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Essabbar A, El Mazouri S, Boumajdi N, Bendani H, Aanniz T, Mouna O, Lahcen B, Ibrahimi A. Temporal Dynamics and Genomic Landscape of SARS-CoV-2 After Four Years of Evolution. Cureus 2024; 16:e53654. [PMID: 38327721 PMCID: PMC10849819 DOI: 10.7759/cureus.53654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2024] [Indexed: 02/09/2024] Open
Abstract
Introduction Since its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive genomic evolution, impacting public health policies, diagnosis, medication, and vaccine development. This study leverages advanced bioinformatics to assess the virus's temporal and regional genomic evolution from December 2019 to October 2023. Methods Our analysis incorporates 16,575 complete SARS-CoV-2 sequences collected from 214 countries. These samples were comparatively analyzed, with a detailed characterization of nucleic mutations, lineages, distribution, and evolutionary patterns during each year, using the Wuhan-Hu-1 strain as the reference. Results Our analysis has identified a total of 21,580 mutations that we classified into transient mutations, which diminished over time, and persistent mutations with steadily increasing frequencies. This mutation landscape led to a notable surge in the evolutionary rate, rising from 13 mutations per sample in 2020 to 96 by 2023, with minor geographic variations. The phylogenetic analysis unveiled three distinct evolutionary branches, each representing unique viral evolution pathways. These lineages exhibited a tendency for a reduced duration of dominance with a shortening prevalence period over time, as dominant strains were consistently replaced by more fit variants. Notably, the emergence of the Alpha and Delta variants in 2021 was followed by the subsequent dominance of Omicron clade variants that have branched into several recombinant variants in 2022, marking a significant shift in the viral landscape. Conclusion This study sheds light on the dynamic nature of SARS-CoV-2 evolution, emphasizing the importance of continuous and vigilant genomic surveillance. The dominance of recombinant lineages, coupled with the disappearance of local variants, underscores the virus's adaptability.
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Affiliation(s)
- Abdelmounim Essabbar
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
- Toulouse Cancer Research Center, Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, FRA
| | - Safae El Mazouri
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Nassma Boumajdi
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Houda Bendani
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Tarik Aanniz
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Ouadghiri Mouna
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
| | - Belyamani Lahcen
- Émergency Department, Military Hospital Rabat Morocco, Rabat, MAR
- Mohammed VI Center For Research and Innovation, Mohammed VI University of Sciences and Health, Rabat, MAR
| | - Azeddine Ibrahimi
- Biotechnology Lab (MedBiotech) Bioinova Research Center, Rabat Medical & Pharmacy School, Mohammed V University, Rabat, MAR
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2
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Gonzalez-Alba JM, Rojo-Alba S, Perez-Martinez Z, Boga JA, Alvarez-Arguelles ME, Gomez J, Herrero P, Costales I, Alba LM, Martin-Rodriguez G, Campo R, Castelló-Abietar C, Sandoval M, Abreu-Salinas F, Coto E, Rodriguez M, Rubianes P, Sanchez ML, Vazquez F, Antuña L, Álvarez V, Melón García S. Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain. Access Microbiol 2023; 5:000573.v4. [PMID: 37841093 PMCID: PMC10569657 DOI: 10.1099/acmi.0.000573.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Mutational analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can quantify the relative importance of variants over time, enable dominant mutations to be identified, and facilitate near real-time detection, comparison and tracking of evolving variants. SARS-CoV-2 in Asturias, an autonomous community of Spain with a large ageing population, and high levels of migration and tourism, was monitored and tracked from the beginning of the pandemic in February 2020 until its decline and stabilization in August 2021, and samples were characterized using whole genomic sequencing and single nucleotide polymorphisms. Data held in the GISAID database were analysed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1 % of the population with SARS-CoV-2 were found, identifying ten major variants worldwide (seven arose before January 2021), 19 regional and one local. In Asturias only 17 different variants were found. After vaccination, no further regional major variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures such as rapid diagnosis, isolation and vaccination were efficient.
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Affiliation(s)
- Jose Maria Gonzalez-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Susana Rojo-Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Zulema Perez-Martinez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Jose A. Boga
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Elena Alvarez-Arguelles
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Juan Gomez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Pablo Herrero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Isabel Costales
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luz Maria Alba
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gabriel Martin-Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rainer Campo
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Cristian Castelló-Abietar
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Marta Sandoval
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fátima Abreu-Salinas
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Eliecer Coto
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Mercedes Rodriguez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Rubianes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Maria Luisa Sanchez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Fernando Vazquez
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Antuña
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Urgencias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Victoria Álvarez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Servicio de Genética Molecular, Oviedo, Spain
| | - Santiago Melón García
- Servicio de Microbiología, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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3
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Chattopadhyay A, Jailani AAK, Mandal B. Exigency of Plant-Based Vaccine against COVID-19 Emergence as Pandemic Preparedness. Vaccines (Basel) 2023; 11:1347. [PMID: 37631915 PMCID: PMC10458178 DOI: 10.3390/vaccines11081347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
After two years since the declaration of COVID-19 as a pandemic by the World Health Organization (WHO), more than six million deaths have occurred due to SARS-CoV-2, leading to an unprecedented disruption of the global economy. Fortunately, within a year, a wide range of vaccines, including pathogen-based inactivated and live-attenuated vaccines, replicating and non-replicating vector-based vaccines, nucleic acid (DNA and mRNA)-based vaccines, and protein-based subunit and virus-like particle (VLP)-based vaccines, have been developed to mitigate the severe impacts of the COVID-19 pandemic. These vaccines have proven highly effective in reducing the severity of illness and preventing deaths. However, the availability and supply of COVID-19 vaccines have become an issue due to the prioritization of vaccine distribution in most countries. Additionally, as the virus continues to mutate and spread, questions have arisen regarding the effectiveness of vaccines against new strains of SARS-CoV-2 that can evade host immunity. The urgent need for booster doses to enhance immunity has been recognized. The scarcity of "safe and effective" vaccines has exacerbated global inequalities in terms of vaccine coverage. The development of COVID-19 vaccines has fallen short of the expectations set forth in 2020 and 2021. Furthermore, the equitable distribution of vaccines at the global and national levels remains a challenge, particularly in developing countries. In such circumstances, the exigency of plant virus-based vaccines has become apparent as a means to overcome supply shortages through fast manufacturing processes and to enable quick and convenient distribution to millions of people without the reliance on a cold chain system. Moreover, plant virus-based vaccines have demonstrated both safety and efficacy in eliciting robust cellular immunogenicity against COVID-19 pathogens. This review aims to shed light on the advantages and disadvantages of different types of vaccines developed against SARS-CoV-2 and provide an update on the current status of plant-based vaccines in the fight against the COVID-19 pandemic.
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Affiliation(s)
- Anirudha Chattopadhyay
- Pulses Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar 385506, India;
| | - A. Abdul Kader Jailani
- Department of Plant Pathology, North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
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4
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Ahmadi K, Hosseinpour M, Rismani E, Hassaniazad M, Mafakher L, Jahantigh HR, Eftekhar E, Gouklani H. Characterization of SARS-CoV-2 isolated from a patient in Iran compared to SARS-CoV-2 different variants. J Biomol Struct Dyn 2023; 41:1217-1232. [PMID: 35007466 DOI: 10.1080/07391102.2021.2017354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Since the onset of the global epidemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), whole genome sequencing of virus in all countries has been considered to track and predict virus transmission and variation patterns. In the current study we reported a novel complete genome sequence of SARS-CoV-2 isolated from Iran. Genomics variations and protein sequences were evaluated for the isolated sequence and seven Iranian complete genome sequences of SARS-CoV-2 from NCBI using the reference genome of the SARS-CoV-2 Wuhan-Hu-1. The results showed six nucleotide substitutions. The multiple sequence alignment of the spike protein of the Wuhan-Hu-1 strain and the emerging variants indicated similar its residue pattern in the current sequence to the Wuhan-Hu-1 strain. There were relatively similar binding affinity and residues involved in the interactions of the spike receptor-binding domain (RBD) of the Wuhan-Hu-1 strain, the variants and Hormozgan With angiotensin-converting enzyme 2 (ACE2). Tracing the phylogeny of virus indicated distinct clustering of Iranian variants in branches close to the Asian countries. The mutation effect study on the function of proteins predicted neutral impact of all six nucleotide substitutions. However, the free energy calculations indicated a decreasing the protein stability related to the mutations. This data, consistent with similar studies, showed that despite the high similarity in the nucleotide sequence of the SARS-CoV-2, the mutation pattern varies from country to country. Therefore, any country can benefit from these studies to track and find appropriate strategies for treating and controlling the epidemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahmood Hosseinpour
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Elham Rismani
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Hassaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hamid Reza Jahantigh
- Interdisciplinary Department of Medicine-Section of Occupational Medicine, University of Bari, Bari, Italy
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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5
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AlMatar M, Ramli ANM, Albarri O, Yi CX. Insights into the Structural Complexities of SARS-CoV-2 for Therapeutic and Vaccine Development. Comb Chem High Throughput Screen 2023; 26:1945-1959. [PMID: 36366840 DOI: 10.2174/1386207326666221108095705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/06/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022]
Abstract
SARS-CoV-2 is a disease that endangers both human life and the economy. There was an 11- month period of relative evolutionary standstill following the appearance of SARS-CoV-2 in late 2019. However, the emergence of clusters of mutations known as' variants of concern 'with variable viral properties such as transmissibility and antigenicity defined the evolution of SARS-CoV-2. Several efforts have been made in recent months to understand the atomic level properties of SARS-CoV-2. A review of the literature on SARS-CoV-2 mutations is offered in this paper. The critical activities performed by different domains of the SARS-CoV-2 genome throughout the virus's entry into the host and overall viral life cycle are discussed in detail. These structural traits may potentially pave the way for the development of a vaccine and medication to combat the SARS-CoV-2 sickness.
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Affiliation(s)
- Manaf AlMatar
- Faculty of Education and Art, Sohar University, Sohar, 311, Sultanate of Oman
| | - Aizi Nor Mazila Ramli
- Faculty of Industrial Science and Technology, University Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitüsü) Çukurova
University, Adana, Turkey
| | - Osman Albarri
- Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Choong Xin Yi
- Faculty of Industrial Science and Technology, University Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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6
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Oliveira FADS, de Holanda MV, Lima LB, Dantas MB, Duarte IO, de Castro LGZ, de Oliveira LLB, Paier CRK, Moreira-Nunes CDFA, Lima NCB, de Moraes MEA, de Moraes Filho MO, Melo VMM, Montenegro RC. Genomic surveillance: Circulating lineages and genomic variation of SARS-CoV-2 in early pandemic in Ceará state, Northeast Brazil. Virus Res 2022; 321:198908. [PMID: 36057416 PMCID: PMC9429123 DOI: 10.1016/j.virusres.2022.198908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/24/2022]
Abstract
In the Northeast of Brazil, Ceará was the second state most impacted by COVID-19 in number of cases and death rate. Despite that, the early dynamics of the pandemic in Ceará was not yet well understood due the low genomic surveillance of SARS-CoV-2 in 2020. In this study, we analyze the circulating lineages and the genomic variation of the virus in Ceará state. Thirty-four genomes were sequenced and combined with sequences available in GISAID database from March 2020 to June 2021 to compose the study dataset. The most prevalent lineages detected were B.1.1.33, in 2020, and P.1, in 2021. Other lineages were found, such as P.2, sublineages of P.1, B.1, B.1.1, B.1.1.28 and B.1.212. Analyzing the mutations, a total of 202 single-nucleotide polymorphisms (SNPs) were identified among the 34 genomes sequenced, of which 127 were missense, 74 synonymous, and one was a nonsense mutation. Among the missense mutations, C14408T, A23403G, T27299C, G28881A G28883C, and T29148C were the most prevalent within the dataset. Although SARS-CoV-2 sequencing data was limited in 2020, our results could provide insights to better understand the genetic diversity of the circulating lineages in Ceará.
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Affiliation(s)
- Francisca Andréa da Silva Oliveira
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil.
| | - Maísa Viana de Holanda
- Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
| | - Luína Benevides Lima
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
| | - Mariana Brito Dantas
- Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
| | - Igor Oliveira Duarte
- Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil
| | - Luzia Gabrielle Zeferino de Castro
- Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil
| | - Laís Lacerda Brasil de Oliveira
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
| | - Carlos Roberto Koscky Paier
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
| | - Caroline de Fátima Aquino Moreira-Nunes
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
| | - Nicholas Costa Barroso Lima
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 907, Pici, 60440-900, Fortaleza, CE, Brazil
| | - Maria Elisabete Amaral de Moraes
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
| | - Manoel Odorico de Moraes Filho
- Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil.
| | - Vânia Maria Maciel Melo
- Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici, s/n, Bloco 909, Pici, 60455-760, Fortaleza, CE, Brazil
| | - Raquel Carvalho Montenegro
- Laboratório de Farmacogenética, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil; Central de Genômica e Bioinformática, Núcleo de Pesquisa e Desenvolvimento de Medicamentos, Universidade Federal do Ceará, Rua Coronel Nunes de Melo, n° 1000, 60430-270, Fortaleza, CE, Brazil
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7
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Madi N, Safar HA, Mustafa AS, Chehadeh W, Asadzadeh M, Sadeq M, Alawadhi E, Al-Muhaini A, Benthani FA. Molecular epidemiology and genetic characterization of SARS-CoV-2 in Kuwait: A descriptive study. Front Microbiol 2022; 13:858770. [PMID: 36090111 PMCID: PMC9459148 DOI: 10.3389/fmicb.2022.858770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been fatal to human health, affecting almost the entire world. Here we reported, for the first time, characterization of the genetic variants of SARS-CoV-2 circulating in Kuwait to understand their genetic diversity and monitor the accumulation of mutations over time. This study randomly enrolled 209 COVID-19 patients whose nasopharyngeal swabs were positive for SARS-CoV-2 between February 2020 and June 2021 using RT-PCR. The whole genomes of SARS-CoV-2 from the nasopharyngeal swabs were sequenced using the Oxford Nanopore sequencing technology following the ARTIC network protocol. Whole-genome sequencing has identified different clades/sub-clades circulating in Kuwait, mimicking the virus’s global spread. Clade 20A was dominant from February 2020 until January 2021, and then clade 20I (Alpha, V1) emerged and dominated. In June 2021, the number of cases infected with clades 21I, 21A, and 21 J (Delta) increased and dominated. We detected several known clade-defining missense and synonymous mutations and other missense mutations in the genes encoding important viral proteins, including ORF1a, S, ORF3a, ORF8 regions and a novel mutation in the N region. ORF1ab region harbored more mutations and deletions (n = 62, 49.2%) compared to the other 12 gene regions, and the most prevalent missense mutations were P314L (97%) in ORF1b and D614G (97%) in the S glycoprotein regions. Detecting and analyzing mutations and monitoring the evolution of SARS-CoV-2 over time is essential to help better understand the spread of various clades/strains of SARS-CoV-2 and their implications for pathogenesis. In addition, knowledge of the circulating variants and genome sequence variability of SARS-CoV-2 may potentially influence the development of vaccines and antiviral drugs to control the COVID-19 pandemic.
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Affiliation(s)
- Nada Madi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
- *Correspondence: Nada Madi,
| | - Hussain A. Safar
- OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | | | - Ebaa Alawadhi
- Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Ali Al-Muhaini
- Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Fahad A. Benthani
- Research Institute for Developmental Medicine, Johannes Kepler University of Linz, Linz, Austria
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8
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Vassilaki N, Papadimitriou K, Ioannidis A, Papandreou NC, Milona RS, Iconomidou VA, Chatzipanagiotou S. SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. Microorganisms 2022; 10:microorganisms10071430. [PMID: 35889149 PMCID: PMC9322066 DOI: 10.3390/microorganisms10071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility rate, albeit a lower case fatality rate, which results in accumulation of a significant number of mutations and a faster evolution rate. Genomic studies on the mutation rate of the virus, as well as the identification of mutations that prevail and their impact on disease severity, are of great importance for pandemic surveillance and vaccine and drug development. Here, we aim to identify mutations on the SARS-CoV-2 viral genome and their effect on the proteins they are located in, in Greek patients infected in the first wave of the pandemic. To this end, we perform SARS-CoV-2 amplicon-based NGS sequencing on nasopharyngeal swab samples from Greek patients and bioinformatic analysis of the results. Although SARS-CoV-2 is considered genetically stable, we discover a variety of mutations on the viral genome. In detail, 18 mutations are detected in total on 10 SARS-CoV-2 isolates. The mutations are located on ORF1ab, S protein, M protein, ORF3a and ORF7a. Sixteen are also detected in patients from other regions around the world, and two are identified for the first time in the present study. Most of them result in amino acid substitutions. These substitutions are analyzed using computational tools, and the results indicate minor or major impact on the proteins’ structural stability, which could probably affect viral transmissibility and pathogenesis. The correlation of these variations with the viral load levels is examined, and their implication for disease severity and the biology of the virus are discussed.
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Affiliation(s)
- Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece; (N.V.); (R.S.M.)
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Anastasios Ioannidis
- Department of Nursing, Faculty of Health Sciences, University of Peloponnese, Sehi Area, 22100 Tripoli, Greece;
| | - Nikos C. Papandreou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (N.C.P.); (V.A.I.)
| | - Raphaela S. Milona
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece; (N.V.); (R.S.M.)
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (N.C.P.); (V.A.I.)
| | - Stylianos Chatzipanagiotou
- Department of Medical Biopathology, Eginition Hospital, Athens Medical School, National and Kapodistrian University of Athens, 72–74 Vasilissis Sofias Avenue, 11528 Athens, Greece
- Correspondence:
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Ahmed I, Jeon G. Enabling Artificial Intelligence for Genome Sequence Analysis of COVID-19 and Alike Viruses. Interdiscip Sci 2022; 14:504-519. [PMID: 34357528 PMCID: PMC8342660 DOI: 10.1007/s12539-021-00465-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/18/2021] [Accepted: 07/23/2021] [Indexed: 12/01/2022]
Abstract
Recent pandemic of COVID-19 (Coronavirus) caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has been growing lethally with unusual speed. It has infected millions of people and continues a mortifying influence on the global population's health and well-being. In this situation, genome sequence analysis and advanced artificial intelligence techniques may help researchers and medical experts to understand the genetic variants of COVID-19 or SARS-CoV-2. Genome sequence analysis of COVID-19 is crucial to understand the virus's origin, behavior, and structure, which might help produce/develop vaccines, antiviral drugs, and efficient preventive strategies. This paper introduces an artificial intelligence based system to perform genome sequence analysis of COVID-19 and alike viruses, e.g., SARS, middle east respiratory syndrome, and Ebola. The system helps to get important information from the genome sequences of different viruses. We perform comparative data analysis by extracting basic information of COVID-19 and other genome sequences, including information of nucleotides composition and their frequency, tri-nucleotide compositions, count of amino acids, alignment between genome sequences, and their DNA similarity information. We use different visualization methods to analyze these viruses' genome sequences and, finally, apply machine learning based classifier support vector machine to classify different genome sequences. The data set of different virus genome sequences are obtained from an online publicly accessible data center repository. The system achieves good classification results with an accuracy of 97% for COVID-19, 96%, SARS, and 95% for MERS and Ebola genome sequences, respectively.
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Affiliation(s)
- Imran Ahmed
- Center of Excellence in IT, Institute of Management Sciences, Hayatabad, Peshawar, 25000 Khyber Pakhtunkhwa Pakistan
| | - Gwanggil Jeon
- Department of Embedded Systems Engineering, Incheon National University, Incheon, Korea
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Martínez-González B, Soria ME, Vázquez-Sirvent L, Ferrer-Orta C, Lobo-Vega R, Mínguez P, de la Fuente L, Llorens C, Soriano B, Ramos R, Cortón M, López-Rodríguez R, García-Crespo C, Gallego I, de Ávila AI, Gómez J, Enjuanes L, Salar-Vidal L, Esteban J, Fernandez-Roblas R, Gadea I, Ayuso C, Ruíz-Hornillos J, Verdaguer N, Domingo E, Perales C. SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes. Microbiol Spectr 2022; 10:e0022122. [PMID: 35348367 PMCID: PMC9045161 DOI: 10.1128/spectrum.00221-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.
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Affiliation(s)
- Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, Universidad de Valencia, Valencia, Spain
| | - Beatriz Soriano
- Biotechvana, “Scientific Park”, Universidad de Valencia, Valencia, Spain
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, Madrid, Spain
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario López-Rodríguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ricardo Fernandez-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruíz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, Madrid, Spain
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Viruses 2022; 14:v14020399. [PMID: 35215992 PMCID: PMC8877413 DOI: 10.3390/v14020399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022] Open
Abstract
In February 2020, the municipality of Vo', a small town near Padua (Italy) was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. To investigate the viral prevalence and clinical features, the entire population was swab tested in two sequential surveys. Here we report the analysis of 87 viral genomes, which revealed that the unique ancestor haplotype introduced in Vo' belongs to lineage B, carrying the mutations G11083T and G26144T. The viral sequences allowed us to investigate the viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo'. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptom severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype that was carried by an index case. The lockdown extinguished both the viral spread and the emergence of new variants.
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Association between Adaptive Evolution of the Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein and Geographically Distinct Virus Epidemiology During the Initial Wave of the Coronavirus Disease 2019 Pandemic. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, putatively caused by the widespread transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in significant mortality worldwide. The highly varied epidemiology of the disease both temporally and geographically has garnered much attention. The present study aimed to gain a deeper understanding of the varied geospatial disease epidemiology during the first wave of the pandemic. The highly mutable spike (S) protein, which confers fitness to SARS-CoV-2 for its survival and spread was studied using representative sequences determined from the initial phase of the pandemic. Adaptive evolution and selection pressure analysis of 311 whole-genome sequences from across the world including Asia (n=105), Europe (n=101), and the United States (n=105) was performed. A high selection pressure at position 614 of the S protein with a dN/dS (non-synonymous/synonymous substitutions per site) ratio of 124.3 for Asia and 867.9 was predicted for Europe. This positively selected site (i.e. 614) was located in the S1 domain (amino acids 14-680), which acts in binding to the angiotensin-converting co-enzyme 2 (ACE2) receptor. The US strains did not exhibit significant positive selection at position 614. In addition, 10 sites (144, 241, 255, 262, 263, 276, 439,517, 528, and 557) in domain 1 and 19 sites (692, 709, 723, 752, 862, 864, 877, 892, 939, 951, 1015, 1060, 1076, 1114, 1116, 1128, 1176, 1235 and 1240) in domain 2 of the S protein mediating viral entry into host cells, exhibited significant negative selection among European strains of (SARS-CoV-2), however, no negative selection was observed in the Asian and US groups. The D614G spike protein variant has been correlated with fatal outcomes in European population and countries including Italy, France, Belgium, and Spain. D614G variants under high selective pressure in the Asian and European strains were also observed. In addition, the presence of 29 negatively selected codon sites under low selection pressure in the European group may imply improved viral fitness compared with strains circulating in other continents. In conclusion, selective pressure on the S protein, with maximum substitution rate, may have facilitated adaptive evolution of the virus and contributed to the worldwide spread of the virus.
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Habibzadeh S, Hashemzadeh N, Baradaran H, Razi Soofiyani S, Jadideslam G, Pahlavan Y. COVID -19: From the Molecular Mechanisms to Treatment. TANAFFOS 2022; 21:113-131. [PMID: 36879738 PMCID: PMC9985119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/20/2021] [Indexed: 03/08/2023]
Abstract
The 2019 novel coronavirus (SARS-CoV-2) causes severe pneumonia called COVID-19 and leads to severe acute respiratory syndrome with a high mortality rate. The SARS-CoV-2 virus in the human body leads to jumpstarting immune reactions and multi-organ inflammation, which has poorer outcomes in the presence of predisposing conditions, including hypertension, dyslipidemia, dysglycemia, abnormal adiposity, and even endothelial dysfunction via biomolecular mechanisms. In addition, leucopenia, hypoxemia, and high levels of both cytokines and chemokines in the acute phase of this disease, as well as some abnormalities in chest CT images, were reported in most patients. The spike protein in SARS-CoV-2, the primary cell surface protein, helps the virus anchor and enter the human host cells. Additionally, new mutations have mainly happened for spike protein, which has promoted the infection's transmissibility and severity, which may influence manufactured vaccines' efficacy. The exact mechanisms of the pathogenesis, besides molecular aspects of COVID-19 related to the disease stages, are not well known. The altered molecular functions in the case of immune responses, including T CD4+, CD8+, and NK cells, besides the overactivity in other components and outstanding factors in cytokines like interleukin-2, were involved in severe cases of SARS-CoV-2. Accordingly, it is highly needed to identify the SARSCoV-2 biomolecular characteristics to help identify the pathogenesis of COVID-19. This study aimed to investigate the biomolecular aspects of SARSCoV-2 infection, focusing on novel SARS-CoV-2 variants and their effects on vaccine efficacy.
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Affiliation(s)
- Shahram Habibzadeh
- Department of Infectious Disease, Imam Khomeini Hospital, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Nastaran Hashemzadeh
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hananeh Baradaran
- Department of clinical pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Saiedeh Razi Soofiyani
- Clinical Research Development Unit, Sina Educational, Research and Treatment Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Golamreza Jadideslam
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yasamin Pahlavan
- Biosensor Sciences and Technologies Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
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14
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Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. Virus Res 2022; 308:198642. [PMID: 34822953 PMCID: PMC8606321 DOI: 10.1016/j.virusres.2021.198642] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Accepted: 11/18/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India. OBJECTIVE Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2. METHODS High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC_045512.2) as reference. RESULTS Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241). CONCLUSION Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic.
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Bano I, Sharif M, Alam S. Genetic drift in the genome of SARS COV-2 and its global health concern. J Med Virol 2022; 94:88-98. [PMID: 34524697 PMCID: PMC8661852 DOI: 10.1002/jmv.27337] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023]
Abstract
The outbreak of the current coronavirus disease (COVID-19) occurred in late 2019 and quickly spread all over the world. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to a genetically diverse group that mutates continuously leading to the emergence of multiple variants. Although a few antiviral agents and anti-inflammatory medicines are available, thousands of individuals have passed away due to emergence of new viral variants. Thus, proper surveillance of the SARS-CoV-2 genome is needed for the rapid identification of developing mutations over time, which are of the major concern if they occur specifically in the surface spike proteins of the virus (neutralizing analyte). This article reviews the potential mutations acquired by the SARS-CoV2 since the pandemic began and their significant impact on the neutralizing efficiency of vaccines and validity of the diagnostic assays.
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Affiliation(s)
- Iqra Bano
- Department of MicrobiologyThe University of HaripurHaripurPakistan
| | - Mehmoona Sharif
- Department of MicrobiologyQuaid I Azam UniversityIslamabadPakistan
| | - Sadia Alam
- Department of MicrobiologyThe University of HaripurHaripurPakistan
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Dahal A, Sonju JJ, Kousoulas KG, Jois SD. Peptides and peptidomimetics as therapeutic agents for Covid-19. Pept Sci (Hoboken) 2022; 114:e24245. [PMID: 34901700 PMCID: PMC8646791 DOI: 10.1002/pep2.24245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.
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Affiliation(s)
- Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Jafrin Jobayer Sonju
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary MedicineLouisiana State UniversityBaton RougeLouisianaUSA
| | - Seetharama D. Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
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Gálvez JM, Chaparro-Solano HM, Pinzón-Rondón ÁM, Albornoz LL, Pardo-Oviedo JM, Zapata-Gómez FA, Patiño-Aldana AF, Hernández-Rodríguez ADP, Díaz-Quiroz M, Ruiz-Sternberg ÁM. Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105192. [PMID: 34933126 PMCID: PMC8684288 DOI: 10.1016/j.meegid.2021.105192] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/18/2021] [Accepted: 12/14/2021] [Indexed: 10/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is the etiopathogenic agent of COVID-19, a condition that has led to a formally recognized pandemic by March 2020 (World Health Organization -WHO). The SARS-CoV-2 genome is constituted of 29,903 base pairs, that code for four structural proteins (N, M, S, and E) and more than 20 non-structural proteins. Mutations in any of these regions, especially in those that encode for the structural proteins, have allowed the identification of diverse lineages around the world, some of them named as Variants of Concern (VOC) and Variants of Interest (VOI), according to the WHO and CDC. In this study, by using Next Generation Sequencing (NGS) technology, we sequenced the SARS-CoV-2 genome of 422 samples from Colombian residents, all of them collected between April 2020 and January 2021. We obtained genetic information from 386 samples, leading us to the identification of 14 new lineages circulating in Colombia, 13 of which were identified for the first time in South America. GH was the predominant GISAID clade in our sample. Most mutations were either missense (53.6%) or synonymous mutations (37.4%), and most genetic changes were located in the ORF1ab gene (63.9%), followed by the S gene (12.9%). In the latter, we identified mutations E484K, L18F, and D614G. Recent evidence suggests that these mutations concede important particularities to the virus, compromising host immunity, the diagnostic test performance, and the effectiveness of some vaccines. Some important lineages containing these mutations are the Alpha, Beta, and Gamma (WHO Label). Further genomic surveillance is important for the understanding of emerging genomic variants and their correlation with disease severity.
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Affiliation(s)
| | - Henry Mauricio Chaparro-Solano
- Genuino Research Group, Gencell Pharma, Colombia; Clinical Investigation Group, Universidad del Rosario, Colombia; Hospital Universitario Mayor - Méderi, Colombia
| | | | | | - Juan Mauricio Pardo-Oviedo
- Clinical Investigation Group, Universidad del Rosario, Colombia; Hospital Universitario Mayor - Méderi, Colombia
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Essabbar A, Kartti S, Alouane T, Hakmi M, Belyamani L, Ibrahimi A. IDbSV: An Open-Access Repository for Monitoring SARS-CoV-2 Variations and Evolution. Front Med (Lausanne) 2021; 8:765249. [PMID: 34966754 PMCID: PMC8710592 DOI: 10.3389/fmed.2021.765249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Ending COVID-19 pandemic requires a collaborative understanding of SARS-CoV-2 and COVID-19 mechanisms. Yet, the evolving nature of coronaviruses results in a continuous emergence of new variants of the virus. Central to this is the need for a continuous monitoring system able to detect potentially harmful variants of the virus in real-time. In this manuscript, we present the International Database of SARS-CoV-2 Variations (IDbSV), the result of ongoing efforts in curating, analyzing, and sharing comprehensive interpretation of SARS-CoV-2's genetic variations and variants. Through user-friendly interactive data visualizations, we aim to provide a novel surveillance tool to the scientific and public health communities. The database is regularly updated with new records through a 4-step workflow (1—Quality control of curated sequences, 2—Call of variations, 3—Functional annotation, and 4—Metadata association). To the best of our knowledge, IDbSV provides access to the largest repository of SARS-CoV-2 variations and the largest analysis of SARS-CoV-2 genomes with over 60 thousand annotated variations curated from the 1,808,613 genomes alongside their functional annotations, first known appearance, and associated genetic lineages, enabling a robust interpretation tool for SARS-CoV-2 variations to help understanding SARS-CoV-2 dynamics across the world.
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Affiliation(s)
- Abdelmounim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Souad Kartti
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Tarek Alouane
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Mohammed Hakmi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical & Pharmacy School, Mohammed Vth University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed Vth University, Rabat, Morocco
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Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Comput Biol Med 2021; 141:105170. [PMID: 34968862 PMCID: PMC8709794 DOI: 10.1016/j.compbiomed.2021.105170] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, an RNA virus, has been prone to high mutations since its first emergence in Wuhan, China, and throughout its spread. Its genome has been sequenced continuously by many countries, including Pakistan, but the results vary. Understanding its genomic patterns and connecting them with phenotypic features will help in devising therapeutic strategies. Thus, in this study, we explored the mutation landscape of 250 Pakistani isolates of SARS-CoV-2 genomes to check the genome diversity and examine the impact of these mutations on protein stability and viral pathogenesis in comparison with a reference sequence (Wuhan NC 045512.2). Our results revealed that structural proteins mainly exhibit more mutations than others in the Pakistani isolates; in particular, the nucleocapsid protein is highly mutated. In comparison, the spike protein is the most mutated protein globally. Furthermore, nsp12 was found to be the most mutated NSP in the Pakistani isolates and worldwide. Regarding accessory proteins, ORF3A is the most mutated in the Pakistani isolates, whereas ORF8 is highly mutated in world isolates. These mutations decrease the structural stability of their proteins and alter different biological pathways. Molecular docking, the dissociation constant (KD), and MM/GBSA analysis showed that mutations in the S protein alter its binding with ACE2. The spike protein mutations D614G-S943T-V622F (−75.17 kcal/mol), D614G-Q677H (−75.78 kcal/mol), and N74K-D614G (−73.84 kcal/mol) exhibit stronger binding energy than the wild type (−66.34 kcal/mol), thus increasing infectivity. Furthermore, the simulation results strongly corroborated the predicted protein servers. Our analysis findings also showed that E, M, ORF6, ORF7A, ORF7B, and ORF10 are the most stable coding genes; they may be suitable targets for vaccine and drug development.
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Kumbhar PS, Pandya AK, Manjappa AS, Disouza JI, Patravale VB. Carbohydrates-based diagnosis, prophylaxis and treatment of infectious diseases: Special emphasis on COVID-19. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2021. [PMCID: PMC7935400 DOI: 10.1016/j.carpta.2021.100052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
COVID-19 pandemic is taking a dangerous turn due to unavailability of approved and effective vaccines and therapy. Currently available diagnostic techniques are time-consuming, expensive, and maybe impacted by the mutations produced in the virus. Therefore, investigation of novel, rapid, and economic diagnosis techniques, prophylactic vaccines and targeted efficacious drug delivery systems as treatment strategy is imperative. Carbohydrates are essential biomolecules which also act as markers in the realization of immune systems. Moreover, they exhibit antiviral, antimicrobial, and antifungal properties. Carbohydrate-based vaccines and therapeutics including stimuli sensitive systems can be developed successfully and used effectively to fight COVID-19. Thus, carbohydrate-based diagnostic, prophylactic and therapeutic alternatives could be promising to defeat COVID-19 propitiously. Morphology of SARS-CoV-2 and its relevance in devising combat strategies has been discussed. Carbohydrate-based approaches for tackling infectious diseases and their importance in the design of various diagnostic and treatment modalities have been reviewed.
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First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia. Epidemiol Infect 2021. [PMCID: PMC8654520 DOI: 10.1017/s095026882100220x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
This study was endeavoured to contribute in furthering our understanding of the molecular epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by sequencing and analysing the first full-length genome sequences obtained from 48 coronavirus disease-2019 (COVID-19) patients in five districts in Western Serbia in the period April 2020–July 2020. SARS-CoV-2 sequences in Western Serbia distinguished from the Wuhan sequence in 128 SNPs in total. The phylogenetic structure of local SARS-CoV-2 isolates suggested the existence of at least four distinct groups of SARS-CoV-2 strains in Western Serbia. The first group is the most similar to the strain from Italy. These isolates included two 20A sequences and 15−30 20B sequences that displayed a newly occurring set of four conjoined mutations. The second group is the most similar to the strain from France, carrying two mutations and belonged to 20A clade. The third group is the most similar to the strain from Switzerland carrying four co-occurring mutations and belonging to 20B clade. The fourth group is the most similar to another strain from France, displaying one mutation that gave rise to a single local isolate that belonged to 20A clade.
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22
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Al-Kuraishy HM, Al-Gareeb AI, Qusti S, Alshammari EM, Atanu FO, Batiha GES. Arginine vasopressin and pathophysiology of COVID-19: An innovative perspective. Biomed Pharmacother 2021; 143:112193. [PMID: 34543987 PMCID: PMC8440235 DOI: 10.1016/j.biopha.2021.112193] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 12/25/2022] Open
Abstract
In Covid-19, systemic disturbances may progress due to development of cytokine storm and dysregulation of and plasma osmolarility due to high release of pro-inflammatory cytokines and neuro-hormonal disorders. Arginine vasopressin (AVP) which is involve in the regulation of body osmotic system, body water content, blood pressure and plasma volume, that are highly disturbed in Covid-19 and linked with poor clinical outcomes. Therefore, this present study aimed to find the potential association between AVP serum level and inflammatory disorders in Covid-19. It has been observed by different recent studies that physiological response due to fever, pain, hypovolemia, dehydration, and psychological stress is characterized by activation release of AVP to counter-balance high blood viscosity in Covid-19 patients. In addition, activated immune cells mainly T and B lymphocytes and released pro-inflammatory cytokines stimulate discharge of stored AVP from immune cells, which in a vicious cycle trigger release of pro-inflammatory cytokines. Vasopressin receptor antagonists have antiviral and anti-inflammatory effects that may inhibit AVP-induced hyponatremia and release of pro-inflammatory cytokines in Covid-19. In conclusion, release of AVP from hypothalamus is augmented in Covid-19 due to stress, high pro-inflammatory cytokines, high circulating AngII and inhibition of GABAergic neurons. In turn, high AVP level leads to induction of hyponatremia, inflammatory disorders, and development of complications in Covid-19 by activation of NF-κB and NLRP3 inflammasome with release of pro-inflammatory cytokines. Therefore, AVP antagonists might be novel potential therapeutic modality in treating Covid-19 through mitigation of AVP-mediated inflammatory disorders and hyponatremia.
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Affiliation(s)
- Hayder M Al-Kuraishy
- Department of Clinical Pharmacology and Medicine, College of Medicine, ALmustansiriyia University, Baghdad, Iraq.
| | - Ali I Al-Gareeb
- Department of Clinical Pharmacology and Medicine, College of Medicine, ALmustansiriyia University, Baghdad, Iraq.
| | - Safaa Qusti
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Eida M Alshammari
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il, Saudi Arabia.
| | - Francis O Atanu
- Department of Biochemistry, Faculty of Natural Sciences, Kogi State University, P.M.B. 1008 Anyigba, Nigeria.
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, AlBeheira, Egypt.
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Di Pasquale A, Radomski N, Mangone I, Calistri P, Lorusso A, Cammà C. SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels. BMC Genomics 2021; 22:782. [PMID: 34717546 PMCID: PMC8556844 DOI: 10.1186/s12864-021-08112-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Faced with the ongoing global pandemic of coronavirus disease, the 'National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis' (GENPAT) formally established at the 'Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise' (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model. RESULTS GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. 'UK variant') are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model. CONCLUSIONS The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
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Affiliation(s)
- Adriano Di Pasquale
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Nicolas Radomski
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Iolanda Mangone
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Paolo Calistri
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Alessio Lorusso
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
| | - Cesare Cammà
- National Reference Centre (NRC) for Whole Genome Sequencing of microbial pathogens: data-base and bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), via Campo Boario, 64100 Teramo, TE Italy
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Martin S, Heslan C, Jégou G, Eriksson LA, Le Gallo M, Thibault V, Chevet E, Godey F, Avril T. SARS-CoV-2 integral membrane proteins shape the serological responses of patients with COVID-19. iScience 2021; 24:103185. [PMID: 34604721 PMCID: PMC8479324 DOI: 10.1016/j.isci.2021.103185] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/16/2021] [Accepted: 09/24/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has elicited a unique mobilization of the scientific community to develop efficient tools to understand and combat the infection. Like other coronavirae, SARS-CoV-2 hijacks host cell secretory machinery to produce viral proteins that compose the nascent virions; including spike (S), envelope (E), and membrane (M) proteins, the most exposed transmembrane proteins to the host immune system. As antibody response is part of the anti-viral immune arsenal, we investigate the immunogenic potential of S, E, and M using a human cell-based system to mimic membrane insertion and N-glycosylation. Both S and M elicit specific Ig production in patients with SARS-CoV-2. Patients with moderate and severe diseases exhibit elevated Ig responses. Finally, reduced Ig binding was observed with spike G614 compared to D614 variant. Altogether, our assay points toward an unexpected immune response against M and represents a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.
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Affiliation(s)
- Sophie Martin
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | | | - Gwénaële Jégou
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | - Leif A. Eriksson
- Department of Chemistry & Molecular Biology, University of Gothenburg, 41390 Göteborg, Sweden
| | - Matthieu Le Gallo
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | | | - Eric Chevet
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | - Florence Godey
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
| | - Tony Avril
- Inserm U1242 Oncogenesis Stress Signaling, 35000 Rennes, France
- Centre Eugène Marquis, 35000 Rennes, France
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Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021; 13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
Abstract
The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+ T cell immunosurveillance during the first year of the pandemic.
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Affiliation(s)
| | - Dominique Fournelle
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jean-Christophe Grenier
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jana Schockaert
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | | | - Peter Kubiniok
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Fatima Mostefai
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | | | - Frederic Saab
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | | | - Martin A Smith
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Sofie Pattijn
- ImmunXperts, a Nexelis Group Company, 6041 Gosselies, Belgium
| | - Hugo Soudeyns
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hélène Decaluwe
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Department of Medicine, Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, QC, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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26
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Wolf JM, Kipper D, Borges GR, Streck AF, Lunge VR. Temporal spread and evolution of SARS-CoV-2 in the second pandemic wave in Brazil. J Med Virol 2021; 94:926-936. [PMID: 34596904 PMCID: PMC8661965 DOI: 10.1002/jmv.27371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil that presented more than 21 million coronavirus disease 2019 cases and 590 000 deaths. The recent emergence of novel lineages carrying several mutations in the spike protein has raised additional public health concerns worldwide. The present study describes the temporal spreading and evolution of SARS‐CoV2 in the beginning of the second pandemic wave in Brazil, highlighting the fast dissemination of the two major concerning variants (P.1 and P.2). A total of 2507 SARS‐CoV‐2 whole‐genome sequences (WGSs) with available information from the country (Brazil) and sampling date (July 2020–February 2021), were obtained and the frequencies of the lineages were evaluated in the period of the growing second pandemic wave. The results demonstrated the increasing prevalence of P.1 and P.2 lineages in the period evaluated. P.2 lineage was first detected in the middle of 2020, but a high increase occurred only in the last trimester of this same year and the spreading to all Brazilian regions. P.1 lineage emerged even later, first in the North region in December 2020 and really fast dissemination to all other Brazilian regions in January and February 2021. All SARS‐CoV‐2 WGSs of P.1 and P.2 were further separately evaluated with a Bayesian approach. The rates of nucleotide and amino acid substitutions were statistically higher in P.1 than P.2 (p < 0.01). The phylodynamic analysis demonstrated that P.2 gradually spread in all the country from September 2020 to January 2021, while P.1 disseminated even faster from December 2020 to February 2021. Skyline plots of both lineages demonstrated a slight rise in the spreading for P.2 and exponential growth for P.1. In conclusion, these data demonstrated that the P.1 (recently renamed as Gamma) and P.2 lineages have predominated in the second pandemic wave due to the very high spreading across all geographic regions in Brazil at the end of 2020 and beginning of 2021. In Brazil, P.1 (Gamma) and P.2 lineages have predominated in the second pandemic wave. The Bayesian approach showed very high spreading for both lineages across all geographic regions at the end of 2020 and the beginning of 2021. P.2 increased only in the last trimester of 2020 and the spreading to all Brazilian regions. P.1 (Gamma) emerged even later with fast dissemination to all Brazilian regions in January and February 2021.
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Affiliation(s)
- Jonas M Wolf
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - Diéssy Kipper
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Gabriela R Borges
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - André F Streck
- Laboratório de Diagnóstico em Medicina Veterinária, Universidade de Caxias do Sul, UCS, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Vagner R Lunge
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, ULBRA, Canoas, Rio Grande do Sul, Brazil.,Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.,Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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Zandi M, Farahani A, Zakeri A, Akhavan Rezayat S, Mohammadi R, Das U, Dimmock JR, Afzali S, Nakhaei MA, Doroudi A, Erfani Y, Soltani S. Clinical Symptoms and Types of Samples Are Critical Factors for the Molecular Diagnosis of Symptomatic COVID-19 Patients: A Systematic Literature Review. Int J Microbiol 2021; 2021:5528786. [PMID: 34545287 PMCID: PMC8449726 DOI: 10.1155/2021/5528786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Currently, a novel coronavirus found in 2019 known as SARS-CoV-2 is the etiological agent of the COVID-19 pandemic. Various parameters including clinical manifestations and molecular evaluation can affect the accuracy of diagnosis. This review aims to discuss the various clinical symptoms and molecular evaluation results in COVID-19 patients, to point out the importance of onset symptoms, type, and timing of the sampling, besides the methods that are used for detection of SARS-CoV-2. METHODS A systematic literature review of current articles in the Web of Science, PubMed, Scopus, and EMBASE was conducted according to the PRISMA guideline. RESULTS Of the 12946 patients evaluated in this investigation, 7643 were confirmed to be COVID-19 positive by molecular techniques, particularly the RT-PCR/qPCR combined technique (qRT-PCR). In most of the studies, all of the enrolled cases had 100% positive results for molecular evaluation. Among the COVID-19 patients who were identified as such by positive PCR results, most of them showed fever or cough as the primary clinical signs. Less common symptoms observed in clinically confirmed cases were hemoptysis, bloody sputum, mental disorders, and nasal congestion. The most common clinical samples for PCR-confirmed COVID-19 patients were obtained from throat, oropharyngeal, and nasopharyngeal swabs, while tears and conjunctival secretions seem to be the least common clinical samples for COVID-19 diagnosis among studies. Also, different conserved SARS-CoV-2 gene sequences could be targeted for qRT-PCR detection. The suggested molecular assay being used by most laboratories for the detection of SARS-CoV-2 is qRT-PCR. CONCLUSION There is a worldwide concern on the COVID-19 pandemic and a lack of well-managed global control. Hence, it is crucial to update the molecular diagnostics protocols for handling the situation. This is possible by understanding the available advances in assays for the detection of the SARS-CoV-2 infection. Good sampling procedure and using samples with enough viral loads, also considering the onset symptoms, may reduce the qRT-PCR false-negative results in symptomatic COVID-19 patients. Selection of the most efficient primer-probe for target genes and samples containing enough viral loads to search for the existence of SARS-CoV-2 helps detecting the virus on time using qRT-PCR.
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Affiliation(s)
- Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Farahani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Armin Zakeri
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sara Akhavan Rezayat
- Department of Health Economics and Management, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Mohammadi
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Umashankar Das
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Jonathan R. Dimmock
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Shervin Afzali
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Mohammadvala Ashtar Nakhaei
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, Iran
| | - Alireza Doroudi
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Yousef Erfani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University Medical Sciences, Tehran, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
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Wang HI, Chuang ZS, Kao YT, Lin YL, Liang JJ, Liao CC, Liao CL, Lai MMC, Yu CY. Small Structural Proteins E and M Render the SARS-CoV-2 Pseudovirus More Infectious and Reveal the Phenotype of Natural Viral Variants. Int J Mol Sci 2021; 22:ijms22169087. [PMID: 34445789 PMCID: PMC8396568 DOI: 10.3390/ijms22169087] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/21/2022] Open
Abstract
The SARS-CoV-2 pseudovirus is a commonly used strategy that mimics certain biological functions of the authentic virus by relying on biological legitimacy at the molecular level. Despite the fact that spike (S), envelope (E), and membrane (M) proteins together wrap up the SARS-CoV-2 virion, most of the reported pseudotype viruses consist of only the S protein. Here, we report that the presence of E and M increased the virion infectivity by promoting the S protein priming. The S, E, and M (SEM)-coated pseudovirion is spherical, containing crown-like spikes on the surface. Both S and SEM pseudoviruses packaged the same amounts of viral RNA, but the SEM virus bound more efficiently to cells stably expressing the viral receptor human angiotensin-converting enzyme II (hACE2) and became more infectious. Using this SEM pseudovirus, we examined the infectivity and antigenic properties of the natural SARS-CoV-2 variants. We showed that some variants have higher infectivity than the original virus and that some render the neutralizing plasma with lower potency. These studies thus revealed possible mechanisms of the dissemination advantage of these variants. Hence, the SEM pseudovirion provides a useful tool to evaluate the viral infectivity and capability of convalescent sera in neutralizing specific SARS-CoV-2 S dominant variants.
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Affiliation(s)
- Hsin-I Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan; (H.-I.W.); (Z.-S.C.); (Y.-T.K.); (C.-L.L.)
| | - Zih-Shiuan Chuang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan; (H.-I.W.); (Z.-S.C.); (Y.-T.K.); (C.-L.L.)
| | - Yu-Ting Kao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan; (H.-I.W.); (Z.-S.C.); (Y.-T.K.); (C.-L.L.)
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (Y.-L.L.); (J.-J.L.); (C.-C.L.)
- Biomedical Translation Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (Y.-L.L.); (J.-J.L.); (C.-C.L.)
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; (Y.-L.L.); (J.-J.L.); (C.-C.L.)
| | - Ching-Len Liao
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan; (H.-I.W.); (Z.-S.C.); (Y.-T.K.); (C.-L.L.)
| | - Michael M. C. Lai
- Research Center for Emerging Viruses, China Medical University Hospital, Taichung 404, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Correspondence: (M.M.C.L.); (C.-Y.Y.)
| | - Chia-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan; (H.-I.W.); (Z.-S.C.); (Y.-T.K.); (C.-L.L.)
- Correspondence: (M.M.C.L.); (C.-Y.Y.)
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Morris CP, Luo CH, Amadi A, Schwartz M, Gallagher N, Ray SC, Pekosz A, Mostafa HH. An Update on SARS-CoV-2 Diversity in the United States National Capital Region: Evolution of Novel and Variants of Concern. Clin Infect Dis 2021; 74:1419-1428. [PMID: 34272947 PMCID: PMC8406876 DOI: 10.1093/cid/ciab636] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/19/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concerning for enhanced transmission, evasion of immune responses, or associated with severe disease have motivated the global increase in genomic surveillance. In the current study, large-scale whole-genome sequencing was performed between November 2020 and the end of March 2021 to provide a phylodynamic analysis of circulating variants over time. In addition, we compared the viral genomic features of March 2020 and March 2021. Methods A total of 1600 complete SARS-CoV-2 genomes were analyzed. Genomic analysis was associated with laboratory diagnostic volumes and positivity rates, in addition to an analysis of the association of selected variants of concern/variants of interest with disease severity and outcomes. Our real-time surveillance features a cohort of specimens from patients who tested positive for SARS-CoV-2 after completion of vaccination. Results Our data showed genomic diversity over time that was not limited to the spike sequence. A significant increase in the B.1.1.7 lineage (alpha variant) in March 2021 as well as a transient circulation of regional variants that carried both the concerning S: E484K and S: P681H substitutions were noted. Lineage B.1.243 was significantly associated with intensive care unit admission and mortality. Genomes recovered from fully vaccinated individuals represented the predominant lineages circulating at specimen collection time, and people with those infections recovered with no hospitalizations. Conclusions Our results emphasize the importance of genomic surveillance coupled with laboratory, clinical, and metadata analysis for a better understanding of the dynamics of viral spread and evolution.
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Affiliation(s)
- C Paul Morris
- Johns Hopkins Hospital, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA.,National Institute of Allergy and Infectious Disease, National Institutes of Health, Rockville, Maryland, USA
| | - Chun Huai Luo
- Johns Hopkins Hospital, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins Hospital, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Johns Hopkins Hospital, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Johns Hopkins Hospital, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Stuart C Ray
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Johns Hopkins Hospital, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
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Pirnay JP, Selhorst P, Hong SL, Cochez C, Potter B, Maes P, Petrillo M, Dudas G, Claes V, Van der Beken Y, Verbeken G, Degueldre J, Dellicour S, Cuypers L, T’Sas F, Van den Eede G, Verhasselt B, Weuts W, Smets C, Mertens J, Geeraerts P, Ariën KK, André E, Neirinckx P, Soentjens P, Baele G. Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and Operations. Viruses 2021; 13:1359. [PMID: 34372565 PMCID: PMC8310367 DOI: 10.3390/v13071359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
More than a year after the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of the 2019 coronavirus disease (COVID-19) in China, the emergence and spread of genomic variants of this virus through travel raise concerns regarding the introduction of lineages in previously unaffected regions, requiring adequate containment strategies. Concomitantly, such introductions fuel worries about a possible increase in transmissibility and disease severity, as well as a possible decrease in vaccine efficacy. Military personnel are frequently deployed on missions around the world. As part of a COVID-19 risk mitigation strategy, Belgian Armed Forces that engaged in missions and operations abroad were screened (7683 RT-qPCR tests), pre- and post-mission, for the presence of SARS-CoV-2, including the identification of viral lineages. Nine distinct viral genotypes were identified in soldiers returning from operations in Niger, the Democratic Republic of the Congo, Afghanistan, and Mali. The SARS-CoV-2 variants belonged to major clades 19B, 20A, and 20B (Nextstrain nomenclature), and included "variant of interest" B.1.525, "variant under monitoring" A.27, as well as lineages B.1.214, B.1, B.1.1.254, and A (pangolin nomenclature), some of which are internationally monitored due to the specific mutations they harbor. Through contact tracing and phylogenetic analysis, we show that isolation and testing policies implemented by the Belgian military command appear to have been successful in containing the influx and transmission of these distinct SARS-CoV-2 variants into military and civilian populations.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (C.C.); (G.V.)
| | - Philippe Selhorst
- Unit of Virology and Outbreak Research Team, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (S.L.H.); (B.P.); (P.M.); (S.D.); (G.B.)
| | - Christel Cochez
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (C.C.); (G.V.)
| | - Barney Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (S.L.H.); (B.P.); (P.M.); (S.D.); (G.B.)
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (S.L.H.); (B.P.); (P.M.); (S.D.); (G.B.)
| | - Mauro Petrillo
- European Commission, Directorate-General Joint Research Centre (JRC), 21027 Ispra, Italy;
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, 413 19 Gothenburg, Sweden;
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Vincent Claes
- Clinical Laboratory, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (V.C.); (Y.V.d.B.); (J.D.); (F.T.)
| | - Yolien Van der Beken
- Clinical Laboratory, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (V.C.); (Y.V.d.B.); (J.D.); (F.T.)
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (C.C.); (G.V.)
| | - Julie Degueldre
- Clinical Laboratory, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (V.C.); (Y.V.d.B.); (J.D.); (F.T.)
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (S.L.H.); (B.P.); (P.M.); (S.D.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, UZ Leuven Hospital, 3000 Leuven, Belgium; (L.C.); (E.A.)
| | - France T’Sas
- Clinical Laboratory, Queen Astrid Military Hospital, 1120 Brussels, Belgium; (V.C.); (Y.V.d.B.); (J.D.); (F.T.)
| | - Guy Van den Eede
- European Commission, Directorate-General Joint Research Centre (JRC), 1050 Brussels, Belgium;
| | - Bruno Verhasselt
- Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium;
| | - Wouter Weuts
- Queen Astrid Military Hospital, 1120 Brussels, Belgium;
| | | | - Jan Mertens
- Medical Component, Ministry of Defense, 1140 Brussels, Belgium; (J.M.); (P.G.); (P.N.)
| | - Philippe Geeraerts
- Medical Component, Ministry of Defense, 1140 Brussels, Belgium; (J.M.); (P.G.); (P.N.)
| | - Kevin K. Ariën
- Unit of Virology, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Emmanuel André
- Department of Laboratory Medicine, UZ Leuven Hospital, 3000 Leuven, Belgium; (L.C.); (E.A.)
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Pierre Neirinckx
- Medical Component, Ministry of Defense, 1140 Brussels, Belgium; (J.M.); (P.G.); (P.N.)
| | - Patrick Soentjens
- Center for Infectious Diseases, Queen Astrid Military Hospital, 1120 Brussels, Belgium;
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (S.L.H.); (B.P.); (P.M.); (S.D.); (G.B.)
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J. Al-Awaida W, Jawabrah Al Hourani B, Swedan S, Nimer R, Alzoughool F, J. Al-Ameer H, E. Al Tamam S, Alashqar R, Al bawareed O, Gushchina Y, Samy Abousenna M, Ayyash AM, Sharab A, M. Alnaimat S, Imraish A, W. Akash M, R. Hadi N. Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Genes (Basel) 2021; 12:1061. [PMID: 34356077 PMCID: PMC8306878 DOI: 10.3390/genes12071061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/21/2021] [Accepted: 07/09/2021] [Indexed: 12/16/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly developed into a worldwide pandemic. Mutations in the SARS-CoV-2 genome may affect various aspects of the disease including fatality ratio. In this study, 553,518 SARS-CoV-2 genome sequences isolated from patients from continents for the period 1 December 2020 to 15 March 2021 were comprehensively analyzed and a total of 82 mutations were identified concerning the reference sequence. In addition, associations between the mutations and the case fatality ratio (CFR), cases per million and deaths per million, were examined. The mutations having the highest frequencies among different continents were Spike_D614G and NSP12_P323L. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR. While the NSP13_Y541C, NSP3_T73I and NSP3_Q180H mutations demonstrated a negative correlation to CFR. The Spike_D614G and NSP12_P323L mutations showed a positive correlation to deaths per million. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million. The NSP12_P323L and Spike_D614G mutations showed a positive correlation to the number of cases per million. In contrast, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of cases per million. In addition, among the identified clades, none showed a significant correlation to CFR. The G, GR, GV, S clades showed a significant positive correlation to deaths per million. The GR and S clades showed a positive correlation to number of cases per million. The clades having the highest frequencies among continents were G, followed by GH and GR. These findings should be taken into consideration during epidemiological surveys of the virus and vaccine development.
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Affiliation(s)
- Wajdy J. Al-Awaida
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | | | - Samer Swedan
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; (S.S.); (R.N.)
| | - Refat Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; (S.S.); (R.N.)
| | - Foad Alzoughool
- Department of Medical Laboratory Sciences, The Hashemite University, Zarqa 13133, Jordan;
| | - Hamzeh J. Al-Ameer
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Sara E. Al Tamam
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Raghad Alashqar
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Omar Al bawareed
- Department of Normal Physiology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia;
| | - Yulia Gushchina
- Department of General and Clinical Pharmacology, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia;
| | - Mohamed Samy Abousenna
- Central Laboratory for Evaluation of Veterinary Biologics, Agricultural Research Center, Cairo 11517, Egypt;
| | - Amani Marwan Ayyash
- Department of Pharmacy, Faculty of Heath Sciences, American University of Madaba, Madaba 11821, Jordan;
| | - Ahmad Sharab
- Department of Biology and Biotechnology, Faculty of Science, American University of Madaba, Madaba 11821, Jordan; (H.J.A.-A.); (S.E.A.T.); (R.A.); (A.S.)
| | - Sulaiman M. Alnaimat
- Biological Department, Faculty of Science, Al Hussein Bin Talal University, Ma’an P.O. Box 20, Jordan;
| | - Amer Imraish
- Department of Biology, Faculty of Science, The University of Jordan, Amman 11942, Jordan;
| | - Muhanad W. Akash
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman 11942, Jordan;
| | - Najah R. Hadi
- Department of Pharmacology and Therapeutics, Faculty of Medicine, University of Kufa, Najaf 540011, Iraq;
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Guijarro-Real C, Plazas M, Rodríguez-Burruezo A, Prohens J, Fita A. Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CL Pro) Activity. Foods 2021; 10:1503. [PMID: 34209659 PMCID: PMC8304378 DOI: 10.3390/foods10071503] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
Antiviral treatments inhibiting Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication may represent a strategy complementary to vaccination to fight the ongoing Coronavirus disease 19 (COVID-19) pandemic. Molecules or extracts inhibiting the SARS-CoV-2 chymotripsin-like protease (3CLPro) could contribute to reducing or suppressing SARS-CoV-2 replication. Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity. Methanolic extracts were evaluated in vitro for inhibition of SARS-CoV-2 3CLPro activity using a quenched fluorescence resonance energy transfer (FRET) assay. Extracts from turmeric (Curcuma longa) rhizomes, mustard (Brassica nigra) seeds, and wall rocket (Diplotaxis erucoides subsp. erucoides) at 500 µg mL-1 displayed significant inhibition of the 3CLPro activity, resulting in residual protease activities of 0.0%, 9.4%, and 14.9%, respectively. Using different extract concentrations, an IC50 value of 15.74 µg mL-1 was calculated for turmeric extract. Commercial curcumin inhibited the 3CLPro activity, but did not fully account for the inhibitory effect of turmeric rhizomes extracts, suggesting that other components of the turmeric extract must also play a main role in inhibiting the 3CLPro activity. Sinigrin, a major glucosinolate present in mustard seeds and wall rocket, did not have relevant 3CLPro inhibitory activity; however, its hydrolysis product allyl isothiocyanate had an IC50 value of 41.43 µg mL-1. The current study identifies plant extracts and molecules that can be of interest in the search for treatments against COVID-19, acting as a basis for future chemical, in vivo, and clinical trials.
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Affiliation(s)
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain; (C.G.-R.); (A.R.-B.); (J.P.); (A.F.)
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Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. Comput Biol Med 2021; 135:104570. [PMID: 34157472 PMCID: PMC8197616 DOI: 10.1016/j.compbiomed.2021.104570] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023]
Abstract
Background The spread of a novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) has affected both the public health and the global economy. The current study was aimed at analysing the genetic sequence of this highly contagious corona virus from an evolutionary perspective, comparing the genetic variation features of different geographic strains, and identifying the key miRNAs as well as their gene targets from the transcriptome data of infected lung tissues. Methods A multilevel robust computational analysis was undertaken for viral genetic sequence alignment, phylogram construction, genome-wide transcriptome data interpretation of virus-infected lung tissues, miRNA mapping, and functional biology networking. Results Our findings show both genetic similarities as well as notable differences in the S protein length among SARS-CoV-1, SARS-CoV-2 and MERS viruses. All SARS-CoV-2 strains showed a high genetic similarity with the parent Wuhan strain, but Saudi Arabian, South African, USA, Russia and New Zealand strains carry 3 additional genetic variations like P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). The infected lung tissues demonstrated the upregulation of 282 (56.51%) antiviral defensive response pathway genes and downregulation of 217 (43.48%) genes involved in autophagy and lung repair pathways. By miRNA mapping, 4 key miRNAs (hsa-miR-342-5p, hsa-miR-432-5p, hsa-miR-98-5p and hsa-miR-17-5p), targeting multiple host genes (MYC, IL6, ICAM1 and VEGFA) as well as SARS-CoV2 gene (ORF1ab) were identified. Conclusion Systems biology methods offer a new perspective in understanding the molecular basis for the faster spread of SARS-CoV-2 infection. The antiviral miRNAs identified in this study may aid in the ongoing search for novel personalized therapeutic avenues for COVID patients.
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Chang PL, Lin CY, Chen CP, Lin YC, Hu HC, Cheng SH, Cheng CY. Clinical validation of an automated reverse transcription-insulated isothermal PCR assay for the detection of severe acute respiratory syndrome coronavirus 2. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:522-526. [PMID: 33582073 PMCID: PMC7849545 DOI: 10.1016/j.jmii.2021.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/27/2022]
Abstract
To determine clinical performance of the single-target SARS-CoV-2 orf 1 ab reverse transcription-insulated isothermal PCR (RT-iiPCR) assay, the positive percentage agreement between this assay and a laboratory real-time RT-PCR assay was 96.8% (30 of 31; 95% confidence interval [CI], 90.5%-100%) and the negative percentage agreement was 97.1% (67 of 69; 95% CI, 93.1%-100%).
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Affiliation(s)
- Pai-Ling Chang
- Department of Laboratory Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan.
| | - Chia-Yi Lin
- Department of Laboratory Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Cheng-Pin Chen
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan; School of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chun Lin
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Hui-Chun Hu
- Department of Nursing, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Shu-Hsing Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan; School of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Chien-Yu Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan; School of Public Health, National Yang-Ming University, Taipei, Taiwan.
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35
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Franceschi VB, Caldana GD, de Menezes Mayer A, Cybis GB, Neves CAM, Ferrareze PAG, Demoliner M, de Almeida PR, Gularte JS, Hansen AW, Weber MN, Fleck JD, Zimerman RA, Kmetzsch L, Spilki FR, Thompson CE. Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. BMC Genomics 2021; 22:371. [PMID: 34016042 PMCID: PMC8136996 DOI: 10.1186/s12864-021-07708-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%). RESULTS We provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologically-related clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions. CONCLUSIONS Our data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19.
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Affiliation(s)
- Vinícius Bonetti Franceschi
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Gabriel Dickin Caldana
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Amanda de Menezes Mayer
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Gabriela Bettella Cybis
- Department of Statistics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Carla Andretta Moreira Neves
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Meriane Demoliner
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | | | - Alana Witt Hansen
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Matheus Nunes Weber
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Juliane Deise Fleck
- Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | | | - Lívia Kmetzsch
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Claudia Elizabeth Thompson
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil. .,Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil. .,Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), 245/200C Sarmento Leite St, Porto Alegre, RS, 90050-170, Brazil.
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36
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Ouadghiri M, Aanniz T, Essabbar A, Seffar M, Kabbaj H, El Amin G, Zouaki A, Amzazi S, Belyamani L, Ibrahimi A. Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. Microbiol Resour Announc 2021; 10:e00240-21. [PMID: 33888505 PMCID: PMC8063648 DOI: 10.1128/mra.00240-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022] Open
Abstract
Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.
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Affiliation(s)
- Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Myriam Seffar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Hakima Kabbaj
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Ghizlane El Amin
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Amal Zouaki
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
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37
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Citarella A, Scala A, Piperno A, Micale N. SARS-CoV-2 M pro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors. Biomolecules 2021; 11:607. [PMID: 33921886 PMCID: PMC8073203 DOI: 10.3390/biom11040607] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
The uncontrolled spread of the COVID-19 pandemic caused by the new coronavirus SARS-CoV-2 during 2020-2021 is one of the most devastating events in the history, with remarkable impacts on the health, economic systems, and habits of the entire world population. While some effective vaccines are nowadays approved and extensively administered, the long-term efficacy and safety of this line of intervention is constantly under debate as coronaviruses rapidly mutate and several SARS-CoV-2 variants have been already identified worldwide. Then, the WHO's main recommendations to prevent severe clinical complications by COVID-19 are still essentially based on social distancing and limitation of human interactions, therefore the identification of new target-based drugs became a priority. Several strategies have been proposed to counteract such viral infection, including the repurposing of FDA already approved for the treatment of HIV, HCV, and EBOLA, inter alia. Among the evaluated compounds, inhibitors of the main protease of the coronavirus (Mpro) are becoming more and more promising candidates. Mpro holds a pivotal role during the onset of the infection and its function is intimately related with the beginning of viral replication. The interruption of its catalytic activity could represent a relevant strategy for the development of anti-coronavirus drugs. SARS-CoV-2 Mpro is a peculiar cysteine protease of the coronavirus family, responsible for the replication and infectivity of the parasite. This review offers a detailed analysis of the repurposed drugs and the newly synthesized molecules developed to date for the treatment of COVID-19 which share the common feature of targeting SARS-CoV-2 Mpro, as well as a brief overview of the main enzymatic and cell-based assays to efficaciously screen such compounds.
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Affiliation(s)
| | | | | | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy; (A.C.); (A.S.); (A.P.)
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38
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Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Int J Biol Sci 2021; 17:1547-1554. [PMID: 33907518 PMCID: PMC8071772 DOI: 10.7150/ijbs.59943] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Suppression of type I interferon (IFN) response is one pathological outcome of the infection of highly pathogenic human coronaviruses. To effect this, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 encode multiple IFN antagonists. In this study, we reported on the IFN antagonism of SARS-CoV-2 main protease NSP5. NSP5 proteins of both SARS-CoV and SARS-CoV-2 counteracted Sendai virus-induced IFN production. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. The suppressive effect of NSP5 on IFN-β gene transcription induced by RIG-I, MAVS, TBK1 and IKKϵ suggested that NSP5 likely acts at a step downstream of IRF3 phosphorylation in the cytoplasm. NSP5 did not influence steady-state expression or phosphorylation of IRF3, suggesting that IRF3, regardless of its phosphorylation state, might not be the substrate of NSP5 protease. However, nuclear translocation of phosphorylated IRF3 was severely compromised in NSP5-expressing cells. Taken together, our work revealed a new mechanism by which NSP5 proteins encoded by SARS-CoV and SARS-CoV-2 antagonize IFN production by retaining phosphorylated IRF3 in the cytoplasm. Our findings have implications in rational design and development of antiviral agents against SARS-CoV-2.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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39
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Periwal N, Rathod SB, Pal R, Sharma P, Nebhnani L, Barnwal RP, Arora P, Srivastava KR, Sood V. In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. J Biomol Struct Dyn 2021; 40:8216-8231. [PMID: 33797336 PMCID: PMC8043164 DOI: 10.1080/07391102.2021.1908170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 has recently emerged as a pandemic that has caused more than 2.4 million deaths worldwide. Since the onset of infections, several full-length sequences of viral genome have been made available which have been used to gain insights into viral dynamics. We utilised a meta-data driven comparative analysis tool for sequences (Meta-CATS) algorithm to identify mutations in 829 SARS-CoV-2 genomes from around the world. The algorithm predicted sixty-one mutations among SARS-CoV-2 genomes. We observed that most of the mutations were concentrated around three protein coding genes viz nsp3 (non-structural protein 3), RdRp (RNA-directed RNA polymerase) and Nucleocapsid (N) proteins of SARS-CoV-2. We used various computational tools including normal mode analysis (NMA), C-α discrete molecular dynamics (DMD) and all-atom molecular dynamic simulations (MD) to study the effect of mutations on functionality, stability and flexibility of SARS-CoV-2 structural proteins including envelope (E), N and spike (S) proteins. PredictSNP predictor suggested that four mutations (L37H in E, R203K and P344S in N and D614G in S) out of seven were predicted to be neutral whilst the remaining ones (P13L, S197L and G204R in N) were predicted to be deleterious in nature thereby impacting protein functionality. NMA, C-α DMD and all-atom MD suggested some mutations to have stabilizing roles (P13L, S197L and R203K in N protein) where remaining ones were predicted to destabilize mutant protein. In summary, we identified significant mutations in SARS-CoV-2 genomes as well as used computational approaches to further characterize the possible effect of highly significant mutations on SARS-CoV-2 structural proteins. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Neha Periwal
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Shravan B Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, India
| | - Ranjan Pal
- Biocatalysis and Enzyme Engineering Lab, Regional Centre for Biotechnology, Faridabad, India
| | - Priya Sharma
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Lata Nebhnani
- Department of Chemistry, Gujarat University, Ahmedabad, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | - Kinshuk Raj Srivastava
- Biocatalysis and Enzyme Engineering Lab, Regional Centre for Biotechnology, Faridabad, India
| | - Vikas Sood
- Department of Biochemistry, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
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40
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Lee S, Lee MK, Na H, Ahn J, Hong G, Lee Y, Park J, Kim Y, Kim YT, Kim CK, Lim HS, Lee KR. Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. GENE REPORTS 2021; 23:101100. [PMID: 33778182 PMCID: PMC7985685 DOI: 10.1016/j.genrep.2021.101100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 11/27/2022]
Abstract
The spike (S) protein mutations of SARS-CoV-2 are of major concern in terms of viral transmission and pathogenesis. Hence, we developed a PCR-based method to rapidly detect the 6 mutational hotspots (H49Y, G476S, V483A, H519Q, A520S, and D614G) in the S protein and applied this method to analyze the hotspots in the viral isolates from different geographical origins. Here, we identified that there was only the D614G mutation in the viral isolates. As of September 30, 2020, the analysis of 113,381 sequences available from the public repositories revealed that the SARS-CoV-2 variant carrying G614 has become the most prevalent form globally. Our results support recent epidemiological and genomic data demonstrating that the viral infectivity and transmission are enhanced by the S protein D614G mutation.
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Key Words
- ACE2, angiotensin-converting enzyme-2
- COVID-19, Coronavirus disease
- CT, cycle threshold
- D614G mutation
- Different geographic origins
- E, envelope
- M, membrane
- Mutational hotspots
- N, nucleocapsid
- NGS, next-generation sequencing
- Nsp3, nonstructural protein
- Orf, open reading frame
- RDB, receptor-binding domain
- RT-qPCR, reverse transcriptase-quantitative polymerase chain reaction
- RdRp, RNA-dependent RNA polymerase
- S, Spike
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Spike gene
- Spike protein
- TMPRSS2, transmembrane serine protease2
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Affiliation(s)
- Sanghoo Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Mi-Kyeong Lee
- Department of Molecular Diagnostics, Seoul Clinical Laboratories, Republic of Korea
| | - Hyeongkyun Na
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Jinwoo Ahn
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Gayeon Hong
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Youngkee Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Jimyeong Park
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Yejin Kim
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea
| | - Yun-Tae Kim
- Center for Technology Innovation, Seoul Clinical Laboratories, Republic of Korea
| | - Chang-Ki Kim
- Center for Clinical Trial, Seoul Clinical Laboratories, Republic of Korea
| | - Hwan-Sub Lim
- Department of Molecular Diagnostics, Seoul Clinical Laboratories, Republic of Korea
| | - Kyoung-Ryul Lee
- Center for Companion Biomarker, Seoul Clinical Laboratories (SCL) Healthcare Inc., Republic of Korea.,Department of Molecular Diagnostics, Seoul Clinical Laboratories, Republic of Korea.,Center for Technology Innovation, Seoul Clinical Laboratories, Republic of Korea.,Center for Clinical Trial, Seoul Clinical Laboratories, Republic of Korea
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41
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First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. Microbiol Resour Announc 2021; 10:10/11/e00027-21. [PMID: 33737349 PMCID: PMC7975867 DOI: 10.1128/mra.00027-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys). We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys).
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42
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Huang SW, Wang SF. SARS-CoV-2 Entry Related Viral and Host Genetic Variations: Implications on COVID-19 Severity, Immune Escape, and Infectivity. Int J Mol Sci 2021; 22:3060. [PMID: 33802729 PMCID: PMC8002537 DOI: 10.3390/ijms22063060] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to display particular patterns of genetic diversity in the genome across geographical regions. These variations in the virus and genetic variation in human populations can determine virus transmissibility and coronavirus disease 2019 (COVID-19) severity. Genetic variations and immune differences in human populations could be the driving forces in viral evolution. Recently emerged SARS-CoV-2 variants show several mutations at the receptor binding domain in the spike (S) glycoprotein and contribute to immune escape and enhanced binding with angiotensin 1-converting enzyme 2 (ACE2). Since ACE2 and transmembrane protease serine 2 (TMPRSS2) play important roles in SARS-CoV-2 entry into the cell, genetic variation in these host entry-related proteins may be a driving force for positive selection in the SARS-CoV-2 S glycoprotein. Dendritic or liver/lymph cell-specific intercellular adhesion molecule (ICAM)-3-grabbing non-integrin is also known to play vital roles in several pathogens. Genetic variations of these host proteins may affect the susceptibility to SARS-CoV-2. This review summarizes the latest research to describe the impacts of genetic variation in the viral S glycoprotein and critical host proteins and aims to provide better insights for understanding transmission and pathogenesis and more broadly for developing vaccine/antiviral drugs and precision medicine strategies, especially for high risk populations with genetic risk variants.
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Affiliation(s)
- Szu-Wei Huang
- Model Development Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Clinical Microbiology Laboratory, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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43
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CRISPR/Cas9-Based Lateral Flow and Fluorescence Diagnostics. Bioengineering (Basel) 2021; 8:bioengineering8020023. [PMID: 33673107 PMCID: PMC7918862 DOI: 10.3390/bioengineering8020023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR/Cas) proteins can be designed to bind specified DNA and RNA sequences and hold great promise for the accurate detection of nucleic acids for diagnostics. We integrated commercially available reagents into a CRISPR/Cas9-based lateral flow assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences with single-base specificity. This approach requires minimal equipment and represents a simplified platform for field-based deployment. We also developed a rapid, multiplex fluorescence CRISPR/Cas9 nuclease cleavage assay capable of detecting and differentiating SARS-CoV-2, influenza A and B, and respiratory syncytial virus in a single reaction. Our findings provide proof-of-principle for CRISPR/Cas9 point-of-care diagnosis as well as a scalable fluorescent platform for identifying respiratory viral pathogens with overlapping symptomology.
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44
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Pattern of genomic variation in SARS-CoV-2 (COVID-19) suggests restricted nonrandom changes: Analysis using Shewhart control charts. J Biosci 2021. [PMID: 33709963 PMCID: PMC7856336 DOI: 10.1007/s12038-020-00131-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is a member of the Coronavirus family which recently originated from the Wuhan province of China and spread very rapidly through the world infecting more than 4 million people. In the past, other Coronaviruses have also been found to cause human infection, but not as widespread as COVID-19. Since Coronavirus sequences constantly change due to mutation and recombination, it is important to understand the pattern of changes and likely path the virus can take in the future. In this study, we have used the Shewhart control chart to identify and analyze hypervariable (hotspots) and hypovariable (coldspots) regions of the virus. Our analysis shows that SARS-CoV-2 has changed in a few regions of the genome. Analysis of SARS-CoV-1 and MERS sequences suggests that over time, mutations start accumulating in different regions and most likely SARS-CoV-2 may also follow a similar path. The results suggest a possible emergence of modified viruses over some time.
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45
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Salpini R, Alkhatib M, Costa G, Piermatteo L, Ambrosio FA, Di Maio VC, Scutari R, Duca L, Berno G, Fabeni L, Alcaro S, Ceccherini-Silberstein F, Artese A, Svicher V. Key genetic elements, single and in clusters, underlying geographically dependent SARS-CoV-2 genetic adaptation and their impact on binding affinity for drugs and immune control. J Antimicrob Chemother 2021; 76:396-412. [PMID: 33254234 PMCID: PMC7799093 DOI: 10.1093/jac/dkaa444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/29/2020] [Indexed: 01/08/2023] Open
Abstract
Objectives To define key genetic elements, single or in clusters, underlying SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) evolutionary diversification across continents, and their impact on drug-binding affinity and viral antigenicity. Methods A total of 12 150 SARS-CoV-2 sequences (publicly available) from 69 countries were analysed. Mutational clusters were assessed by hierarchical clustering. Structure-based virtual screening (SBVS) was used to select the best inhibitors of 3-chymotrypsin-like protease (3CL-Pr) and RNA-dependent RNA polymerase (RdRp) among the FDA-approved drugs and to evaluate the impact of mutations on binding affinity of these drugs. The impact of mutations on epitope recognition was predicted following Grifoni et al. (Cell Host Microbe 2020; 27 671–80.) Results Thirty-five key mutations were identified (prevalence: ≥0.5%), residing in different viral proteins. Sixteen out of 35 formed tight clusters involving multiple SARS-CoV-2 proteins, highlighting intergenic co-evolution. Some clusters (including D614GSpike + P323LRdRp + R203KN + G204RN) occurred in all continents, while others showed a geographically restricted circulation (T1198KPL-Pr + P13LN + A97VRdRp in Asia, L84SORF-8 + S197LN in Europe, Y541CHel + H504CHel + L84SORF-8 in America and Oceania). SBVS identified 20 best RdRp inhibitors and 21 best 3CL-Pr inhibitors belonging to different drug classes. Notably, mutations in RdRp or 3CL-Pr modulate, positively or negatively, the binding affinity of these drugs. Among them, P323LRdRp (prevalence: 61.9%) reduced the binding affinity of specific compounds including remdesivir while it increased the binding affinity of the purine analogues penciclovir and tenofovir, suggesting potential hypersusceptibility. Finally, specific mutations (including Y541CHel + H504CHel) strongly hampered recognition of Class I/II epitopes, while D614GSpike profoundly altered the structural stability of a recently identified B cell epitope target of neutralizing antibodies (amino acids 592–620). Conclusions Key genetic elements reflect geographically dependent SARS-CoV-2 genetic adaptation, and may play a potential role in modulating drug susceptibility and hampering viral antigenicity. Thus, a close monitoring of SARS-CoV-2 mutational patterns is crucial to ensure the effectiveness of treatments and vaccines worldwide.
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Affiliation(s)
- Romina Salpini
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università 'Magna Græcia', Catanzaro, Italy.,Net4Science srl, Università 'Magna Græcia', Catanzaro, Italy
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | | | - Velia Chiara Di Maio
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases 'Lazzaro Spallanzani'-IRCCS, Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases 'Lazzaro Spallanzani'-IRCCS, Rome, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università 'Magna Græcia', Catanzaro, Italy.,Net4Science srl, Università 'Magna Græcia', Catanzaro, Italy
| | | | - Anna Artese
- Dipartimento di Scienze della Salute, Università 'Magna Græcia', Catanzaro, Italy.,Net4Science srl, Università 'Magna Græcia', Catanzaro, Italy
| | - Valentina Svicher
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
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46
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Azad GK. The molecular assessment of SARS-CoV-2 Nucleocapsid Phosphoprotein variants among Indian isolates. Heliyon 2021; 7:e06167. [PMID: 33553784 PMCID: PMC7848562 DOI: 10.1016/j.heliyon.2021.e06167] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/05/2020] [Accepted: 01/28/2021] [Indexed: 11/28/2022] Open
Abstract
Coronavirus disease- 2019 (COVID-19) has rapidly become a major threat to humans due to its high infection rate and deaths caused worldwide. This disease is caused by an RNA virus, Severe Acquired Respiratory Syndrome -Corona Virus-2 (SARS-CoV-2). This class of viruses have a high rate of mutation than DNA viruses that enables them to adapt and also evade host immune system. Here, we compared the first known Nucleocapsid Phosphoprotein (N protein) sequence of SARS-CoV-2 from China with the sequences from Indian COVID-19 patients to understand, if this virus is also mutating, as it is spreading to new locations. Our data revealed twenty mutations present among Indian isolates. Out of these, mutation at six positions led to changes in the secondary structure of N protein. Further, we also show that these mutations are primarily destabilising the protein structure. The candidate mutations identified in this study may help to speed up the understanding of variations occurring in SARS-CoV-2.
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47
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Bogani G, Ditto A, De Cecco L, Lopez S, Guerrisi R, Piccioni F, Micali A, Daidone MG, Raspagliesi F. Transmission of SARS-CoV-2 in Surgical Smoke during Laparoscopy: A Prospective, Proof-of-concept Study. J Minim Invasive Gynecol 2020; 28:1519-1525. [PMID: 33373728 PMCID: PMC7833707 DOI: 10.1016/j.jmig.2020.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 01/19/2023]
Abstract
STUDY OBJECTIVE There are growing concerns regarding the potential risk of coronavirus disease transmission during surgery and in particular during minimally invasive procedures owing to the aerosolization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particles. However, no study has demonstrated this hypothesis. Here, we aimed to investigate the presence of SARS-CoV-2 in surgical smoke. DESIGN A prospective pilot study. SETTING A tertiary cancer center in northern Italy. PATIENTS Overall, 17 patients underwent laparoscopic procedures for the management of suspected or documented gynecologic malignancies. The median age was 57 years (range 26-77). The surgical indications included endometrial cancer (n = 11), borderline ovarian tumor (n = 3), early-stage ovarian cancer (n = 1), stage IA cervical cancer after diagnostic conization (n = 1), and an ovarian cyst that turned out to be benign at final histologic examination (n = 1). INTERVENTIONS We evaluated all consecutive women scheduled to have laparoscopic procedures for suspected or documented gynecologic cancers. The patients underwent planned laparoscopic surgery. At the end of the laparoscopic procedures (after extubation), we performed reverse transcription-polymerase chain reaction (RT-PCR) tests for the detection of SARS-CoV-2 from both the endotracheal tube and the filter applied on the trocar valve. MEASUREMENTS AND MAIN RESULTS In 1 patient, both swab tests (endotracheal tube and trocar valve filter) showed amplification of the N gene on RT-PCR analysis. This case was considered to be a presumptive positive case. In another case, the RT-PCR analysis showed an amplification curve for the N gene only in the swab test performed on the filter. No ORF1ab amplification was detected. CONCLUSION Our study suggested the proof of principle that SARS-CoV-2 might be transmitted through surgical smoke and aerosolized native fluid from the abdominal cavity.
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Affiliation(s)
- Giorgio Bogani
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Antonino Ditto
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Loris De Cecco
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Salvatore Lopez
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Rocco Guerrisi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)..
| | - Federico Piccioni
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Arianna Micali
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Maria Grazia Daidone
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
| | - Francesco Raspagliesi
- Department of Gynecologic Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy (all authors)
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48
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Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Genes (Basel) 2020; 12:genes12010016. [PMID: 33374416 PMCID: PMC7824201 DOI: 10.3390/genes12010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein D614G mutation became the predominant globally circulating variant after its emergence in the early coronavirus disease 2019 (COVID-19) pandemic. Studies showed that this mutation results in an open conformation of the S glycoprotein receptor-binding domain (RBD), and increased angiotensin 1-converting enzyme 2 (ACE2) binding and fusion, which result in an increase in SARS-CoV-2 transmissibility and infectivity. Dynamic tracking of SARS-CoV-2 showed that the D614G variant became predominant after emergence in Europe and North America, but not in China. The current absence of selective pressures from antiviral treatment suggests that the driving force for viral evolution could be variations in human population genetics. Results show that ACE2 expression is higher in Asian populations than that in European, North American, and African populations. This supports the idea that lower ACE2 expression is a driving force in the positive selection for the D614G mutation. This study suggests that the dynamics of the SARS-CoV-2 D614G mutation during the early-to-mid pandemic is associated with enhanced transmission efficiency in populations with lower ACE2 expression. Understanding the role that human genetic diversity plays in the adaptive evolution of SARS-CoV-2 may have an important impact on public health and measures to control the pandemic.
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49
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Chand GB, Banerjee A, Azad GK. Identification of twenty-five mutations in surface glycoprotein (Spike) of SARS-CoV-2 among Indian isolates and their impact on protein dynamics. GENE REPORTS 2020; 21:100891. [PMID: 33015411 PMCID: PMC7521409 DOI: 10.1016/j.genrep.2020.100891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/28/2020] [Accepted: 09/23/2020] [Indexed: 01/20/2023]
Abstract
SARS-CoV-2, the causative agent of the COVID-19 pandemic, is an RNA virus that has inherent high rate of mutation. Due to the mutations, the virus evolves at a rapid pace that helps them to survive better inside the host. One of the hotspots of pharmacological interventions is to inhibit binding of virus with the host cells, which is mediated by Spike glycoprotein of SARS-CoV-2 and ACE2 receptors present on the human cells. This study was conducted with an aim to identify and characterise the mutation (s) present in the Spike glycoprotein of the SARS-CoV-2. Towards this, an in silico methodology was used, and the mutations on Spike glycoprotein were identified by comparing the Spike glycoprotein of first reported sequence from Wuhan wet seafood market virus with the available sequences of SARS-CoV-2 from Indian isolates. Our analysis revealed the presence of twenty-five mutations in Spike glycoprotein among Indian SARS-CoV-2 isolates. These mutations spread all over the protein and can be clustered at least into four distinct positions. Further, mutations at eleven positions exhibited alterations in the secondary structure of the polypeptide chain. We also investigated the influence of these mutations on overall protein dynamics and have shown that they affect the dynamic stability of the Spike glycoprotein.
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Affiliation(s)
| | - Atanu Banerjee
- Department of Zoology, Samastipur College, Samastipur 848134, Bihar, India
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50
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Zhang L, Jackson CB, Mou H, Ojha A, Peng H, Quinlan BD, Rangarajan ES, Pan A, Vanderheiden A, Suthar MS, Li W, Izard T, Rader C, Farzan M, Choe H. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun 2020; 11:6013. [PMID: 33243994 PMCID: PMC7693302 DOI: 10.1038/s41467-020-19808-4] [Citation(s) in RCA: 632] [Impact Index Per Article: 158.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 variants with spike (S)-protein D614G mutations now predominate globally. We therefore compare the properties of the mutated S protein (SG614) with the original (SD614). We report here pseudoviruses carrying SG614 enter ACE2-expressing cells more efficiently than those with SD614. This increased entry correlates with less S1-domain shedding and higher S-protein incorporation into the virion. Similar results are obtained with virus-like particles produced with SARS-CoV-2 M, N, E, and S proteins. However, D614G does not alter S-protein binding to ACE2 or neutralization sensitivity of pseudoviruses. Thus, D614G may increase infectivity by assembling more functional S protein into the virion.
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Affiliation(s)
- Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Cody B Jackson
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Huihui Mou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Amrita Ojha
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Brian D Quinlan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Erumbi S Rangarajan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Andi Pan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Abigail Vanderheiden
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Yerkes National Primate Research Center, Atlanta, GA, USA
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA
| | - Mehul S Suthar
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
- Yerkes National Primate Research Center, Atlanta, GA, USA
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta, GA, USA
| | - Wenhui Li
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Tina Izard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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