecular diagnostic methods have gained importance
due to the devastating effects of the COVID-19 pandemic. Various isothermal
one-pot COVID-19 detection methods have been proposed as favorable
alternatives to standard RT-qPCR methods as they do not require sophisticated
and/or expensive devices. However, as one-pot reactions are highly
complex with a large number of variables, determining the optimum
conditions to maximize sensitivity while minimizing diagnostic cost
can be cumbersome. Here, statistical design of experiments (DoE) was
employed to accelerate the development and optimization of a CRISPR/Cas12a-RPA-based
one-pot detection method for the first time. Using a definitive screening
design, factors with a significant effect on performance were elucidated
and optimized, facilitating the detection of two copies/μL of
full-length SARS-CoV-2 (COVID-19) genome using simple instrumentation.
The screening revealed that the addition of a reverse transcription
buffer and an RNase inhibitor, components generally omitted in one-pot
reactions, improved performance significantly, and optimization of
reverse transcription had a critical impact on the method’s
sensitivity. This strategic method was also applied in a second approach
involving a DNA sequence of the N gene from the COVID-19 genome. The
slight differences in optimal conditions for the methods using RNA
and DNA templates highlight the importance of reaction-specific optimization
in ensuring robust and efficient diagnostic performance. The proposed
detection method is automation-compatible, rendering it suitable for
high-throughput testing. This study demonstrated the benefits of DoE
for the optimization of complex one-pot molecular diagnostics methods
to increase detection sensitivity.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, Edinburgh EH9 3BD, United Kingdom
| | - Laura E. Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, Edinburgh EH9 3BD, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, Edinburgh EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K
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Situmorang DDB. The efficacy of "rapid tele-psychotherapy" with single-session music therapy: A personal reflection as a founder. Palliat Support Care 2022;:1-2. [PMID: 35317880 DOI: 10.1017/S1478951522000293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Samanta A, Alam SSM, Ali S, Hoque M. Analyzing the interaction of human ACE2 and RBD of spike protein of SARS-CoV-2 in perspective of Omicron variant. EXCLI J 2022; 21:610-620. [PMID: 35651657 PMCID: PMC9149974 DOI: 10.17179/excli2022-4721] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/25/2022] [Indexed: 01/18/2023]
Abstract
The newly identified Omicron (B.1.1.529) variant of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has steered concerns across the world due to the possession of a large number of mutations leading to high infectivity and vaccine escape potential. The Omicron variant houses 32 mutations in spike (S) protein alone. The viral infectivity is determined mainly by the ability of S protein Receptor Binding Domain (RBD) to bind to the human Angiotensin I Converting Enzyme 2 (hACE2) receptor. In this paper, the interaction of the RBDs of SARS-CoV-2 variants with hACE2 was analyzed by using protein-protein docking and compared with the novel Omicron variant. Our findings reveal that the Omicron RBD interacts strongly with hACE2 receptor via unique amino acid residues as compared to the Wuhan and many other variants. However, the interacting residues of RBD are found to be the same in Lamda (C.37) variant. This unique binding of Omicron RBD with hACE2 suggests an increased potential of infectivity and vaccine evasion potential of the new variant. The evolutionary drive of the SARS-CoV-2 may not be exclusively driven by RBD variants but surely provides for the platform for emergence of new variants.
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Affiliation(s)
- Arijit Samanta
- Applied Bio-Chemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
| | | | - Safdar Ali
- Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
| | - Mehboob Hoque
- Applied Bio-Chemistry Laboratory, Department of Biological Sciences, Aliah University, Kolkata 700160, India
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Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G, Chakraborty C. Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. GeroScience 2022. [PMID: 35258772 DOI: 10.1007/s11357-022-00532-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023] Open
Abstract
The Omicron variant has been detected in nearly 150 countries. We analyzed the mutational landscape of Omicron throughout the genome, focusing the S-glycoprotein. We also evaluated mutations in the antibody-binding regions and observed some important mutations overlapping those of previous variants including N501Y, D614G, H655Y, N679K, and P681H. Various new receptor-binding domain mutations were detected, including Q493K, G496S, Q498R, S477N, G466S, N440K, and Y505H. New mutations were found in the NTD (Δ143-145, A67V, T95I, L212I, and Δ211) including one new mutation in fusion peptide (D796Y). There are several mutations in the antibody-binding region including K417N, E484A, Q493K, Q498R, N501Y, and Y505H and several near the antibody-binding region (S477N, T478K, G496S, G446S, and N440K). The impact of mutations in regions important for the affinity between spike proteins and neutralizing antibodies was evaluated. Furthermore, we examined the effect of significant antibody-binding mutations (K417N, T478K, E484A, and N501Y) on antibody affinity, stability to ACE2 interaction, and possibility of amino acid substitution. All the four mutations destabilize the antibody-binding affinity. This study reveals future directions for developing neutralizing antibodies against the Omicron variant.
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Lundberg AL, Lorenzo-Redondo R, Hultquist JF, Hawkins CA, Ozer EA, Welch SB, Prasad PVV, Achenbach CJ, White JI, Oehmke JF, Murphy RL, Havey RJ, Post LA. Overlapping Delta and Omicron Outbreaks: Dynamic Panel Data (Preprint). JMIR Public Health Surveill 2022; 8:e37377. [PMID: 35500140 PMCID: PMC9169703 DOI: 10.2196/37377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 11/17/2022] Open
Abstract
Background The Omicron variant of SARS-CoV-2 is more transmissible than prior variants of concern (VOCs). It has caused the largest outbreaks in the pandemic, with increases in mortality and hospitalizations. Early data on the spread of Omicron were captured in countries with relatively low case counts, so it was unclear how the arrival of Omicron would impact the trajectory of the pandemic in countries already experiencing high levels of community transmission of Delta. Objective The objective of this study is to quantify and explain the impact of Omicron on pandemic trajectories and how they differ between countries that were or were not in a Delta outbreak at the time Omicron occurred. Methods We used SARS-CoV-2 surveillance and genetic sequence data to classify countries into 2 groups: those that were in a Delta outbreak (defined by at least 10 novel daily transmissions per 100,000 population) when Omicron was first sequenced in the country and those that were not. We used trend analysis, survival curves, and dynamic panel regression models to compare outbreaks in the 2 groups over the period from November 1, 2021, to February 11, 2022. We summarized the outbreaks in terms of their peak rate of SARS-CoV-2 infections and the duration of time the outbreaks took to reach the peak rate. Results Countries that were already in an outbreak with predominantly Delta lineages when Omicron arrived took longer to reach their peak rate and saw greater than a twofold increase (2.04) in the average apex of the Omicron outbreak compared to countries that were not yet in an outbreak. Conclusions These results suggest that high community transmission of Delta at the time of the first detection of Omicron was not protective, but rather preluded larger outbreaks in those countries. Outbreak status may reflect a generally susceptible population, due to overlapping factors, including climate, policy, and individual behavior. In the absence of strong mitigation measures, arrival of a new, more transmissible variant in these countries is therefore more likely to lead to larger outbreaks. Alternately, countries with enhanced surveillance programs and incentives may be more likely to both exist in an outbreak status and detect more cases during an outbreak, resulting in a spurious relationship. Either way, these data argue against herd immunity mitigating future outbreaks with variants that have undergone significant antigenic shifts.
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Affiliation(s)
- Alexander L Lundberg
- Buehler Center for Health Policy and Economics, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Center for Pathogen Genomics and Microbial Evolution, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Center for Pathogen Genomics and Microbial Evolution, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Claudia A Hawkins
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Center for Global Communicable and Emerging Infectious Diseases, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Center for Pathogen Genomics and Microbial Evolution, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Sarah B Welch
- Buehler Center for Health Policy and Economics, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Chad J Achenbach
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Robert J Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Janine I White
- Buehler Center for Health Policy and Economics, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - James F Oehmke
- Buehler Center for Health Policy and Economics, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Robert L Murphy
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Robert J Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Robert J Havey
- Robert J Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Department of Medicine, General Internal Medicine and Geriatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Lori A Post
- Buehler Center for Health Policy and Economics, Robert J Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
- Department of Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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