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mimouni H, Bouchlarhem A, Lafkih A, Haddar L, Lamzouri O, Bkiyar H, Housni B. Factors influencing the length of stay in the moroccan intensive care unit in patients surviving critical COVID-19 infection. Ann Med Surg (Lond) 2022; 79:104108. [PMID: 35784951 PMCID: PMC9238020 DOI: 10.1016/j.amsu.2022.104108] [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] [Received: 05/08/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Methods Results Conclusion Our objective is to determine the factors that influence the length of hospitalization of patients admitted to an intensive care unit. The average length of hospitalization for a critical infection with COVID-19 is 6 days (SD = 7Days). The length of time between the consultation and the onset of symptoms higher than 8 days affects the length of hospitalization. During hospitalization, the use of mechanical ventilation, the use of tocilizumab, having a billateral nosocomial pneumonia are all factors that impact the length of hospitalization.
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Affiliation(s)
- Hamza mimouni
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
- Corresponding author. Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco.
| | - Amine Bouchlarhem
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
| | - Amine Lafkih
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
| | - Leila Haddar
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
| | - Oussama Lamzouri
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
| | - Houssam Bkiyar
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
- Mohammed First University, Faculty of Medecine and Pharmacy, LAMCESM, Oujda, Morocco
| | - Brahim Housni
- Faculty of Medicine and Pharmacy, Mohammed I University, Oujda, Morocco
- Department of Anesthesiology and Intensive Care Unit, Mohammed VI University Hospital Mohammed I University, Oujda, Morocco
- Mohammed First University, Faculty of Medecine and Pharmacy, LAMCESM, Oujda, Morocco
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Nasereddin A, Al-Jawabreh A, Dumaidi K, Al-Jawabreh A, Al-Jawabreh H, Ereqat S. Tracking of SARS-CoV-2 Alpha variant (B.1.1.7) in Palestine. INFECTION, GENETICS AND EVOLUTION 2022; 101:105279. [PMID: 35390503 PMCID: PMC8978447 DOI: 10.1016/j.meegid.2022.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022]
Abstract
As surges of the COVID-19 pandemic continue globally, including in Palestine, several new SARS-CoV-2 variants have been introduced. This expansion has impacted transmission, disease severity, virulence, diagnosis, therapy, and natural and vaccine-induced immunity. Here, 183 whole genome sequences (WGS) were analyzed, of which 129 were from Palestinian cases, 62 of which were collected in 11 Palestinian districts between October 2020 and April 2021 and sequenced completely. A dramatic shift from the wild type to the Alpha variant (B 1.1.7) was observed within a short period of time. Cluster mapping revealed statistically significant clades in two main Palestinian cities, Al-Khalil (Monte Carlo hypothesis test-Poisson model, P = 0.00000000012) and Nablus (Monte Carlo hypothesis test-Poisson model, P = 0.014 and 0.015). The phylogenetic tree showed three main clusters of SARS-CoV-2 with high bootstrap values (>90). However, population genetics analysis showed a genetically homogenous population supported by low Wright's F-statistic values (Fst <0.25), high gene flow (Nm > 3), and statistically insignificant Tajima's D values (Tajima's test, neutrality model prediction, P = 0.02). The Alpha variant, rapidly replaced the wild type, causing a major surge that peaked in April 2021, with an increased COVID-19 mortality rate, especially, in the Al-Khalil and Nablus districts. The source of introduction remains uncertain, despite the minimal genetic variation. The study substantiates the use of WGS for SARS-CoV-2 surveillance as an early warning system to track down new variants requiring effective control.
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Saag M. Wonder of wonders, miracle of miracles: the unprecedented speed of COVID-19 science. Physiol Rev 2022; 102:1569-1577. [PMID: 35446679 PMCID: PMC9169823 DOI: 10.1152/physrev.00010.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Michael Saag
- University of Alabama at Birmingham, Birmingham, Alabama
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54
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Villa-Parra AC, Criollo I, Valadão C, Silva L, Coelho Y, Lampier L, Rangel L, Sharma G, Delisle-Rodríguez D, Calle-Siguencia J, Urgiles-Ortiz F, Díaz C, Caldeira E, Krishnan S, Bastos-Filho T. Towards Multimodal Equipment to Help in the Diagnosis of COVID-19 Using Machine Learning Algorithms. SENSORS 2022; 22:s22124341. [PMID: 35746121 PMCID: PMC9228002 DOI: 10.3390/s22124341] [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] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/29/2022]
Abstract
COVID-19 occurs due to infection through respiratory droplets containing the SARS-CoV-2 virus, which are released when someone sneezes, coughs, or talks. The gold-standard exam to detect the virus is Real-Time Polymerase Chain Reaction (RT-PCR); however, this is an expensive test and may require up to 3 days after infection for a reliable result, and if there is high demand, the labs could be overwhelmed, which can cause significant delays in providing results. Biomedical data (oxygen saturation level—SpO2, body temperature, heart rate, and cough) are acquired from individuals and are used to help infer infection by COVID-19, using machine learning algorithms. The goal of this study is to introduce the Integrated Portable Medical Assistant (IPMA), which is a multimodal piece of equipment that can collect biomedical data, such as oxygen saturation level, body temperature, heart rate, and cough sound, and helps infer the diagnosis of COVID-19 through machine learning algorithms. The IPMA has the capacity to store the biomedical data for continuous studies and can be used to infer other respiratory diseases. Quadratic kernel-free non-linear Support Vector Machine (QSVM) and Decision Tree (DT) were applied on three datasets with data of cough, speech, body temperature, heart rate, and SpO2, obtaining an Accuracy rate (ACC) and Area Under the Curve (AUC) of approximately up to 88.0% and 0.85, respectively, as well as an ACC up to 99% and AUC = 0.94, respectively, for COVID-19 infection inference. When applied to the data acquired with the IMPA, these algorithms achieved 100% accuracy. Regarding the easiness of using the equipment, 36 volunteers reported that the IPMA has a high usability, according to results from two metrics used for evaluation: System Usability Scale (SUS) and Post Study System Usability Questionnaire (PSSUQ), with scores of 85.5 and 1.41, respectively. In light of the worldwide needs for smart equipment to help fight the COVID-19 pandemic, this new equipment may help with the screening of COVID-19 through data collected from biomedical signals and cough sounds, as well as the use of machine learning algorithms.
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Affiliation(s)
- Ana Cecilia Villa-Parra
- Biomedical Engineering Research Group—GIIB, Universidad Politécnica Salesiana (UPS), Cuenca 010105, Ecuador; (A.C.V.-P.); (I.C.); (J.C.-S.); (F.U.-O.)
| | - Ismael Criollo
- Biomedical Engineering Research Group—GIIB, Universidad Politécnica Salesiana (UPS), Cuenca 010105, Ecuador; (A.C.V.-P.); (I.C.); (J.C.-S.); (F.U.-O.)
| | - Carlos Valadão
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Leticia Silva
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Yves Coelho
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Lucas Lampier
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Luara Rangel
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Garima Sharma
- Department of Electrical, Computer, and Biomedical Engineering, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada; (G.S.); (S.K.)
| | - Denis Delisle-Rodríguez
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - John Calle-Siguencia
- Biomedical Engineering Research Group—GIIB, Universidad Politécnica Salesiana (UPS), Cuenca 010105, Ecuador; (A.C.V.-P.); (I.C.); (J.C.-S.); (F.U.-O.)
| | - Fernando Urgiles-Ortiz
- Biomedical Engineering Research Group—GIIB, Universidad Politécnica Salesiana (UPS), Cuenca 010105, Ecuador; (A.C.V.-P.); (I.C.); (J.C.-S.); (F.U.-O.)
| | - Camilo Díaz
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Eliete Caldeira
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
| | - Sridhar Krishnan
- Department of Electrical, Computer, and Biomedical Engineering, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada; (G.S.); (S.K.)
| | - Teodiano Bastos-Filho
- Department of Electrical Engineering, Universidade Federal do Espírito Santo (UFES), Vitoria 29075-910, Brazil; (C.V.); (L.S.); (Y.C.); (L.L.); (L.R.); (D.D.-R.); (C.D.); (E.C.)
- Correspondence: ; Tel.: +593-98-441-2586
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Troyano-Hernáez P, Reinosa R, Holguín Á. Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins. Int J Mol Sci 2022; 23:6394. [PMID: 35742840 PMCID: PMC9223475 DOI: 10.3390/ijms23126394] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Monitoring SARS-CoV-2’s genetic diversity and emerging mutations in this ongoing pandemic is crucial to understanding its evolution and ensuring the performance of COVID-19 diagnostic tests, vaccines, and therapies. Spain has been one of the main epicenters of COVID-19, reaching the highest number of cases and deaths per 100,000 population in Europe at the beginning of the pandemic. This study aims to investigate the epidemiology of SARS-CoV-2 in Spain and its 18 Autonomous Communities across the six epidemic waves established from February 2020 to January 2022. We report on the circulating SARS-CoV-2 variants in each epidemic wave and Spanish region and analyze the mutation frequency, amino acid (aa) conservation, and most frequent aa changes across each structural/non-structural/accessory viral protein among the Spanish sequences deposited in the GISAID database during the study period. The overall SARS-CoV-2 mutation frequency was 1.24 × 10−5. The aa conservation was >99% in the three types of protein, being non-structural the most conserved. Accessory proteins had more variable positions, while structural proteins presented more aa changes per sequence. Six main lineages spread successfully in Spain from 2020 to 2022. The presented data provide an insight into the SARS-CoV-2 circulation and genetic variability in Spain during the first two years of the pandemic.
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Affiliation(s)
| | | | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology Department and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) in Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), 28034 Madrid, Spain; (P.T.-H.); (R.R.)
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56
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Arévalo MT, Karavis MA, Katoski SE, Harris JV, Hill JM, Deshpande SV, Roth PA, Liem AT, Bernhards RC. A Rapid, Whole Genome Sequencing Assay for Detection and Characterization of Novel Coronavirus (SARS-CoV-2) Clinical Specimens Using Nanopore Sequencing. Front Microbiol 2022; 13:910955. [PMID: 35733956 PMCID: PMC9207459 DOI: 10.3389/fmicb.2022.910955] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 12/22/2022] Open
Abstract
A new human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged at the end of 2019 in Wuhan, China that caused a range of disease severities; including fever, shortness of breath, and coughing. This disease, now known as coronavirus disease 2019 (COVID-19), quickly spread throughout the world, and was declared a pandemic by the World Health Organization in March of 2020. As the disease continues to spread, providing rapid characterization has proven crucial to better inform the design and execution of control measures, such as decontamination methods, diagnostic tests, antiviral drugs, and prophylactic vaccines for long-term control. Our work at the United States Army’s Combat Capabilities Development Command Chemical Biological Center (DEVCOM CBC) is focused on engineering workflows to efficiently identify, characterize, and evaluate the threat level of any potential biological threat in the field and more remote, lower resource settings, such as forward operating bases. While we have successfully established untargeted sequencing approaches for detection of pathogens for rapid identification, our current work entails a more in-depth sequencing analysis for use in evolutionary monitoring. We are developing and validating a SARS-CoV-2 nanopore sequencing assay, based on the ARTIC protocol. The standard ARTIC, Illumina, and nanopore sequencing protocols for SARS-CoV-2 are elaborate and time consuming. The new protocol integrates Oxford Nanopore Technology’s Rapid Sequencing Kit following targeted RT-PCR of RNA extracted from human clinical specimens. This approach decreases sample manipulations and preparation times. Our current bioinformatics pipeline utilizes Centrifuge as the classifier for quick identification of SARS-CoV-2 and RAMPART software for verification and mapping of reads to the full SARS-CoV-2 genome. ARTIC rapid sequencing results, of previous RT-PCR confirmed patient samples, showed that the modified protocol produces high quality data, with up to 98.9% genome coverage at >1,000x depth for samples with presumably higher viral loads. Furthermore, whole genome assembly and subsequent mutational analysis of six of these sequences identified existing and unique mutations to this cluster, including three in the Spike protein: V308L, P521R, and D614G. This work suggests that an accessible, portable, and relatively fast sample-to-sequence process to characterize viral outbreaks is feasible and effective.
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Affiliation(s)
- Maria T. Arévalo
- Defense Threat Reduction Agency, Aberdeen Proving Ground, MD, United States
- United States Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, United States
- *Correspondence: Maria T. Arévalo,
| | - Mark A. Karavis
- United States Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, United States
| | - Sarah E. Katoski
- United States Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, United States
| | - Jacquelyn V. Harris
- United States Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, United States
| | | | - Samir V. Deshpande
- United States Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, United States
| | | | | | - R. Cory Bernhards
- United States Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, MD, United States
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57
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McHenry A, Iyer K, Wang J, Liu C, Harigopal M. Detection of SARS-CoV-2 in tissue: the comparative roles of RT-qPCR, in situ RNA hybridization, and immunohistochemistry. Expert Rev Mol Diagn 2022; 22:559-574. [PMID: 35658709 DOI: 10.1080/14737159.2022.2085508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The emergence of SARS-CoV-2, the causative agent the COVID-19 pandemic, has led to a rapidly expanding arsenal of molecular diagnostic assays for the detection of viral material in tissue specimens. AREAS COVERED We review the value and shortcomings of available tissue-based assays for SARS-CoV-2 detection in formalin-fixed paraffin-embedded (FFPE) tissue, including immunohistochemistry, in situ hybridization, and quantitative reverse transcription PCR (RT-qPCR). The validation, accuracy, and comparative utility of each method is discussed. Subsequently, we identify commercially available antibodies which render the greatest specificity and reproducibility of staining in FFPE specimens. EXPERT OPINION We offer expert opinion on the efficacy of such techniques and guidance for future implementation, both clinical and experimental.
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Affiliation(s)
- Austin McHenry
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Krishna Iyer
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Jianhi Wang
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Chen Liu
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
| | - Malini Harigopal
- Yale University School of Medicine, Department of Pathology, New Haven, CT, 06520, United States
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Ciubotariu II, Dorman J, Perry NM, Gorenstein L, Kattoor JJ, Fola AA, Zine A, Hendrix GK, Wilkes RP, Kitchen A, Carpi G. Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant. Open Forum Infect Dis 2022; 9:ofac268. [PMID: 35818365 PMCID: PMC9213861 DOI: 10.1093/ofid/ofac268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Using a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis we tracked the spread and introduction events of SARS-CoV-2 variants focusing on a large university community.
Methods
Here, we sequenced and analyzed 677 high-quality SARS-CoV-2 genomes from positive RNA samples collected from Purdue University students, faculty, and staff who tested positive for the virus between January 2021 and May 2021, comprising an average of 32% of weekly cases across the time frame.
Results
Our analysis of circulating SARS-CoV-2 variants over time revealed periods when Variant of Concern (VOC) Alpha (B.1.1.7) and Iota (B.1.526) reached rapid dominance and documented that VOC Gamma (P.1) was increasing in frequency as campus surveillance was ending. Phylodynamic analysis of Gamma genomes from campus alongside a subsampling of >20,000 previously published P.1 genomes revealed ten independent introductions of this variant into the Purdue community, predominantly from elsewhere in the United States, with introductions from within the state of Indiana and from Illinois, and possibly Washington and New York, suggesting a degree of domestic spread.
Conclusions
We conclude that a robust and sustained active and passive surveillance program coupled with genomic sequencing during a pandemic offers important insights into the dynamics of pathogen arrival and spread in a campus community and can help guide mitigation measures.
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Affiliation(s)
- Ilinca I. Ciubotariu
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Jack Dorman
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Nicole M. Perry
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Lev Gorenstein
- Purdue University Information Technology Research Computing, , West Lafayette, Indiana 47907, USA
| | - Jobin J. Kattoor
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Abebe A. Fola
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
| | - Amy Zine
- University of Iowa Department of Anthropology, , Iowa City, Iowa, USA
| | - G. Kenitra Hendrix
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Rebecca P. Wilkes
- Purdue University College of Veterinary Medicine Department of Comparative Biology, Animal Disease Diagnostic Laboratory, , West Lafayette, Indiana 47907, USA
| | - Andrew Kitchen
- University of Iowa Department of Anthropology, , Iowa City, Iowa, USA
| | - Giovanna Carpi
- Purdue University Department of Biological Sciences, , West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation , Immunology and Infectious Disease, West Lafayette, Indiana 47907, USA
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Petersen JD, Lu J, Fitzgerald W, Zhou F, Blank PS, Matthies D, Zimmerberg J. Unique Aggregation of Retroviral Particles Pseudotyped with the Delta Variant SARS-CoV-2 Spike Protein. Viruses 2022; 14:1024. [PMID: 35632764 PMCID: PMC9147488 DOI: 10.3390/v14051024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped viral particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped viral particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spike's unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.
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Affiliation(s)
- Jennifer D. Petersen
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (J.D.P.); (P.S.B.)
| | - Jianming Lu
- Codex BioSolutions, Inc., Department of Research and Development, Cell Biology, 12358 Parklawn Dr., Suite 250, North Bethesda, MD 20852, USA;
| | - Wendy Fitzgerald
- Section on Intercellular Interactions, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (F.Z.); (D.M.)
| | - Paul S. Blank
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (J.D.P.); (P.S.B.)
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (F.Z.); (D.M.)
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (J.D.P.); (P.S.B.)
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60
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Morris CP, Luo CH, Amadi A, Schwartz M, Gallagher N, Ray SC, Pekosz A, Mostafa HH. An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Clin Infect Dis 2022; 74:1419-1428. [PMID: 34272947 PMCID: PMC8406876 DOI: 10.1093/cid/ciab636] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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 School of Medicine, 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 School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Adannaya Amadi
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Johns Hopkins School of Medicine, 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 School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
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61
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Jamir E, Sarma H, Priyadarsinee L, Nagamani S, Kiewhuo K, Gaur AS, Rawal RK, Murugan NA, Subramanian V, Sastry GN. Applying polypharmacology approach for drug repurposing for SARS-CoV2. J CHEM SCI 2022; 134:57. [PMID: 35498548 PMCID: PMC9028909 DOI: 10.1007/s12039-022-02046-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 02/06/2023]
Abstract
Exploring the new therapeutic indications of known drugs for treating COVID-19, popularly known as drug repurposing, is emerging as a pragmatic approach especially owing to the mounting pressure to control the pandemic. Targeting multiple targets with a single drug by employing drug repurposing known as the polypharmacology approach may be an optimised strategy for the development of effective therapeutics. In this study, virtual screening has been carried out on seven popular SARS-CoV-2 targets (3CLpro, PLpro, RdRp (NSP12), NSP13, NSP14, NSP15, and NSP16). A total of 4015 approved drugs were screened against these targets. Four drugs namely venetoclax, tirilazad, acetyldigitoxin, and ledipasvir have been selected based on the docking score, ability to interact with four or more targets and having a reasonably good number of interactions with key residues in the targets. The MD simulations and MM-PBSA studies showed reasonable stability of protein-drug complexes and sustainability of key interactions between the drugs with their respective targets throughout the course of MD simulations. The identified four drug molecules were also compared with the known drugs namely elbasvir and nafamostat. While the study has provided a detailed account of the chosen protein-drug complexes, it has explored the nature of seven important targets of SARS-CoV-2 by evaluating the protein-drug complexation process in great detail.
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Affiliation(s)
- Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kikrusenuo Kiewhuo
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anamika Singh Gaur
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ravindra K Rawal
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Natarajan Arul Murugan
- Department of Computer Science, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Venkatesan Subramanian
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Center for High Computing, CSIR- Central Leather Research Institute (CLRI), Chennai, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR – North East Institute of Science and Technology, Jorhat, Assam 785006 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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62
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Combating Viral Diseases in the Era of Systems Medicine. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2486:87-104. [PMID: 35437720 DOI: 10.1007/978-1-0716-2265-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Viruses can cause many diseases resulting in disabilities and death. Fortunately, advances in systems medicine enable the development of effective therapies for treating viral diseases, of vaccines to prevent viral infections, as well as of diagnostic tools to mitigate the risk and reduce the death toll. Characterizing the SARS-CoV-2 gene sequence and the role of its spike protein in infection informs development of small molecule drugs, antibodies, and vaccines to combat infection and complication, as well as to end the pandemic. Drug repurposing of small molecule drugs is a viable strategy to combat viral diseases; the key concepts include (1) linking a drug candidate's pharmacological network to its pharmacodynamic response in patients; (2) linking a drug candidate's physicochemical properties to its pharmacokinetic characteristics; and (3) optimizing the safe and effective dosing regimen within its therapeutic window. Computational integration of drug-induced signaling pathways with clinical outcomes is useful to inform selection of potential drug candidates with respect to safety and effectiveness. Key pharmacokinetic and pharmacodynamic principles for computational optimization of drug development include a drug candidate's Cminss/IC95 ratio, pharmacokinetic characteristics, and systemic exposure-response relationship, where Cminss is the trough concentration following multiple dosing. In summary, systems medicine approaches play a vital role in global success in combating viral diseases, including global real-time information sharing, development of test kits, drug repurposing, discovery and development of safe, effective therapies, detection of highly transmissible and deadly variants, and development of vaccines.
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63
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Ramm F, Dondapati SK, Trinh HA, Wenzel D, Walter RM, Zemella A, Kubick S. The Potential of Eukaryotic Cell-Free Systems as a Rapid Response to Novel Zoonotic Pathogens: Analysis of SARS-CoV-2 Viral Proteins. Front Bioeng Biotechnol 2022; 10:896751. [PMID: 35519622 PMCID: PMC9061942 DOI: 10.3389/fbioe.2022.896751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
The ongoing pandemic caused by the novel coronavirus (SARS-CoV-2) has led to more than 445 million infections and the underlying disease, COVID-19, resulted in more than 6 million deaths worldwide. The scientific world is already predicting future zoonotic diseases. Hence, rapid response systems are needed to tackle future epidemics and pandemics. Here, we present the use of eukaryotic cell-free systems for the rapid response to novel zoonotic diseases represented by SARS-CoV-2. Non-structural, structural and accessory proteins encoded by SARS-CoV-2 were synthesized by cell-free protein synthesis in a fast and efficient manner. The inhibitory effect of the non-structural protein 1 on protein synthesis could be shown in vitro. Structural proteins were quantitatively detected by commercial antibodies, therefore facilitating cell-free systems for the validation of available antibodies. The cytotoxic envelope protein was characterized in electrophysiological planar lipid bilayer measurements. Hence, our study demonstrates the potential of eukaryotic cell-free systems as a rapid response mechanism for the synthesis, functional characterization and antibody validation against a viral pathogen.
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Affiliation(s)
- Franziska Ramm
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Srujan K. Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Hoai Anh Trinh
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Department of Applied Biochemistry, Institute of Biotechnology, Technical University Berlin, Berlin, Germany
| | - Dana Wenzel
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Ruben M. Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Department of Applied Biochemistry, Institute of Biotechnology, Technical University Berlin, Berlin, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus–Senftenberg, The Brandenburg Medical School Theodor Fontane, The University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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64
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Choi S, Kim KW, Ku KB, Kim SJ, Park C, Park D, Kim S, Yi H. Human Alphacoronavirus Universal Primers for Genome Amplification and Sequencing. Front Microbiol 2022; 13:789665. [PMID: 35401489 PMCID: PMC8990890 DOI: 10.3389/fmicb.2022.789665] [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: 10/05/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate sequencing covering the entire genome is essential to identify genetic variations of viral pathogens. However, due to the low viral titers in clinical samples, certain amplification steps are required for viral genome sequencing. At present, there are no universal primers available for alphacoronaviruses and that, since these viruses have diverse strains, new primers specific to the target strain must be continuously developed for sequencing. Thus, in this study, we aimed to develop a universal primer set valid for all human alphacoronaviruses and applicable to samples containing trace amounts of the virus. To this aim, we designed overlapping primer pairs capable of amplifying the entire genome of all known human alphacoronaviruses. The selected primers, named the AC primer set, were composed of 10 primer pairs stretching over the entire genome of alphacoronaviruses, and produced PCR products of the expected size (3-5 kb) from both the HCoV-229E and HCoV-NL63 strains. After genome amplification, an evaluation using various sequencing platforms was carried out. The amplicon library sequencing data were assembled into complete genome sequences in all sequencing strategies examined in this study. The sequencing accuracy varied depending on the sequencing technology, but all sequencing methods showed a sequencing error of less than 0.01%. In the mock clinical specimen, the detection limit was 10-3 PFU/ml (102 copies/ml). The AC primer set and experimental procedure optimized in this study may enable the fast diagnosis of mutant alphacoronaviruses in future epidemics.
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Affiliation(s)
- Sungmi Choi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Kwan Woo Kim
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Changwoo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Dongju Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Biological Science, Chungnam National University, Daejeon, South Korea
| | - Seil Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Bio-Analysis Science, University of Science and Technology, Daejeon, South Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea.,School of Biosystems and Biomedical Sciences, Korea University, Seoul, South Korea
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65
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Petersen JD, Lu J, Fitzgerald W, Zhou F, Blank PS, Matthies D, Zimmerberg J. The Delta variant SARS-CoV-2 spike protein uniquely promotes aggregation of pseudotyped viral particles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.07.487415. [PMID: 35441171 PMCID: PMC9016642 DOI: 10.1101/2022.04.07.487415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spike’s unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.
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Affiliation(s)
- Jennifer D Petersen
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Jianming Lu
- Codex BioSolutions, Inc., 12358 Parklawn Dr., Suite 250, North Bethesda, MD, USA
| | - Wendy Fitzgerald
- Section on Intercellular Interactions, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul S Blank
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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66
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Figueiredo DLA, Ximenez JPB, Seiva FRF, Panis C, Bezerra RDS, Ferrasa A, Cecchini AL, de Medeiros AI, Almeida AMF, Ramão A, Boldt ABW, Moya CF, Chin CM, de Paula D, Rech D, Gradia DF, Malheiros D, Venturini D, Tavares ER, Carraro E, Ribeiro EMDSF, Pereira EM, Tuon FF, Follador FAC, Fernandes GSA, Volpato H, Cólus IMDS, de Oliveira JC, Rodrigues JHDS, dos Santos JL, Visentainer JEL, Brandi JC, Serpeloni JM, Bonini JS, de Oliveira KB, Fiorentin K, Lucio LC, Faccin-Galhardi LC, Ferreto LED, Lioni LMY, Consolaro MEL, Vicari MR, Arbex MA, Pileggi M, Watanabe MAE, Costa MAR, Giannini MJSM, Amarante MK, Khalil NM, de Lima QA, Herai RH, Guembarovski RL, Shinsato RN, Mainardes RM, Giuliatti S, Yamada-Ogatta SF, Gerber VKDQ, Pavanelli WR, da Silva WC, Petzl-Erler ML, Valente V, Soares CP, Cavalli LR, Silva WA. COVID-19: The question of genetic diversity and therapeutic intervention approaches. Genet Mol Biol 2022; 44:e20200452. [PMID: 35421211 PMCID: PMC9075701 DOI: 10.1590/1678-4685-gmb-2020-0452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/24/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), is the largest pandemic in modern history with very high infection rates and considerable mortality. The disease, which emerged in China's Wuhan province, had its first reported case on December 29, 2019, and spread rapidly worldwide. On March 11, 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic and global health emergency. Since the outbreak, efforts to develop COVID-19 vaccines, engineer new drugs, and evaluate existing ones for drug repurposing have been intensively undertaken to find ways to control this pandemic. COVID-19 therapeutic strategies aim to impair molecular pathways involved in the virus entrance and replication or interfere in the patients' overreaction and immunopathology. Moreover, nanotechnology could be an approach to boost the activity of new drugs. Several COVID-19 vaccine candidates have received emergency-use or full authorization in one or more countries, and others are being developed and tested. This review assesses the different strategies currently proposed to control COVID-19 and the issues or limitations imposed on some approaches by the human and viral genetic variability.
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Affiliation(s)
- David Livingstone Alves Figueiredo
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina, Guarapuava, PR, Brazil
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - João Paulo Bianchi Ximenez
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicologia e Ciência de Alimentos, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Fábio Rodrigues Ferreira Seiva
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carolina Panis
- Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rafael dos Santos Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Adriano Ferrasa
- Universidade Estadual de Ponta Grossa, Ponta Grossa, Programa de Pós Graduação em Computação Aplicada, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alessandra Lourenço Cecchini
- Universidade Estadual de Londrina, Departamento de Patologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alexandra Ivo de Medeiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ana Marisa Fusco Almeida
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Anelisa Ramão
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Ciências Biológicas, Guarapuava, PR, Brazil
| | - Angelica Beate Winter Boldt
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carla Fredrichsen Moya
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina Veterinária, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Chung Man Chin
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- União das Faculdades dos Grandes Lagos (UNILAGO), Centro de Pesquisa Avançada em Medicina, São José do Rio Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel de Paula
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel Rech
- Universidade Estadual do Oeste do Paraná (UNIOESTE), Hospital do Câncer Francisco Beltrão, Laboratório de Biologia de Tumores, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniela Fiori Gradia
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Malheiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Venturini
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de patologia, clínica e toxicologia, Laboratório de bioquímica clínica, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Eliandro Reis Tavares
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Emerson Carraro
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Virologia Clínica, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Enilze Maria de Souza Fonseca Ribeiro
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Evani Marques Pereira
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Felipe Francisco Tuon
- Universidade Católica do Paraná, Laboratório de Doenças Infecciosas Emergentes, Pontifícia Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Franciele Aní Caovilla Follador
- Universidade Estadual do Oeste do Paraná, Departamento de Ciências da Vida, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Glaura Scantamburlo Alves Fernandes
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Hélito Volpato
- Universidade Estadual do Paraná (UNESPAR), Faculdade de Ciências Biológicas, Centro de Ciências Humanas e Educação, Paranavaí, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ilce Mara de Syllos Cólus
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jaqueline Carvalho de Oliveira
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Henrique da Silva Rodrigues
- Universidade do Estado de São Paulo (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Leandro dos Santos
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jeane Eliete Laguila Visentainer
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Cristina Brandi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Mara Serpeloni
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Sartori Bonini
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karen Brajão de Oliveira
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Genética Molecular e Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karine Fiorentin
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Léia Carolina Lucio
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ligia Carla Faccin-Galhardi
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lirane Elize Defante Ferreto
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lucy Megumi Yamauchi Lioni
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Marcia Edilaine Lopes Consolaro
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Abdo Arbex
- Universidade de Araraquara, Faculdade de Medicina, Área temática de Pneumologia, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Pileggi
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Angelica Ehara Watanabe
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Antônia Ramos Costa
- Universidade do Estado do Paraná, Colegiada de Enfermagem, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria José S. Mendes Giannini
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marla Karine Amarante
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Najeh Maissar Khalil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Quirino Alves de Lima
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberto H. Herai
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberta Losi Guembarovski
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rogério N. Shinsato
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rubiana Mara Mainardes
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Silvana Giuliatti
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Viviane Knuppel de Quadros Gerber
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wander Rogério Pavanelli
- Universidade Estadual de Londrina, Laboratório de Imunoparasitologia de Doenças Negligenciadas e Câncer, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Weber Claudio da Silva
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Luiza Petzl-Erler
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Valeria Valente
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Christiane Pienna Soares
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Luciane Regina Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wilson Araujo Silva
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular (INCT/CNPq), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
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Salih RA, Mohamed NS, Taha AA. Genetic Sequence of Coronavirus Strains Isolated from Iraqi Patients and their Relationship with some Liver Enzymes and Interleukins. ARCHIVES OF RAZI INSTITUTE 2022; 77:809-819. [PMID: 36284985 PMCID: PMC9548273 DOI: 10.22092/ari.2022.357089.1967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/16/2022] [Indexed: 05/24/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a positive-sense single-stranded RNA virus from the genus Betacoronavirus causes COVID-19 (coronavirus disease 2019). According to daily reports issued by the Iraqi Ministry of Health, the SARS-COV-2 was firstly detected in Al-Najaf city in February 2020 and identified in the Central Public Health Laboratory (CPHL) in Baghdad, Iraq. The outcomes of this study were based on 100 nasopharyngeal swaps and venous blood samples from hospitalized patients in Al-Kindy and CPHL. Patients were assigned to five groups (Asymptomatic, Mild, Moderate, Severe, and Deceased) based on disease severity as indicated by World Health Organization (WHO). The positive samples were identified by real-time quantitative polymerase chain reaction (RT-PCR) and subjected to some liver enzyme assays and interleukins measurements, and the correlation with the genetic sequence was determined by Illumina Miseq technology. Liver enzymes levels of Aspartate aminotransferase (AST), Alanine aminotransferase (ALT), and lactate dehydrogenase (LDH) showed statistically significant differences, especially between the deceased groups. Interleukins (IL-10, IL-18, and TNF- α) significantly differed among groups. This study revealed that three isolates belonging to the original strain isolated from Wuhan (A19) and characterized by their virulence caused severe symptoms and led to admission to isolation hospitals and intensive care units, and the last two isolates of (UK alpha V1) appeared in Iraq in early 2021. These strains which were less virulent than the Wuhan strain spread faster and appear in moderate and asymptomatic patients.
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Affiliation(s)
- R A Salih
- Central Public Health Laboratory, Ministry of Health, Baghdad, Iraq
| | - N S Mohamed
- Pharmacy College, Al- Nahrain University, Baghdad, Iraq
| | - A A Taha
- Department of Applied Science, University of Technology, Baghdad, Iraq
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68
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End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection. Sci Rep 2022; 12:4759. [PMID: 35306521 PMCID: PMC8933765 DOI: 10.1038/s41598-022-07756-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/24/2022] [Indexed: 11/09/2022] Open
Abstract
End-point RT-PCR is a suitable alternative diagnostic technique since it is cheaper than RT-qPCR tests and can be implemented on a massive scale in low- and middle-income countries. In this work, a bioinformatic approach to guide the design of PCR primers was developed, and an alternative diagnostic test based on end-point PCR was designed. End-point PCR primers were designed through conservation analysis based on kmer frequency in SARS-CoV-2 and human respiratory pathogen genomes. Highly conserved regions were identified for primer design, and the resulting PCR primers were used to amplify 871 nasopharyngeal human samples with a previous RT-qPCR based SARS-CoV-2 diagnosis. The diagnostic test showed high accuracy in identifying SARS-CoV-2-positive samples including B.1.1.7, P.1, B.1.427/B.1.429 and B.1.617.2/ AY samples with a detection limit of 7.2 viral copies/µL. In addition, this test could discern SARS-CoV-2 infection from other viral infections with COVID-19-like symptomatology. The designed end-point PCR diagnostic test to detect SARS-CoV-2 is a suitable alternative to RT-qPCR. Since the proposed bioinformatic approach can be easily applied in thousands of viral genomes and over highly divergent strains, it can be used as a PCR design tool as new SARS-CoV-2 variants emerge. Therefore, this end-point PCR test could be employed in epidemiological surveillance to detect new SARS-CoV-2 variants as they emerge and propagate.
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Kuchi A, Wu J, Fuloria J, Hicks C. Landscape of Molecular Crosstalk Perturbation between Lung Cancer and COVID-19. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:3454. [PMID: 35329141 PMCID: PMC8953719 DOI: 10.3390/ijerph19063454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Lung cancer patients have the worst outcomes when affected by coronavirus disease 2019 (COVID-19). The molecular mechanisms underlying the association between lung cancer and COVID-19 remain unknown. The objective of this investigation was to determine whether there is crosstalk in molecular perturbation between COVID-19 and lung cancer, and to identify a molecular signature, molecular networks and signaling pathways shared by the two diseases. METHODS We analyzed publicly available gene expression data from 52 severely affected COVID-19 human lung samples, 594 lung tumor samples and 54 normal disease-free lung samples. We performed network and pathways analysis to identify molecular networks and signaling pathways shared by the two diseases. RESULTS The investigation revealed a signature of genes associated with both diseases and signatures of genes uniquely associated with each disease, confirming crosstalk in molecular perturbation between COVID-19 and lung cancer. In addition, the analysis revealed molecular networks and signaling pathways associated with both diseases. CONCLUSIONS The investigation revealed crosstalk in molecular perturbation between COVID-19 and lung cancer, and molecular networks and signaling pathways associated with the two diseases. Further research on a population impacted by both diseases is recommended to elucidate molecular drivers of the association between the two diseases.
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Affiliation(s)
- Aditi Kuchi
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Jiande Wu
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA
| | - Jyotsna Fuloria
- University Medical Center New Orleans, 2000 Canal Street, New Orleans, LA 70112, USA
| | - Chindo Hicks
- Department of Genetics and the Bioinformatics and Genomics Program, Louisiana State University Health Sciences Center, School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA
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Papanikolaou V, Chrysovergis A, Ragos V, Tsiambas E, Katsinis S, Manoli A, Papouliakos S, Roukas D, Mastronikolis S, Peschos D, Batistatou A, Kyrodimos E, Mastronikolis N. From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants. Gene 2022; 814:146134. [PMID: 34990799 PMCID: PMC8725615 DOI: 10.1016/j.gene.2021.146134] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus-related Severe Acute Respiratory Syndrome (SARS-CoV) in 2002/2003, Middle-East Respiratory Syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 Severe Acute Respiratory Syndrome-2 (SARS-CoV-2) affected negatively the national health systems’ endurance worldwide. SARS-Cov-2 virus belongs to lineage b of beta-CoVs demonstrating a strong phylogenetic similarity with BatCoVRaTG13 type. Spike (S) glycoprotein projections -consisting of two subunits S1/S2- provide a unique crown-like formation (corona) on virion’s surface. Concerning their functional role, S1 represents the main receptor-binding domain (RBD), whereas S2 is involved in the virus-cell membrane fusion mechanism. On Nov 26th 2021, WHO designated the new SARS-CoV-2 strain – named Omicron, from letter ‘’όμικρον’’ in the Greek alphabet - as a variant of concern (B.1.1529 variant). Potentially this new variant is associated with high transmissibility leading to elevated infectivity and probably increased re-infection rates. Its impact on morbidity/mortality remains under investigation. In the current paper, analyzing and comparing the alterations of SARS-CoV-2 S RNA sequences in the defined variants (Alpha to Omicron), we observed some interesting findings regarding the S1-RBD/S2 mutation/deletion equilibrium that maybe affect and modify its activity.
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Affiliation(s)
| | - Aris Chrysovergis
- 1ST ENT Department, Hippocration Hospital, University of Athens, Athens, Greece
| | - Vasileios Ragos
- Dept of Maxillofacial, Medical School, University of Ioannina, Greece
| | - Evangelos Tsiambas
- Dept of Maxillofacial, Medical School, University of Ioannina, Greece; Department of Cytology, Molecular Unit, 417 Veterans Army Hospital (NIMTS), Athens, Greece.
| | - Spyros Katsinis
- Department of Otorhinolaryngology, Thoracic Diseases General Hospital "Sotiria", Athens, Greece
| | - Arezina Manoli
- Department of Otorhinolaryngology, Thoracic Diseases General Hospital "Sotiria", Athens, Greece
| | | | - Dimitrios Roukas
- Department of Psychiatry, 417 Veterans Army Hospital (NIMTS), Athens, Greece
| | | | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Greece
| | - Anna Batistatou
- ENT Department, Medical School, University of Patras, Greece
| | - Efthimios Kyrodimos
- 1ST ENT Department, Hippocration Hospital, University of Athens, Athens, Greece
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Iwasaki Y, Abe T, Wada K, Wada Y, Ikemura T. Unsupervised explainable AI for molecular evolutionary study of forty thousand SARS-CoV-2 genomes. BMC Microbiol 2022; 22:73. [PMID: 35272618 PMCID: PMC8907386 DOI: 10.1186/s12866-022-02484-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 02/28/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established unsupervised AI, a BLSOM (batch-learning SOM), which can analyze five million genomic sequences simultaneously. The present study applied the BLSOM to the oligonucleotide compositions of forty thousand SARS-CoV-2 genomes. RESULTS While only the oligonucleotide composition was given, the obtained clusters of genomes corresponded primarily to known main clades and internal divisions in the main clades. Since the BLSOM is explainable AI, it reveals which features of the oligonucleotide composition are responsible for clade clustering. Additionally, BLSOM also provided information concerning the special genomic region possibly undergoing RNA modifications. CONCLUSIONS The BLSOM has powerful image display capabilities and enables efficient knowledge discovery about viral evolutionary processes, and it can complement phylogenetic methods based on sequence alignment.
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Affiliation(s)
- Yuki Iwasaki
- Nagahama Institute of Bio-Science and Technology, Shiga-ken, Nagahama, 526-0829, Japan
| | - Takashi Abe
- Faculty of Engineering, Niigata University, Niigata-ken, 950-2181, Japan
| | - Kennosuke Wada
- Nagahama Institute of Bio-Science and Technology, Shiga-ken, Nagahama, 526-0829, Japan
| | - Yoshiko Wada
- Nagahama Institute of Bio-Science and Technology, Shiga-ken, Nagahama, 526-0829, Japan
| | - Toshimichi Ikemura
- Nagahama Institute of Bio-Science and Technology, Shiga-ken, Nagahama, 526-0829, Japan. .,National Institute of Genetics, Mishima, Shizuoka-ken, 411-8540, Japan.
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Amara U, Rashid S, Mahmood K, Nawaz MH, Hayat A, Hassan M. Insight into prognostics, diagnostics, and management strategies for SARS CoV-2. RSC Adv 2022; 12:8059-8094. [PMID: 35424750 PMCID: PMC8982343 DOI: 10.1039/d1ra07988c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 01/08/2023] Open
Abstract
The foremost challenge in countering infectious diseases is the shortage of effective therapeutics. The emergence of coronavirus disease (COVID-19) outbreak has posed a great menace to the public health system globally, prompting unprecedented endeavors to contain the virus. Many countries have organized research programs for therapeutics and management development. However, the longstanding process has forced authorities to implement widespread infrastructures for detailed prognostic and diagnostics study of severe acute respiratory syndrome (SARS CoV-2). This review discussed nearly all the globally developed diagnostic methodologies reported for SARS CoV-2 detection. We have highlighted in detail the approaches for evaluating COVID-19 biomarkers along with the most employed nucleic acid- and protein-based detection methodologies and the causes of their severe downfall and rejection. As the variable variants of SARS CoV-2 came into the picture, we captured the breadth of newly integrated digital sensing prototypes comprised of plasmonic and field-effect transistor-based sensors along with commercially available food and drug administration (FDA) approved detection kits. However, more efforts are required to exploit the available resources to manufacture cheap and robust diagnostic methodologies. Likewise, the visualization and characterization tools along with the current challenges associated with waste-water surveillance, food security, contact tracing, and their role during this intense period of the pandemic have also been discussed. We expect that the integrated data will be supportive and aid in the evaluation of sensing technologies not only in current but also future pandemics.
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Affiliation(s)
- Umay Amara
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Sidra Rashid
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Khalid Mahmood
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
| | - Mian Hasnain Nawaz
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Akhtar Hayat
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Maria Hassan
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
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Nashed NT, Aniana A, Ghirlando R, Chiliveri SC, Louis JM. Modulation of the monomer-dimer equilibrium and catalytic activity of SARS-CoV-2 main protease by a transition-state analog inhibitor. Commun Biol 2022; 5:160. [PMID: 35233052 PMCID: PMC8888643 DOI: 10.1038/s42003-022-03084-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/28/2022] [Indexed: 12/17/2022] Open
Abstract
The role of dimer formation for the onset of catalytic activity of SARS-CoV-2 main protease (MProWT) was assessed using a predominantly monomeric mutant (MProM). Rates of MProWT and MProM catalyzed hydrolyses display substrate saturation kinetics and second-order dependency on the protein concentration. The addition of the prodrug GC376, an inhibitor of MProWT, to MProM leads to an increase in the dimer population and catalytic activity with increasing inhibitor concentration. The activity reaches a maximum corresponding to a dimer population in which one active site is occupied by the inhibitor and the other is available for catalytic activity. This phase is followed by a decrease in catalytic activity due to the inhibitor competing with the substrate. Detailed kinetics and equilibrium analyses are presented and a modified Michaelis-Menten equation accounts for the results. These observations provide conclusive evidence that dimer formation is coupled to catalytic activity represented by two equivalent active sites.
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Affiliation(s)
- Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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Laghdaf SM, El Baraa A, Mohamed Beydjeu A. Characterization of a cluster of COVID-19 cases linked to the Omicron variant, in Mauritania. LA TUNISIE MEDICALE 2022; 100:217-221. [PMID: 36005913 PMCID: PMC9387648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To describe the epidemiological and genomic profile of COVID-19 during the 4th epidemic wave in Mauritania. METHODS This is a cross-sectional study in Mauritania, from October 1, 2021, to February 28, 2022. Were included all people in the process of travel, performing an RT-PCR, at the level of the National Research Institute in Public Health and patients who have been sampled for sequencing by teams from the Department of Strategic Information and Epidemiological Surveillance. RESULTS Out of 37,574 RT-PCR tests collected on March 3, 2022, during the study period, 1,465 cases were diagnosed positive for COVID-19 (3.9%), with an average age of 39±14,6 years and a sex ratio of 2.08. Of the 112 genomic sequences performed, 75 were of the Omicron variant (66.9%). The average age was 40±15 years, with extremes of 15 to 82 years and a sex ratio of 0.97. The vaccination status was assured in 67.7% of patients and the peak of the Omicron variant was reached during the first week of January 2022. CONCLUSION The Omicron variant was predominant during the 4th wave in Mauritania. As part of its response plan against COVID-19, the installation of new sequencing units inside the country and the strengthening of the training of technicians in the virology laboratory will be essential.
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Affiliation(s)
- Sidi Mohamed Laghdaf
- 1. Professeur assistant de Santé Publique, à la Faculté de Médecine de Nouakchott. Directeur de l’Institut National de Recherche en Santé Publique (INRSP) en Mauritanie
| | - Ahmed El Baraa
- 2. Professeur assistant de Parasitologie à la Faculté de Médecine de Nouakchott (Mauritanie)
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75
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Zhang M, Gong Y, Jiao S. Neutralization heterogeneity of circulating SARS-CoV-2 variants to sera elicited by a vaccinee or convalescent. Future Virol 2022; 17:10.2217/fvl-2021-0100. [PMID: 35492429 PMCID: PMC9041375 DOI: 10.2217/fvl-2021-0100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
Abstract
COVID-19, which was first reported in December 2019 in China, has caused a global outbreak. Five variants of concern (VOCs) have been identified in different countries since the global pandemic, namely, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.529). Although multiple vaccines have been found to be effective, some of the amino acid changes may increase the infectivity of virus and decrease the sensitivity to antibodies. Here we characterize the VOCs and discuss their sensitivity to antibodies elicited by convalescent and vaccinee sera. In conclusion, several variants display a reduction in the susceptibility to neutralization antibodies generated by natural infection or vaccination, which threatens the containment of the epidemic.
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Affiliation(s)
- Meng Zhang
- Department of Research & Development, Beijing DCTY Biotech Co., Ltd, 86 Shuangying West Road, Beijing, 102200, People's Republic of China
| | - Yixin Gong
- Department of Research & Development, Beijing DCTY Biotech Co., Ltd, 86 Shuangying West Road, Beijing, 102200, People's Republic of China
| | - Shunchang Jiao
- Department of Oncology, Chinese PLA General Hospital, 28 Fuxing Road, Haidian, Beijing, 100853, People's Republic of China
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76
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Wu X, Chen Q, Li J, Liu Z. Diagnostic techniques for COVID-19: A mini-review. J Virol Methods 2022; 301:114437. [PMID: 34933045 PMCID: PMC8684097 DOI: 10.1016/j.jviromet.2021.114437] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023]
Abstract
COVID-19, a new respiratory infectious disease, was first reported at the end of 2019, in Wuhan, China. Now, COVID-19 is still causing major loss of human life and economic productivity in almost all countries around the world. Early detection, early isolation, and early diagnosis of COVID-19 patients and asymptomatic carriers are essential to blocking the spread of the pandemic. This paper briefly reviewed COVID-19 diagnostic assays for clinical application, including nucleic acid tests, immunological methods, and Computed Tomography (CT) imaging. Nucleic acid tests (NAT) target the virus genome and indicates the existence of the SARS-CoV-2 virus. Currently, real-time quantitative PCR (qPCR) is the most widely used NAT and, basically, is the most used diagnostic assay for COVID-19. Besides qPCR, many novel rapid and sensitive NAT assays were also developed. Serological testing (detection of serum antibodies specific to SARS-CoV-2), which belongs to the immunological methods, is also used in the diagnosis of COVID-19. The positive results of serological testing indicate the presence of antibodies specific to SARS-CoV-2 resulting from being infected with the virus. Viral antigen detection assays are also important immunological methods used mainly for rapid virus detection. However, only a few of these assays had been reported. CT imaging is still an important auxiliary diagnosis tool for COVID-19 patients, especially for symptomatic patients in the early stage, whose viral load is low and different to be identified by NAT. These diagnostic techniques are all good in some way and applying a combination of them will greatly improve the accuracy of COVID-19 diagnostics.
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Affiliation(s)
- Xianyong Wu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Qiming Chen
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Junhai Li
- Department of Oncology, No. 215 Hospital of Shaanxi Nuclear Industry, Xianyang City, Shaanxi Province, 712000, China.
| | - Zhanmin Liu
- School of Life Sciences, Shanghai University, Shanghai, 200444, China.
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Zhao LP, Lybrand T, Gilbert P, Payne TH, Pyo CW, Geraghty D, Jerome K. Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. RESEARCH SQUARE 2022:rs.3.rs-1280819. [PMID: 35233566 PMCID: PMC8887078 DOI: 10.21203/rs.3.rs-1280819/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Extensive mutations in the Omicron spike protein appear to accelerate the transmission of SARS-CoV-2, and rapid infections increase the odds that additional mutants will emerge. To build an investigative framework, we have applied an unsupervised machine learning approach to 4296 Omicron viral genomes collected and deposited to GISAID as of December 14, 2021, and have identified a core haplotype of 28 polymutants (A67V, T95I, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, K796Y, N856K, Q954H, N69K, L981F) in the spike protein and a separate core haplotype of 17 polymutants in non-spike genes: (K38, A1892) in nsp3, T492 in nsp4, (P132, V247, T280, S284) in 3C-like proteinase, I189 in nsp6, P323 in RNA-dependent RNA polymerase, I42 in Exonuclease, T9 in envelope protein, (D3, Q19, A63) in membrane glycoprotein, and (P13, R203, G204) in nucleocapsid phosphoprotein. Using these core haplotypes as reference, we have identified four newly emerging polymutants (R346, A701, I1081, N1192) in the spike protein (p-value=9.37*10 -4 , 1.0*10 -15 , 4.76*10 -7 and 1.56*10 -4 , respectively), and five additional polymutants in non-spike genes (D343G in nucleocapsid phosphoprotein, V1069I in nsp3, V94A in nsp4, F694Y in the RNA-dependent RNA polymerase and L106L/F of ORF3a) that exhibit significant increasing trajectories (all p-values < 1.0*10 -15 ). In the absence of relevant clinical data for these newly emerging mutations, it is important to monitor them closely. Two emerging mutations may be of particular concern: the N1192S mutation in spike protein locates in an extremely highly conserved region of all human coronaviruses that is integral to the viral fusion process, and the F694Y mutation in the RNA polymerase may induce conformational changes that could impact Remdesivir binding.
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Hemlali M, Chouati T, Ghammaz H, Melloul M, Alaoui Amine S, Rhoulam S, Touil N, Ennibi K, Oumzil H, Mohamed R, Hassan A, El Fahime E. Coding-Complete Genome Sequences of a Delta Subvariant (AY.33) of SARS-CoV-2 Obtained from Moroccan COVID-19 Patients. Microbiol Resour Announc 2022; 11:e0109921. [PMID: 35112895 PMCID: PMC8812311 DOI: 10.1128/mra.01099-21] [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: 11/20/2021] [Accepted: 01/06/2022] [Indexed: 11/20/2022] Open
Abstract
We report here the complete genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains obtained from Moroccan patients with COVID-19. The analysis of these sequences indicates that the identified strains belong to the AY.33 sublineage of the Delta variant.
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Affiliation(s)
- Mouhssine Hemlali
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Neuroscience and Neurogenetics Research Team, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Taha Chouati
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Neuroscience and Neurogenetics Research Team, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Hamza Ghammaz
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity, and Environment, Faculty of Sciences, Mohammed V University of Rabat, Rabat, Morocco
| | - Marouane Melloul
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity, and Environment, Faculty of Sciences, Mohammed V University of Rabat, Rabat, Morocco
| | - Sanaâ Alaoui Amine
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Neuroscience and Neurogenetics Research Team, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Safaa Rhoulam
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Nadia Touil
- Cell Culture Unit, Center of Virology, Infectious, and Tropical Diseases, Med V Military Hospital, Rabat, Morocco
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Khalid Ennibi
- Virology and Infectious Tropical Diseases Center, Med V Military Hospital, Rabat, Morocco
| | - Hicham Oumzil
- National Influenza Center, Virology Department, Institut National d’Hygiène, Rabat, Morocco
| | | | - Aguenaou Hassan
- Ibn Tofaïl University-CNESTEN, Joint Research Unit in Nutrition and Food, RDC-Nutrition AFRA/IAEA, Rabat-Kénitra, Morocco
| | - Elmostafa El Fahime
- Molecular Biology and Functional Genomics Platform, National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
- Neuroscience and Neurogenetics Research Team, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
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Mallick R, Duttaroy AK. Origin and Structural Biology of Novel Coronavirus (SARS-CoV-2). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1352:1-13. [PMID: 35132591 DOI: 10.1007/978-3-030-85109-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION A recent rapid outbreak of infection around the globe has been caused by a novel coronavirus, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first identified in December 2019 in Wuhan city of Hubei province, People's Republic of China. METHODS We reviewed the currently available literature on coronaviruses. RESULTS Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. Although 13 variation sites in open reading frames have been identified among SARS-CoV-2 strains, no mutation has been observed so far in envelop protein. The origin and structural biology of SARS-CoV-2 in details are discussed. CONCLUSIONS Origin and structural biology will help the researchers identify the virus's mechanism in the host and drug design. Currently, no clinical treatments or prevention strategies are available for any human coronavirus.
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Affiliation(s)
- Rahul Mallick
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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80
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Bagri A, Assis RR, Tsai C, Simmons G, Mei ZW, Von Goetz M, Gatmaitan M, Stone M, Di Germanio C, Martinelli R, Darst O, Rioveros J, Robinson PV, Ward D, Ziman A, Seftel D, Khan S, Busch MP, Felgner PL, Corash LM. Antibody profiles in
COVID
‐19 convalescent plasma prepared with Amotosalen/
UVA
pathogen reduction treatment. Transfusion 2022; 62:570-583. [PMID: 35128658 PMCID: PMC9115453 DOI: 10.1111/trf.16819] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 01/08/2023]
Abstract
Background COVID‐19 convalescent plasma (CCP), from donors recovered from severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection, is one of the limited therapeutic options currently available for the treatment of critically ill patients with COVID‐19. There is growing evidence that CCP may reduce viral loads and disease severity; and reduce mortality. However, concerns about the risk of transfusion‐transmitted infections (TTI) and other complications associated with transfusion of plasma, remain. Amotosalen/UVA pathogen reduction treatment (A/UVA‐PRT) of plasma offers a mitigation of TTI risk, and when combined with pooling has the potential to increase the diversity of the polyclonal SARS‐CoV‐2 neutralizing antibodies. Study design and methods This study assessed the impact of A/UVA‐PRT on SARS‐CoV‐2 antibodies in 42 CCP using multiple complimentary assays including antigen binding, neutralizing, and epitope microarrays. Other mediators of CCP efficacy were also assessed. Results A/UVA‐PRT did not negatively impact antibodies to SARS‐CoV‐2 and other viral epitopes, had no impact on neutralizing activity or other potential mediators of CCP efficacy. Finally, immune cross‐reactivity with other coronavirus antigens was observed raising the potential for neutralizing activity against other emergent coronaviruses. Conclusion The findings of this study support the selection of effective CCP combined with the use of A/UVA‐PRT in the production of CCP for patients with COVID‐19.
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Affiliation(s)
- Anil Bagri
- Cerus Corporation Concord California United States
| | - Rafael R. Assis
- Department of Physiology and Biophysics School of Medicine, University of California Irvine Irvine California United States
| | - Cheng‐ting Tsai
- ENable Biosciences Inc South San Francisco California United States
| | - Graham Simmons
- Vitalant Research Institute San Francisco California United States
| | - Zhen W. Mei
- Wing‐Kwai and Alice Lee‐Tsing Chung Transfusion Service, Department of Pathology and Laboratory Medicine David Geffen School of Medicine at University of California Los Angeles California USA
| | | | | | - Mars Stone
- Vitalant Research Institute San Francisco California United States
| | | | | | - Orsolya Darst
- Vitalant Research Institute San Francisco California United States
| | - Jowin Rioveros
- Wing‐Kwai and Alice Lee‐Tsing Chung Transfusion Service, Department of Pathology and Laboratory Medicine David Geffen School of Medicine at University of California Los Angeles California USA
| | | | - Dawn Ward
- Wing‐Kwai and Alice Lee‐Tsing Chung Transfusion Service, Department of Pathology and Laboratory Medicine David Geffen School of Medicine at University of California Los Angeles California USA
| | - Alyssa Ziman
- Wing‐Kwai and Alice Lee‐Tsing Chung Transfusion Service, Department of Pathology and Laboratory Medicine David Geffen School of Medicine at University of California Los Angeles California USA
| | - David Seftel
- ENable Biosciences Inc South San Francisco California United States
| | - Saahir Khan
- Division of Infectious Diseases, Department of Medicine University of California Irvine Health Orange California United States
| | - Michael P. Busch
- Vitalant Research Institute San Francisco California United States
| | - Philip L. Felgner
- Department of Physiology and Biophysics School of Medicine, University of California Irvine Irvine California United States
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81
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Malik JA, Ahmed S, Mir A, Shinde M, Bender O, Alshammari F, Ansari M, Anwar S. The SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges. J Infect Public Health 2022; 15:228-240. [PMID: 35042059 PMCID: PMC8730674 DOI: 10.1016/j.jiph.2021.12.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/13/2021] [Accepted: 12/25/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The SARS-CoV-2 coronavirus epidemic is hastening the discovery of the most efficient vaccines. The development of cost-effective vaccines seems to be the only solution to terminate this pandemic. However, the vaccines' effectiveness has been questioned due to recurrent mutations in the SARS-CoV-2 genome. Most of the mutations are associated with the spike protein, a vital target for several marketed vaccines. Many countries were highly affected by the 2nd wave of the SARS-CoV-2, like the UK, India, Brazil and France. Experts are also alarming the further COVID-19 wave with the emergence of Omicron, which is highly affecting the South African populations. This review encompasses the detailed description of all vaccine candidates and COVID-19 mutants that will add value to design further studies to combat the COVID-19 pandemic. METHODS The information was generated using various search engines like google scholar, PubMed, clinicaltrial.gov.in, WHO database, ScienceDirect, and news portals by using keywords SARS-CoV-2 mutants, COVID-19 vaccines, efficacy of SARS-CoV-2 vaccines, COVID-19 waves. RESULTS This review has highlighted the evolution of SARS-CoV-2 variants and the vaccine efficacy. Currently, various vaccine candidates are undergoing several phases of development. Their efficacy still needs to check for newly emerged variants. We have focused on the evolution, multiple mutants, waves of the SARS-CoV-2, and different marketed vaccines undergoing various clinical trials and the design of the trials to determine vaccine efficacy. CONCLUSION Various mutants of SARS-CoV-2 arrived, mainly concerned with the spike protein, a key component to design the vaccine candidates. Various vaccines are undergoing clinical trial and show impressive results, but their efficacy still needs to be checked in different SARS-CoV-2 mutants. We discussed all mutants of SARS-CoV-2 and the vaccine's efficacy against them. The safety concern of these vaccines is also discussed. It is important to understand how coronavirus gets mutated to design better new vaccines, providing long-term protection and neutralizing broad mutant variants. A proper study approach also needs to be considered while designing the vaccine efficacy trials, which further improved the study outcomes. Taking preventive measures to protect from the virus is also equally important, like vaccine development.
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Affiliation(s)
- Jonaid Ahmad Malik
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Guwahati, India; Department of Biomedical Engineering, Indian Institute of Technology (IIT), Ropar 140001, India
| | - Sakeel Ahmed
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Ahmedabad, India
| | - Aroosa Mir
- Department of Pharmacology, Jamia Hamdard, New Delhi, India
| | - Mrunal Shinde
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research, Guwahati, India
| | - Onur Bender
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Mukhtar Ansari
- Department of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Sirajudheen Anwar
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Hail, Hail, Saudi Arabia.
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Ahmed-Abakur EH, Ullah MF, Elssaig EH, Alnour TM. In-Silico genomic landscape characterization and evolution of SARS- CoV- 2 variants isolated in India shows significant drift with high frequency of mutations. Saudi J Biol Sci 2022; 29:3494-3501. [PMID: 35233173 PMCID: PMC8875766 DOI: 10.1016/j.sjbs.2022.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/27/2022] [Accepted: 02/20/2022] [Indexed: 01/09/2023] Open
Abstract
In-silico studies on SARS-CoV-2 genome are considered important to identify the significant pattern of variations and its possible effects on the structural and functional characteristics of the virus. The current study determined such genetic variations and their possible impact among SARS-CoV-2 variants isolated in India. A total of 546 SARS-CoV-2 genomic sequences (India) were retrieved from the gene bank (NCBI) and subjected to alignment against the Wuhan variant (NC_045512.2), the corresponding amino acid changes were analyzed using NCBI Protein-BLAST. These 546 variants revealed 841 mutations; most of these were non-synonymous 464/841 (55.1%), there was no identical variant compared to the original strain. All genes; coding and non-coding showed nucleotide changes, most of the structural genes showed frequent nonsynonymous mutations. The most affected genes were ORF1a/b followed by the S gene which showed 515/841 (61.2%) and 120/841 (14.3%) mutations, respectively. The most frequent non-synonymous mutation 486/546 (89.01%) occurred in the S gene (structural gene) at position 23,403 where A changed to G leading to the replacement of aspartic acid by glycine in position (D614G). Interestingly, four variants also showed deletion. The variants MT800923 and MT800925 showed 12 consecutive nucleotide deletion in position 21982–21993 resulting in 4 consecutive amino acid deletions that were leucine, glycine, valine, and tyrosine in positions 141, 142, 143, and 144 respectively. The present study exhibited a higher mutations rate per variant compared to other studies carried out in India.
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Affiliation(s)
- Eltayib H. Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
- Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
- Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Elmutuz H. Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
- Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Tarig M.S. Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
- Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
- Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum North 11111, Sudan
- Corresponding author at: Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.
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83
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Barros FR, Leite DC, Guimarães LJ, Lopes JM, Vasconcelos MW, Ferreira LX, Gonçalves S, Pastre VG, Pereira G, Trentin AB, Gabiatti NC, Kuhn BC, Perseguini JM, Wendt SN, Ghisi NC. Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene Allplex TM 2019-nCoV protocol. J Virol Methods 2022; 300:114429. [PMID: 34919975 PMCID: PMC8668600 DOI: 10.1016/j.jviromet.2021.114429] [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: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen's Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.
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Affiliation(s)
- Flavia R.O. Barros
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | - Deborah C.A. Leite
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nédia C. Ghisi
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
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Lucas B, Vahedi B, Karimzadeh M. A spatiotemporal machine learning approach to forecasting COVID-19 incidence at the county level in the USA. INTERNATIONAL JOURNAL OF DATA SCIENCE AND ANALYTICS 2022; 15:247-266. [PMID: 35071733 PMCID: PMC8760128 DOI: 10.1007/s41060-021-00295-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/19/2021] [Indexed: 01/06/2023]
Abstract
With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper, we approach the forecasting task with an alternative technique-spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a long short-term memory deep learning architecture for forecasting COVID-19 incidence at the county level in the USA. We use the weekly number of new positive cases as temporal input, and hand-engineered spatial features from Facebook movement and connectedness datasets to capture the spread of the disease in time and space. COVID-LSTM outperforms the COVID-19 Forecast Hub's Ensemble model (COVIDhub-ensemble) on our 17-week evaluation period, making it the first model to be more accurate than the COVIDhub-ensemble over one or more forecast periods. Over the 4-week forecast horizon, our model is on average 50 cases per county more accurate than the COVIDhub-ensemble. We highlight that the underutilization of data-driven forecasting of disease spread prior to COVID-19 is likely due to the lack of sufficient data available for previous diseases, in addition to the recent advances in machine learning methods for spatiotemporal forecasting. We discuss the impediments to the wider uptake of data-driven forecasting, and whether it is likely that more deep learning-based models will be used in the future.
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Affiliation(s)
- Benjamin Lucas
- Department of Geography, University of Colorado Boulder, Boulder, CO USA
| | - Behzad Vahedi
- Department of Geography, University of Colorado Boulder, Boulder, CO USA
| | - Morteza Karimzadeh
- Department of Geography, University of Colorado Boulder, Boulder, CO USA
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85
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Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. Curr Microbiol 2022; 79:48. [PMID: 34982246 PMCID: PMC8750362 DOI: 10.1007/s00284-021-02743-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022]
Abstract
This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains.
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86
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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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87
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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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88
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Aimrane A, Laaradia MA, Sereno D, Perrin P, Draoui A, Bougadir B, Hadach M, Zahir M, Fdil N, El Hiba O, El Hidan MA, Kahime K. Insight into COVID-19's epidemiology, pathology, and treatment. Heliyon 2022; 8:e08799. [PMID: 35071819 PMCID: PMC8767941 DOI: 10.1016/j.heliyon.2022.e08799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/08/2021] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
The newly emerged 2019 coronavirus disease (COVID-19) has urged scientific and medical communities to focus on epidemiology, pathophysiology, and treatment of SARS-CoV-2. Indeed, little is known about the virus causing this severe acute respiratory syndrome pandemic, coronavirus (SARS-CoV-2). Data already collected on viruses belonging to the coronaviridae family are of interest to improve our knowledge rapidly on this pandemic. The current review aims at delivering insight into the fundamental advances inSARS-CoV-2 epidemiology, pathophysiology, life cycle, and treatment.
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Affiliation(s)
- Abdelmohcine Aimrane
- Metabolics Platform, Biochemistry Laboratory, Faculty of Medicine, Cadi Ayad University, Marrakech, Morocco
- Nutritional Physiopathology Team, Faculty of Sciences, ChouaibDoukkali University, El Jadida, 24000, Morocco
| | - Mehdi Ait Laaradia
- Laboratory of Pharmacology, Neurobiology and Behavior, Semlalia Faculty of Sciences, Cadi Ayyad University, Marrakech, Morocco
| | - Denis Sereno
- IRD, University of Montpellier, InterTryp, Parasite Infectiology Research Group, 34000, Montpellier, France
| | - Pascale Perrin
- IRD, University of Montpellier, MiVeGec, Parasite Infectiology Research Group, 34000, Montpellier, France
| | - Ahmed Draoui
- Laboratory of Clinical and Experimental Neurosciences and Environment, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Morocco
| | - Blaid Bougadir
- SAEDD Laboratory, School of Technology Essaouira, Cadi Ayyad University of Marrakesh, Morocco
| | - Mohamed Hadach
- SAEDD Laboratory, School of Technology Essaouira, Cadi Ayyad University of Marrakesh, Morocco
| | - Mustapha Zahir
- SAEDD Laboratory, School of Technology Essaouira, Cadi Ayyad University of Marrakesh, Morocco
| | - Naima Fdil
- Metabolics Platform, Biochemistry Laboratory, Faculty of Medicine, Cadi Ayad University, Marrakech, Morocco
| | - Omar El Hiba
- Nutritional Physiopathology Team, Faculty of Sciences, ChouaibDoukkali University, El Jadida, 24000, Morocco
| | | | - Kholoud Kahime
- SAEDD Laboratory, School of Technology Essaouira, Cadi Ayyad University of Marrakesh, Morocco
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SARS-CoV-2 ORF10 suppresses the antiviral innate immune response by degrading MAVS through mitophagy. Cell Mol Immunol 2022; 19:67-78. [PMID: 34845370 PMCID: PMC8628139 DOI: 10.1038/s41423-021-00807-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/04/2021] [Indexed: 12/29/2022] Open
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused severe morbidity and mortality in humans. It is urgent to understand the function of viral genes. However, the function of open reading frame 10 (ORF10), which is uniquely expressed by SARS-CoV-2, remains unclear. In this study, we showed that overexpression of ORF10 markedly suppressed the expression of type I interferon (IFN-I) genes and IFN-stimulated genes. Then, mitochondrial antiviral signaling protein (MAVS) was identified as the target via which ORF10 suppresses the IFN-I signaling pathway, and MAVS was found to be degraded through the ORF10-induced autophagy pathway. Furthermore, overexpression of ORF10 promoted the accumulation of LC3 in mitochondria and induced mitophagy. Mechanistically, ORF10 was translocated to mitochondria by interacting with the mitophagy receptor Nip3-like protein X (NIX) and induced mitophagy through its interaction with both NIX and LC3B. Moreover, knockdown of NIX expression blocked mitophagy activation, MAVS degradation, and IFN-I signaling pathway inhibition by ORF10. Consistent with our observations, in the context of SARS-CoV-2 infection, ORF10 inhibited MAVS expression and facilitated viral replication. In brief, our results reveal a novel mechanism by which SARS-CoV-2 inhibits the innate immune response; that is, ORF10 induces mitophagy-mediated MAVS degradation by binding to NIX.
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Sequence analysis for SNP detection and phylogenetic reconstruction of SARS-cov-2 isolated from Nigerian COVID-19 cases. New Microbes New Infect 2022; 45:100955. [PMID: 35070322 PMCID: PMC8763411 DOI: 10.1016/j.nmni.2022.100955] [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
Background Coronaviruses are a group of viruses that belong to the Family Coronaviridae, genus Betacoronavirus. In December 2019, a new coronavirus disease (COVID-19) characterized by severe respiratory symptoms was discovered. The causative pathogen was a novel coronavirus known as 2019-nCoV and later as SARS-CoV-2. Within two months of its discovery, COVID-19 became a pandemic causing widespread morbidity and mortality. Methodology Whole genome sequence data of SARS-CoV-2 isolated from Nigerian COVID-19 cases were retrieved by downloading from GISAID database. A total of 18 sequences that satisfied quality assurance (length ≥29,700 nts and number of unknown bases denoted as “N” ≤ 5%) were used for the study. In addition, genome sequence of SARS-CoV-2 obtained from Nigeria's COVID-19 index case (Accession ID: EPI_ISL_413550) and the reference genome (Accession NC_ 045512.2) were obtained from GISAID and the GenBank databases, respectively. Multiple sequence alignment (MSA) was done in MAFFT (Version 7.471) while SNP calling was implemented in DnaSP (Version 6.12.03), respectively and then visualized in Jalview (Version 2.11.1.0). Phylogenetic analysis was with MEGA X software. Results Nigerian SARS-CoV-2 had 99.9% genomic similarity with four large conserved genomic regions. A total of 66 SNPs were identified out of which 31 were informative. Nucleotide diversity assessment gave Pi = 0.00048 and average SNP frequency of 2.22 SNPs per 1000 nts. Non-coding genomic regions particularly 5′UTR and 3′UTR had a SNP density of 3.77 and 35.4, respectively. The region with the highest SNP density was ORF10 with a frequency of 8.55 SNPs/1000 nts). This value was significantly higher (P < 0.01) than that of the spike gene, the region of greatest interest in SARS-CoV-2 genomics. Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. Nigeria SARS-CoV-2 revealed 3 major clades namely Oyo, Ekiti and Osun on a maximum likelihood phylogenetic tree. Conclusion and Recommendation There was a preponderance of L lineage (to include the new lineage scheme) and D614G mutants. Nigerian SARS-CoV-2 genome revealed ORF1ab as the region containing the highest SNP density as compared to the spike gene. The implication of this distribution of SNPs for the empirical lower infectivity of SARS-CoV-2 in Nigeria is discussed. This also underscores the need for more aggressive testing and treatment of COVID-19 in Nigeria. Additionally, attempt to produce testing kits for COVID-19 in Nigeria should consider the conserved regions identified in this study. Strict adherence to COVID-19 preventive measure is recommended in view of Nigerian SARS-CoV-2 phylogenetic clustering pattern, which suggests intensive community transmission possibly rooted in communal culture characteristic of many ethnicities in Nigeria.
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91
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Zhao LP, Lybrand TP, Gilbert PB, Hawn TR, Schiffer JT, Stamatatos L, Payne TH, Carpp LN, Geraghty DE, Jerome KR. Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. Viruses 2021; 14:9. [PMID: 35062214 PMCID: PMC8777887 DOI: 10.3390/v14010009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022] Open
Abstract
The emergence and establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest (VOIs) and variants of concern (VOCs) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We analyzed 167,893 Spike protein sequences from coronavirus disease 2019 (COVID-19) cases in the United States (excluding 21,391 sequences from VOI/VOC strains) deposited at GISAID from 19 January 2020 to 15 March 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution compared to the reference strain. Next, generalized additive models were applied to model VRV temporal dynamics and to identify VRVs with significant and substantial dynamics (false discovery rate q-value < 0.01; maximum VRV proportion >10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modeling was performed to gain insight into the potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which had not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identified 17 VRVs ~91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of four VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported a potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods.
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Affiliation(s)
- Lue Ping Zhao
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA 98109, USA
| | - Terry P. Lybrand
- Quintepa Computing LLC, Nashville, TN 37205, USA;
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Peter B. Gilbert
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
| | - Thomas R. Hawn
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; (T.R.H.); (T.H.P.)
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Joshua T. Schiffer
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; (T.R.H.); (T.H.P.)
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Thomas H. Payne
- Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA; (T.R.H.); (T.H.P.)
| | - Lindsay N. Carpp
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
| | - Daniel E. Geraghty
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA;
| | - Keith R. Jerome
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA; (P.B.G.); (J.T.S.); (L.S.); (L.N.C.); (K.R.J.)
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92
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Tarig M S Alnour, Ullah MF, Elssaig EH, Ahmed-Abakur EH. Unique SARS-CoV-2 Variant Exhibiting Plenteous Missense Mutations in Structural and Nonstructural Genes. CYTOL GENET+ 2021; 55:606-612. [PMID: 34924640 PMCID: PMC8672854 DOI: 10.3103/s0095452721060153] [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: 04/12/2021] [Revised: 04/28/2021] [Accepted: 09/08/2021] [Indexed: 12/03/2022]
Abstract
Determining the variations in SARS-CoV-2 variant is considered main factor for understanding the pathogenic mechanisms, aid in diagnosis, prevention and treatment. The present study aimed to determine the genetic variations of SARS-CoV-2. The sequences of SARS-CoV-2 were obtained from National Center for Biotechnology Information (NCBI) and studied according to the time of isolation and their origin. The genome sequence of SARS-CoV-2 accession number NC_045512 which represented the first isolated sequence of SARS-CoV-2 (Wuhan strain) was used as the reference sequence. The obtained genome sequences of SARS-CoV-2 were aligned against this Wuhan strain and variations among nucleotides and proteins were examined. The sequence of SARS-CoV-2 accession number MT577016 showed very low homology 98.75% compared to Wuhan strain NC_045512. The analysis identified 301 nucleotide changes, which correspond to 258 different mutations; most of them 80% (207/258) were missense point mutations followed by 17.1% (44/258) silent point mutations. The critical mutations occurred in viral structural genes; 16.7% (43/258) mutations reported in S gene and 1 missense mutation was observed in E gene. Our finding showed the lowest homology and relatively distant phylogenetic relation of this SARS-CoV-2 variant with Wuhan strain along with high frequency of mutations including those in spike S and envelope E genes.
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Affiliation(s)
- Tarig M S Alnour
- Faculty of Medical Laboratory Science, Department of Microbiology and Immunology Alzaiem Alazhari University, 11111 Khartoum North, Sudan.,Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia
| | - Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia
| | - Elmutuz H Elssaig
- Faculty of Medical Laboratory Science, Department of Microbiology and Immunology Alzaiem Alazhari University, 11111 Khartoum North, Sudan.,Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia
| | - Eltayib H Ahmed-Abakur
- Faculty of Medical Laboratory Science, Department of Microbiology and Immunology Alzaiem Alazhari University, 11111 Khartoum North, Sudan.,Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, 71411 Tabuk, Saudi Arabia
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93
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Ullah MF, Alnour TMS, Elssaig EH, Ahmed-Abakur EH. Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Saudi J Biol Sci 2021; 28:6803-6807. [PMID: 34866979 PMCID: PMC8626222 DOI: 10.1016/j.sjbs.2021.07.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/17/2021] [Accepted: 07/17/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico, cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.
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Affiliation(s)
- Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Tarig M S Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum North 11111, Sudan
| | - Elmutuz H Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Eltayib H Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum North 11111, Sudan
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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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95
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Dastar S, Gharesouran J, Mortazavi D, Hosseinzadeh H, Kian SJ, Taheri M, Ghafouri-Fard S, Jamali E, Rezazadeh M. COVID-19 pandemic: Insights into genetic susceptibility to SARS-CoV-2 and host genes implications on virus spread, disease severity and outcomes. Hum Antibodies 2021; 30:1-14. [PMID: 34864654 DOI: 10.3233/hab-211506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The outbreak of the newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) all over the world has caused global public health emergencies, international concern and economic crises. The systemic SARS-CoV-2 disease (COVID-19) can lead to death through causing unrestrained cytokines-storm and subsequent pulmonary shutdown among the elderly and patients with pre-existing comorbidities. Additionally, in comparison with poor nations without primary health care services, in developed countries with advanced healthcare system we can witness higher number of infections per one million people. In this review, we summarize the latest studies on genes associated with SARS-CoV-2 pathogenesis and propose possible mechanisms of the virus replication cycle and its triggered signaling pathways to encourage researchers to investigate genetic and immune profiles of the disease and try strategies for its treatment. Our review shows that immune response in people with different genetic background might vary as African and then Asian populations have lowest number of affected cases compared with European and American nations. Considering SARS-CoV-2 pathogenesis, we put forward some potentially important genetic gateways to COVID-19 infection including genes involved in the entry and replication of SARS-CoV-2 and the regulation of host immune response which might represent explanation for its spread, severity, and morality. Finally, we suggest that genetic alterations within these gateways could be critical factors in influencing geographical discrepancies of the virus, so it is essential to fully study them and design appropriated and reliable therapeutic agents against COVID-19.
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Affiliation(s)
- Saba Dastar
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Fatih, Istanbul, Turkey
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Deniz Mortazavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Jalal Kian
- Department of Virology, Iran University of Medical Sciences, School of Medicine, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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96
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Yu J, Sun S, Tang Q, Wang C, Yu L, Ren L, Li J, Zhang Z. Establishing reference sequences for each clade of SARS-CoV-2 to provide a basis for virus variation and function research. J Med Virol 2021; 94:1494-1501. [PMID: 34821382 PMCID: PMC9015442 DOI: 10.1002/jmv.27476] [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: 06/17/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022]
Abstract
Coronavirus disease 2019 (COVID‐19) is a severe respiratory disease caused by the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). As the COVID‐19 pandemic continues, mutations of SARS‐CoV‐2 accumulate. These mutations may not only make the virus spread faster, but also render current vaccines less effective. In this study, we established a reference sequence for each clade defined using the GISAID typing method. Homology analysis of each reference sequence confirmed a low mutation rate for SARS‐CoV‐2, with the latest clade GRY having the lowest homology with other clades (99.89%–99.93%), and the homology between other clade being greater than or equal to 99.95%. Variation analyses showed that the earliest genotypes S, V, and G had 2, 3, and 3 characterizing mutations in the genome respectively. The G‐derived clades GR, GH, and GV had 5, 6, and 13 characterizing mutations in the genome respectively. A total of 28 characterizing mutations existed in the genome of the latest clades GRY. In addition, we found differences in the geographic distribution of different clades. G, GH, and GR are popular in the USA, while GV and GRY are common in the UK. Our work may facilitate the custom design of antiviral strategies depending on the molecular characteristics of SARS‐CoV‐2. We established reference sequences for GISAID typing in order to provide suitable reference standards for studies on the molecular biology and virology of SARS‐CoV‐2. Based on established reference sequences, we identified characterizing mutations and high‐frequency mutations in each clade.
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Affiliation(s)
- Jian Yu
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.,Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, The School of Pharmacy, Anhui Medical University, Hefei, China
| | - Shanshan Sun
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.,Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Qianqian Tang
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.,Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Chengzhuo Wang
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.,Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China
| | - Liangchen Yu
- The Second Clinical Medical School, Anhui Medical University, Hefei, China
| | - Lulu Ren
- The Second Clinical Medical School, Anhui Medical University, Hefei, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, The School of Pharmacy, Anhui Medical University, Hefei, China
| | - Zhenhua Zhang
- Department of Infectious Diseases, The Second Hospital of Anhui Medical University, Hefei, China.,Institute of Clinical Virology, The Second Hospital of Anhui Medical University, Hefei, China
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97
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Ghosh M, Basak S, Dutta S. Underlying selection for the diversity of spike protein sequences of SARS-CoV-2. IUBMB Life 2021; 74:213-220. [PMID: 34780121 PMCID: PMC8652778 DOI: 10.1002/iub.2577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023]
Abstract
The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present article, we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.
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Affiliation(s)
- Manisha Ghosh
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Surajit Basak
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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98
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Dong H, Wang S, Zhang J, Zhang K, Zhang F, Wang H, Xie S, Hu W, Gu L. Structure-Based Primer Design Minimizes the Risk of PCR Failure Caused by SARS-CoV-2 Mutations. Front Cell Infect Microbiol 2021; 11:741147. [PMID: 34760717 PMCID: PMC8573093 DOI: 10.3389/fcimb.2021.741147] [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: 07/14/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused and is still causing tremendous damage to the global economy and human health. Qualitative reverse transcription-PCR (RT-qPCR) is the golden standard for COVID-19 test. However, the SARS-CoV-2 variants may not only make vaccine less effective but also evade RT-qPCR test. Here we suggest an innovative primer design strategy for the RT-qPCR test of SARS-CoV-2. The principle is that the primers should be designed based on both the nucleic acid sequence and the structure of the protein encoded. The three nucleotides closest to the 3′ end of the primer should be the codon which encodes the tryptophan in the structure core. Based on this principle, we designed a pair of primers targeting the nucleocapsid (N) gene. Since tryptophan is encoded by only one codon, any mutation that occurs at this position would change the amino acid residue, resulting in an unstable N protein. This means that this kind of SARS-CoV-2 variant could not survive. In addition, both our data and previous reports all indicate that the mutations occurring at other places in the primers do not significantly affect the RT-qPCR result. Consequently, no SARS-CoV-2 variant can escape detection by the RT-qPCR kit containing the primers designed based on our strategy.
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Affiliation(s)
- Hongjie Dong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shuai Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Junmei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,Research and Development Department, Shandong Shtars Medical Technology Co., Ltd, Jinan, China
| | - Kundi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hongwei Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shiling Xie
- Research and Development Department, Shandong Shtars Medical Technology Co., Ltd, Jinan, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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99
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Pal A, Dobhal S, Dey KK, Sharma AK, Savani V, Negi VS. Polymorphic landscape of SARS-CoV-2 genomes isolated from Indian population in 2020 demonstrates rapid evolution in ORF3a, ORF8, nucleocapsid phosphoprotein and spike glycoprotein. Comput Biol Chem 2021; 95:107594. [PMID: 34736125 PMCID: PMC8547785 DOI: 10.1016/j.compbiolchem.2021.107594] [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: 08/04/2021] [Revised: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 11/18/2022]
Abstract
India, with around 15 million COVID-19 cases, recently became the second worst-hit nation by the SARS-CoV-2 pandemic. In this study, we analyzed the mutation and selection landscape of 516 unique and complete genomes of SARS-CoV-2 isolates from India in a 12-month span (from Jan to Dec 2020) to understand how the virus is evolving in this geographical region. We identified 953 genome-wide loci displaying single nucleotide polymorphism (SNP) and the Principal Component Analysis and mutation plots of the datasets indicate an increase in genetic variance with time. The 42% of the polymorphic sites display substitutions in the third nucleotide position of codons indicating that non-synonymous substitutions are more prevalent. These isolates displayed strong evidence of purifying selection in ORF1ab, spike, nucleocapsid, and membrane glycoprotein. We also find some evidence of localized positive selections ORF1ab, spike glycoprotein, and nucleocapsid. The CDSs for ORF3a, ORF8, nucleocapsid phosphoprotein, and spike glycoprotein were found to evolve at rapid rate. This study will be helpful in understanding the dynamics of rapidly evolving SARS-CoV-2.
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Affiliation(s)
- Archana Pal
- School of Sciences, P P Savani University, Surat, Gujarat 394125, India
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Kishore Kumar Dey
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL 32608, USA
| | | | - Vivek Savani
- School of Sciences, P P Savani University, Surat, Gujarat 394125, India
| | - Vishal Singh Negi
- School of Sciences, P P Savani University, Surat, Gujarat 394125, India.
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100
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Zekri ARN, Bahnasy AA, Hafez MM, Hassan ZK, Ahmed OS, Soliman HK, El-Sisi ER, Dine MHSE, Solimane MS, Latife LSA, Seadawy MG, Elsafty AS, Abouelhoda M. Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection. Sci Rep 2021; 11:21632. [PMID: 34732835 PMCID: PMC8566477 DOI: 10.1038/s41598-021-99014-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/05/2021] [Indexed: 12/26/2022] Open
Abstract
At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021.
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Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt.
| | - Abeer A Bahnasy
- Surgical Pathology Department, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Mohamed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Enas R El-Sisi
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, 11796, Egypt
| | - Mona H Salah El Dine
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - May S Solimane
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Lamyaa S Abdel Latife
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, 12613, Egypt
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