1
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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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2
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Terrazos Miani MA, Borcard L, Gempeler S, Baumann C, Bittel P, Leib SL, Neuenschwander S, Ramette A. NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples. Pathogens 2024; 13:61. [PMID: 38251368 PMCID: PMC10818518 DOI: 10.3390/pathogens13010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/23/2024] Open
Abstract
Whole-genome sequencing (WGS) represents the main technology for SARS-CoV-2 lineage characterization in diagnostic laboratories worldwide. The rapid, near-full-length sequencing of the viral genome is commonly enabled by high-throughput sequencing of PCR amplicons derived from cDNA molecules. Here, we present a new approach called NASCarD (Nanopore Adaptive Sampling with Carrier DNA), which allows a low amount of nucleic acids to be sequenced while selectively enriching for sequences of interest, hence limiting the production of non-target sequences. Using COVID-19 positive samples available during the omicron wave, we demonstrate how the method may lead to >99% genome completeness of the SARS-CoV-2 genome sequences within 7 h of sequencing at a competitive cost. The new approach may have applications beyond SARS-CoV-2 sequencing for other DNA or RNA pathogens in clinical samples.
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Affiliation(s)
| | | | | | | | | | | | | | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 25, 3001 Bern, Switzerland
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3
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Salazar-Ardiles C, Asserella-Rebollo L, Cornejo C, Arias D, Vasquez-Muñoz M, Toledo C, Andrade DC. Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences. Mol Biol Rep 2023; 50:10367-10382. [PMID: 37817022 DOI: 10.1007/s11033-023-08844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.
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Affiliation(s)
- Camila Salazar-Ardiles
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | | | - Carlos Cornejo
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Dayana Arias
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile
| | - Manuel Vasquez-Muñoz
- Dirección de Docencia de Especialidades Médicas, Dirección de Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
| | - Camilo Toledo
- Laboratory of Cardiorespiratory and Sleep Physiology, Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - David C Andrade
- Exercise Applied Physiology Laboratory, Centro de Investigación en Fisiología y Medicina de Altura (FIMEDALT), Biomedical Department, Faculty of Health Sciences, Universidad de Antofagasta, Av. Universidad de Antofagasta #02800, Antofagasta, Chile.
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4
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Faghihkhorasani A, Ahmed HH, Mashool NM, Alwan M, Assefi M, Adab AH, Yasamineh S, Gholizadeh O, Baghani M. The potential use of bacteria and bacterial derivatives as drug delivery systems for viral infection. Virol J 2023; 20:222. [PMID: 37789431 PMCID: PMC10548687 DOI: 10.1186/s12985-023-02183-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023] Open
Abstract
Viral infections in humans are responsible for fatalities worldwide and contribute to the incidence of various human ailments. Controllable targeted medicine delivery against many illnesses, including viral infection, may be significantly aided by using bacteria and bacteria-derived products. They may accumulate in diseased tissues despite physical obstacles, where they can launch antiviral immunity. The ability to genetically and chemically modify them means that vaccinations against viral infections may be manufactured and delivered to affected tissues more safely and effectively. The objective of this study is to provide an overview of the latest advancements in the field of utilizing bacteria and bacterial derivatives as carriers for administering medication to treat viral diseases such as SARS-CoV-2, hepatitis B virus, hepatitis C virus, human immunodeficiency virus, human papillomavirus, influenza, and Ebola virus.
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Affiliation(s)
| | | | | | - Mariem Alwan
- Pharmacy College, Al-Farahidi University, Baghdad, Iraq
| | - Marjan Assefi
- University of North Carolina at Greensboro, Greensboro, USA
| | - Aya Hussein Adab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
| | - Saman Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Omid Gholizadeh
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
| | - Moein Baghani
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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5
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Li X, Yan H, Wong G, Ouyang W, Cui J. Identifying featured indels associated with SARS-CoV-2 fitness. Microbiol Spectr 2023; 11:e0226923. [PMID: 37698427 PMCID: PMC10580940 DOI: 10.1128/spectrum.02269-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/14/2023] [Indexed: 09/13/2023] Open
Abstract
As an RNA virus, severe acute respiratory coronavirus 2 (SARS-CoV-2) is known for frequent substitution mutations, and substitutions in important genome regions are often associated with viral fitness. However, whether indel mutations are related to viral fitness is generally ignored. Here we developed a computational methodology to investigate indels linked to fitness occurring in over 9 million SARS-CoV-2 genomes. Remarkably, by analyzing 31,642,404 deletion records and 1,981,308 insertion records, our pipeline identified 26,765 deletion types and 21,054 insertion types and discovered 65 indel types with a significant association with Pango lineages. We proposed the concept of featured indels representing the population of specific Pango lineages and variants as substitution mutations and termed these 65 indels as featured indels. The selective pressure of all indel types is assessed using the Bayesian model to explore the importance of indels. Our results exhibited higher selective pressure of indels like substitution mutations, which are important for assessing viral fitness and consistent with previous studies in vitro. Evaluation of the growth rate of each viral lineage indicated that indels play key roles in SARS-CoV-2 evolution and deserve more attention as substitution mutations. IMPORTANCE The fitness of indels in pathogen genome evolution has rarely been studied. We developed a computational methodology to investigate the severe acute respiratory coronavirus 2 genomes and analyze over 33 million records of indels systematically, ultimately proposing the concept of featured indels that can represent specific Pango lineages and identifying 65 featured indels. Machine learning model based on Bayesian inference and viral lineage growth rate evaluation suggests that these featured indels exhibit selection pressure comparable to replacement mutations. In conclusion, indels are not negligible for evaluating viral fitness.
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Affiliation(s)
- Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongliang Yan
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Wanli Ouyang
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
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6
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Taha BA, Al-Jubouri Q, Al Mashhadany Y, Hafiz Mokhtar MH, Bin Zan MSD, Bakar AAA, Arsad N. Density estimation of SARS-CoV2 spike proteins using super pixels segmentation technique. Appl Soft Comput 2023; 138:110210. [PMID: 36960080 PMCID: PMC10019041 DOI: 10.1016/j.asoc.2023.110210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/14/2022] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
The worldwide outbreak of COVID-19 disease was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2). The existence of spike proteins, which allow these viruses to infect host cells, is one of the distinctive biological traits of various prior viruses. As a result, the process by which these viruses infect people is largely dependent on spike proteins. The density of SARS-CoV-2 spike proteins must be estimated to better understand and develop diagnostics and vaccines against the COVID-19 pandemic. CT scans and X-rays have three issues: frosted glass, consolidation, and strange roadway layouts. Each of these issues can be graded separately or together. Although CT scan is sensitive to COVID-19, it is not very specific. Therefore, patients who obtain these results should have more comprehensive clinical and laboratory tests to rule out other probable reasons. This work collected 586 SARS-CoV 2 transmission electron microscopy (TEM) images from open source for density estimation of virus spike proteins through a segmentation approach based on the superpixel technique. As a result, the spike density means of SARS-CoV2 and SARS-CoV were 21,97 nm and 22,45 nm, respectively. Furthermore, in the future, we aim to include this model in an intelligent system to enhance the accuracy of viral detection and classification. Moreover, we can remotely connect hospitals and public sites to conduct environmental hazard assessments and data collection.
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Affiliation(s)
- Bakr Ahmed Taha
- UKM-Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Malaysia
| | - Qussay Al-Jubouri
- Department of Communication Engineering, University of Technology, Baghdad, Iraq
| | - Yousif Al Mashhadany
- Department of Electrical Engineering, College of Engineering, University of Anbar, Anbar, 00964, Iraq
| | - Mohd Hadri Hafiz Mokhtar
- UKM-Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Malaysia
| | - Mohd Saiful Dzulkefly Bin Zan
- UKM-Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Malaysia
| | - Ahmad Ashrif A Bakar
- UKM-Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Malaysia
| | - Norhana Arsad
- UKM-Department of Electrical, Electronic and Systems Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Malaysia
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7
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Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
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Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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8
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Saade C, Brengel-Pesce K, Gaymard A, Trabaud MA, Destras G, Oriol G, Cheynet V, Debombourg M, Mokdad B, Billaud G, Oblette A, Créhalet H, Giannoli JM, Garrigou C, Generenaz L, Compagnon C, Boibieux A, Lina B, Morfin F, Pozzetto B, Josset L, Touillet-Assant S, Bal A, On Behalf Of Lyon Covid Study Group A. Dynamics of viral shedding during ancestral or Omicron BA.1 SARS-CoV-2 infection and enhancement of pre-existing immunity during breakthrough infections. Emerg Microbes Infect 2022; 11:2423-2432. [PMID: 36098494 PMCID: PMC9621261 DOI: 10.1080/22221751.2022.2122578] [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] [Indexed: 11/22/2022]
Abstract
Omicron variant is circulating in the presence of a globally acquired immunity unlike the ancestral SARS-CoV-2 isolate. Herein, we investigated the normalized viral load dynamics and viral culture status in 44 fully vaccinated healthcare workers (HCWs) infected with the Omicron BA.1 variant. Viral load dynamics of 38 unvaccinated HCWs infected with the 20A variant during the first pandemic wave was also studied. We then explored the impact of Omicron infection on pre-existing immunity assessing anti-RBD IgG levels, neutralizing antibody titres against 19A, Delta and Omicron isolates, as well as IFN-γ release following cell stimulation with SARS-CoV-2 peptides. We reported that two weeks after diagnosis a greater proportion of HCWs infected with 20A (78.9%, 15/19) than with Omicron BA.1 (44.7%, 17/38; p = 0.02) were still positive by RT-qPCR. We found that Omicron breakthrough infections led to an overall enhancement of vaccine-induced humoral and cellular immunity as soon as a median [interquartile range] of 8 [7–9] days post symptom onset. Among samples with similar high viral loads, non-culturable samples exhibited higher neutralizing antibody titres and anti-RBD IgG levels than culturable samples. Additionally, Omicron infection led to an enhancement of antibodies neutralization capacity against other SARS-CoV-2 isolates. Taken together, the results suggest that Omicron BA.1 vaccine breakthrough infection is associated with a faster viral clearance than that of the ancestral SARS-CoV-2, in addition this new variant leads to a rapid enhancement of the humoral response against multiple SARS-CoV-2 variants, and of the cellular response.
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Affiliation(s)
- Carla Saade
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Karen Brengel-Pesce
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Alexandre Gaymard
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Mary-Anne Trabaud
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Gregory Destras
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.,GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Guy Oriol
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Valérie Cheynet
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Marion Debombourg
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Bouchra Mokdad
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Geneviève Billaud
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Antoine Oblette
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.,GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | | | | | - Christine Garrigou
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Laurence Generenaz
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - Christelle Compagnon
- Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France
| | - André Boibieux
- Infectious and Tropical Diseases Unit, Hospices Civil de Lyon, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.,GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Florence Morfin
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.,GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Bruno Pozzetto
- Team GIMAP, CIRI-Centre International de Recherche en Infectiologie, Université Jean Monnet de Saint-Etienne, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS de Lyon, F-42023 Saint-Etienne, France.,Laboratoire des Agents Infectieux, Centre Hospitalier Universitaire de Saint-Étienne, F-42055 Saint-Etienne, France
| | - Laurence Josset
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.,GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Sophie Touillet-Assant
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Joint Research Unit Civils Hospices of Lyon-bioMérieux, Civils Hospices of Lyon, Lyon Sud Hospital, Pierre-Bénite, 69310, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France
| | - Antonin Bal
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, F-69004, Lyon, France.,GenEPII sequencing platform, Institut des Agents Infectieux, Hospices Civils de Lyon, F-69004, Lyon, France
| | - A On Behalf Of Lyon Covid Study Group
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
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9
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Nicot F, Trémeaux P, Latour J, Jeanne N, Ranger N, Raymond S, Dimeglio C, Salin G, Donnadieu C, Izopet J. Whole-genome sequencing of SARS-CoV-2: Comparison of target capture and amplicon single molecule real-time sequencing protocols. J Med Virol 2022; 95:e28123. [PMID: 36056719 PMCID: PMC9539136 DOI: 10.1002/jmv.28123] [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: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS-CoV-2.
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Affiliation(s)
- Florence Nicot
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | | | - Justine Latour
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Nicolas Jeanne
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Noémie Ranger
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Stéphanie Raymond
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Chloé Dimeglio
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Gérald Salin
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Cécile Donnadieu
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Jacques Izopet
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
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10
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Shi FS, Yu Y, Li YL, Cui L, Zhao Z, Wang M, Wang B, Zhang R, Huang YW. Expression Profile and Localization of SARS-CoV-2 Nonstructural Replicase Proteins in Infected Cells. Microbiol Spectr 2022; 10:e0074422. [PMID: 35730969 PMCID: PMC9431475 DOI: 10.1128/spectrum.00744-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is responsible for the COVID-19 pandemic that has caused unprecedented loss of life and economic trouble all over the world, though the mechanism of its replication remains poorly understood. In this study, antibodies were generated and used to systematically determine the expression profile and subcellular distribution of 11 SARS-CoV-2 nonstructural replicase proteins (nsp1, nsp2, nsp3, nsp5, nsp7, nsp8, nsp9, nsp10, nsp13, nsp14, and nsp15) by Western blot and immunofluorescence assay. Nsp3, nsp5, and nsp8 were detected in perinuclear foci at different time points, with diffusion and stronger fluorescence observed over time. In particular, colocalization of nsp8 and nsp13 with different replicase proteins suggested viral protein-protein interaction, which may be key to understanding their functions and potential molecular mechanisms. Viral intermediate dsRNA was detected in perinuclear foci as early as 2-h postinfection, indicating the initiation of virus replication. With the passage of time, these perinuclear dsRNA foci became larger and brighter, and nearly all colocalized with N protein, consistent with viral growth over time. Thus, the development of these anti-nsp antibodies provides basic tools for the further study of replication and diagnosis of SARS-CoV-2. IMPORTANCE The intracellular localization of SARS-CoV-2 replicase nonstructural proteins (nsp) during infection has not been fully elucidated. In this study, we systematically analyzed the expression and subcellular localization of 11 distinct viral nsp and dsRNA over time in SARS-CoV-2-infected cells by using individual antibody against these replicase proteins. The data indicated that nsp gene expression is highly regulated in space and time, which could be useful to understand the function of viral replicases and future development of diagnostics and potential antiviral strategies against SARS-CoV-2.
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Affiliation(s)
- Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Yin Yu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, China
| | - Ya-Li Li
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Lilan Cui
- Novoprotein Scientific Inc., Shanghai, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Mi Wang
- Novoprotein Scientific Inc., Shanghai, China
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Rong Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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11
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Katowa B, Kalonda A, Mubemba B, Matoba J, Shempela DM, Sikalima J, Kabungo B, Changula K, Chitanga S, Kasonde M, Kapona O, Kapata N, Musonda K, Monze M, Tembo J, Bates M, Zumla A, Sutcliffe CG, Kajihara M, Yamagishi J, Takada A, Sawa H, Chilengi R, Mukonka V, Muleya W, Simulundu E. Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern. Viruses 2022; 14:v14091865. [PMID: 36146671 PMCID: PMC9504048 DOI: 10.3390/v14091865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.
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Affiliation(s)
- Ben Katowa
- Macha Research Trust, Choma 20100, Zambia
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Benjamin Mubemba
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe 50100, Zambia
- Department of Biomedical Sciences, School of Medicine, Copperbelt University, Ndola 50100, Zambia
| | | | | | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia
| | - Boniface Kabungo
- Southern Provincial Health Office, Ministry of Health, Choma 20100, Zambia
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Simbarashe Chitanga
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Preclinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek Private Bag 13301, Namibia
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Mpanga Kasonde
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Otridah Kapona
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Nathan Kapata
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Mwaka Monze
- Virology Laboratory, University Teaching Hospital, Lusaka 10101, Zambia
| | - John Tembo
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka 10101, Zambia
| | - Matthew Bates
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka 10101, Zambia
- School of Life and Environmental Sciences, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, UK
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London NW3 2PF, UK
| | - Catherine G. Sutcliffe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Division of International Research Promotion, Hokkaido University International Institute for Zoonosis Control, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
- Republic of Zambia State House, Lusaka 10101, Zambia
| | - Victor Mukonka
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Edgar Simulundu
- Macha Research Trust, Choma 20100, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Correspondence:
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12
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Probing the Immune System Dynamics of the COVID-19 Disease for Vaccine Designing and Drug Repurposing Using Bioinformatics Tools. IMMUNO 2022. [DOI: 10.3390/immuno2020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The pathogenesis of COVID-19 is complicated by immune dysfunction. The impact of immune-based therapy in COVID-19 patients has been well documented, with some notable studies on the use of anti-cytokine medicines. However, the complexity of disease phenotypes, patient heterogeneity and the varying quality of evidence from immunotherapy studies provide problems in clinical decision-making. This review seeks to aid therapeutic decision-making by giving an overview of the immunological responses against COVID-19 disease that may contribute to the severity of the disease. We have extensively discussed theranostic methods for COVID-19 detection. With advancements in technology, bioinformatics has taken studies to a higher level. The paper also discusses the application of bioinformatics and machine learning tools for the diagnosis, vaccine design and drug repurposing against SARS-CoV-2.
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13
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Al-Qahtani AA. Mutations in the genome of severe acute respiratory syndrome coronavirus 2: implications for COVID-19 severity and progression. J Int Med Res 2022; 50:3000605221086433. [PMID: 35352580 PMCID: PMC8973081 DOI: 10.1177/03000605221086433] [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] [Indexed: 01/02/2023] Open
Abstract
Coronaviridae is a large family of enveloped, positive-strand RNA viruses that has plagued the world since it was discovered in humans in the 1960s. The recent severe acute respiratory syndrome coronavirus (SARS-CoV)-2 pandemic has already exceeded the number of combined cases and deaths witnessed during previous SARS-CoV and Middle East respiratory syndrome-CoV epidemics in the last two decades. This narrative review focuses on genomic mutations in SARS-CoV-2 and their impact on the severity and progression of COVID-19 in light of reported data in the literature. Notable SARS-CoV-2 mutations associated with open reading frames, the S glycoprotein, and nucleocapsid protein, currently circulating globally, are discussed along with emerging mutations such as those in the SARS-CoV-2 VUI 202012/01 variant in the UK and other European countries, the 484K.V2 and P.1 variants in Brazil, the B.1.617 variant in India, and South African variants 501Y.V2 and B.1.1.529 (omicron). These variants have the potential to influence the receptor binding domain, host-virus fusion, and SARS-CoV-2 replication. Correlating these mutations with disease dynamics could help us understand their pathogenicity and design appropriate therapeutics.
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Affiliation(s)
- Ahmed Ali Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University, School of Medicine, Riyadh, Saudi Arabia
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14
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Liu X, Guo L, Xu T, Lu X, Ma M, Sheng W, Wu Y, Peng H, Cao L, Zheng F, Huang S, Yang Z, Du J, Shi M, Guo D. A comprehensive evolutionary and epidemiological characterization of insertion and deletion mutations in SARS-CoV-2 genomes. Virus Evol 2022; 7:veab104. [PMID: 35039785 PMCID: PMC8754802 DOI: 10.1093/ve/veab104] [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: 11/07/2021] [Revised: 11/29/2021] [Accepted: 12/11/2021] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2, which causes the current pandemic of respiratory illness, is evolving continuously and generating new variants. Nevertheless, most of the sequence analyses thus far focused on nucleotide substitutions despite the fact that insertions and deletions (indels) are equally important in the evolution of SARS-CoV-2. In this study, we analyzed 1,099,664 high-quality sequences of SARS-CoV-2 genomes to re-construct the evolutionary and epidemiological histories of indels. Our analysis revealed 289 circulating indel types (237 deletion and 52 insertion types, each represented by more than ten genomic sequences), among which eighteen were recurrent indel types, each represented by more than 500 genome sequences. Although indels were identified across the entire genome, most of them were identified in nsp6, S, ORF8, and N genes, among which ORF8 indel types had the highest frequencies of frameshift. Geographical and temporal analyses of these variants revealed a few alterations of dominant indel types, each accompanied by geographic expansion to different countries and continents, which resulted in the fixation of several types of indels in the field, including the current variants of concern. Evolutionary and structural analyses revealed that indels involving S N-terminal domain regions were linked to the 3/4 variants of concern, resulting in significantly altered S protein that might contribute to the selective advantage of the corresponding variant. In sum, our study highlights the important role of insertions and deletions in the evolution and spread of SARS-CoV-2.
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Affiliation(s)
- Xue Liu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Liping Guo
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Tiefeng Xu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xiaoyu Lu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mingpeng Ma
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wenyu Sheng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yinxia Wu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Hong Peng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Liu Cao
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Fuxiang Zheng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siyao Huang
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zixiao Yang
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jie Du
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mang Shi
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Deyin Guo
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
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15
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Panzera Y, Ramos N, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Frabasile S, Fuques E, Coppola L, Goñi N, Ramas V, Sorhouet C, Bormida V, Burgueño A, Brasesco M, Garland MR, Molinari S, Perez MT, Somma R, Somma S, Morel MN, Mogdasy C, Chiparelli H, Arbiza J, Delfraro A, Pérez R. Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion. Mem Inst Oswaldo Cruz 2022; 116:e210275. [PMID: 35019072 PMCID: PMC8752050 DOI: 10.1590/0074-02760210275] [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: 08/15/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels’ importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.
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Affiliation(s)
- Yanina Panzera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Natalia Ramos
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Lucía Calleros
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Ana Marandino
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Gonzalo Tomás
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Claudia Techera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sofía Grecco
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sandra Frabasile
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Eddie Fuques
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Leticia Coppola
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Natalia Goñi
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Viviana Ramas
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Victoria Bormida
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Analía Burgueño
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - María Brasesco
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Rosa Garland
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Sylvia Molinari
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Teresa Perez
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Rosina Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Silvana Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Noelia Morel
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cristina Mogdasy
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Héctor Chiparelli
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Juan Arbiza
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Adriana Delfraro
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Ruben Pérez
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
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16
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Lhomme S, Latour J, Jeanne N, Trémeaux P, Ranger N, Migueres M, Salin G, Donnadieu C, Izopet J. Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Viruses 2021; 13:v13122544. [PMID: 34960813 PMCID: PMC8707593 DOI: 10.3390/v13122544] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.
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Affiliation(s)
- Sébastien Lhomme
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
- Correspondence: ; Tel.: +33-5-67-69-04-24
| | - Justine Latour
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Nicolas Jeanne
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Pauline Trémeaux
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Noémie Ranger
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Marion Migueres
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Gérald Salin
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France; (G.S.); (C.D.)
| | - Cécile Donnadieu
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France; (G.S.); (C.D.)
| | - Jacques Izopet
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
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17
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Perez-Gomez R. The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. J Dev Biol 2021; 9:58. [PMID: 34940505 PMCID: PMC8705434 DOI: 10.3390/jdb9040058] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
A novel coronavirus (SARS-CoV-2) emerged towards the end of 2019 that caused a severe respiratory disease in humans called COVID-19. It led to a pandemic with a high rate of morbidity and mortality that is ongoing and threatening humankind. Most of the mutations occurring in SARS-CoV-2 are synonymous or deleterious, but a few of them produce improved viral functions. The first known mutation associated with higher transmissibility, D614G, was detected in early 2020. Since then, the virus has evolved; new mutations have occurred, and many variants have been described. Depending on the genes affected and the location of the mutations, they could provide altered infectivity, transmissibility, or immune escape. To date, mutations that cause variations in the SARS-CoV-2 spike protein have been among the most studied because of the protein's role in the initial virus-cell contact and because it is the most variable region in the virus genome. Some concerning mutations associated with an impact on viral fitness have been described in the Spike protein, such as D614G, N501Y, E484K, K417N/T, L452R, and P681R, among others. To understand the impact of the infectivity and antigenicity of the virus, the mutation landscape of SARS-CoV-2 has been under constant global scrutiny. The virus variants are defined according to their origin, their genetic profile (some characteristic mutations prevalent in the lineage), and the severity of the disease they produce, which determines the level of concern. If they increase fitness, new variants can outcompete others in the population. The Alpha variant was more transmissible than previous versions and quickly spread globally. The Beta and Gamma variants accumulated mutations that partially escape the immune defenses and affect the effectiveness of vaccines. Nowadays, the Delta variant, identified around March 2021, has spread and displaced the other variants, becoming the most concerning of all lineages that have emerged. The Delta variant has a particular genetic profile, bearing unique mutations, such as T478K in the spike protein and M203R in the nucleocapsid. This review summarizes the current knowledge of the different mutations that have appeared in SARS-CoV-2, mainly on the spike protein. It analyzes their impact on the protein function and, subsequently, on the level of concern of different variants and their importance in the ongoing pandemic.
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Affiliation(s)
- Raquel Perez-Gomez
- Translational Genomics Group, Institut Universitari de Biotecnologia y Biomedicina BIOTECMED, Universitat de Valencia, 46100 Valencia, Spain
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18
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Quéromès G, Destras G, Bal A, Regue H, Burfin G, Brun S, Fanget R, Morfin F, Valette M, Trouillet-Assant S, Lina B, Frobert E, Josset L. Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France. Emerg Microbes Infect 2021; 10:167-177. [PMID: 33399033 PMCID: PMC7850418 DOI: 10.1080/22221751.2021.1872351] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/10/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022]
Abstract
During routine molecular surveillance of SARS-CoV-2 performed at the National Reference Center of Respiratory Viruses (Lyon, France) (n = 229 sequences collected February-April 2020), two frameshifting deletions were detected in the open reading frame 6, at the same position (27267). While a 26-nucleotide deletion variant (D26) was only found in one nasopharyngeal sample in March 2020, the 34-nucleotide deletion (D34) was found within a single geriatric hospital unit in 5/9 patients and one health care worker in April 2020. Phylogeny analysis strongly suggested a nosocomial transmission of D34, with potential fecal transmission, as also identified in a stool sample. No difference in disease severity was observed between patients hospitalized in the geriatric unit infected with WT or D34. In vitro D26 and D34 characterization revealed comparable replication kinetics with the wild-type (WT), but differential host immune responses. While interferon-stimulated genes were similarly upregulated after infection with WT and ORF6 variants, the latter specifically induced overexpression of 9 genes coding for inflammatory cytokines in the NF-kB pathway, including CCL2/MCP1, PTX3, and TNFα, for which high plasma levels have been associated with severe COVID-19. Our findings emphasize the need to monitor the occurrence of ORF6 deletions and assess their impact on the host immune response.
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Affiliation(s)
- Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
| | - Grégory Destras
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Antonin Bal
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Solenne Brun
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Rémi Fanget
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Florence Morfin
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Martine Valette
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | | | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
- Centre National de Référence des virus des infections respiratoires, Lyon, Fracne
| | - Emilie Frobert
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Lyon, Fracne
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Lyon, France
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19
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Yuan F, Wang L, Fang Y, Wang L. Global SNP analysis of 11,183 SARS-CoV-2 strains reveals high genetic diversity. Transbound Emerg Dis 2021; 68:3288-3304. [PMID: 33207070 PMCID: PMC7753349 DOI: 10.1111/tbed.13931] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/19/2020] [Accepted: 11/13/2020] [Indexed: 02/05/2023]
Abstract
Since first identified in December of 2019, COVID-19 has been quickly spreading to the world in few months and COVID-19 cases are still undergoing rapid surge in most countries worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), adapts and evolves rapidly in nature. With the availability of 16,092 SARS-CoV-2 full genomes in GISAID as of 13 May, we removed the poor-quality genomes and performed mutational profiling analysis for the remaining 11,183 viral genomes. Global analysis of all sequences identified all single nucleotide polymorphisms (SNPs) across the whole genome and critical SNPs with high mutation frequency that contributes to five-clade classification of global strains. A total of 119 SNPs were found with 74 non-synonymous mutations, 43 synonymous mutations and two mutations in intergenic regions. Analysis of geographic pattern of mutational profiling for the whole genome reveals differences between each continent. A transition mutation from C to T represents the most mutation types across the genome, suggesting rapid evolution and adaptation of the virus in host. Amino acid (AA) deletions and insertions found across the genome results in changes in viral protein length and potential function alteration. Mutational profiling for each gene was analysed, and results show that nucleocapsid gene demonstrates the highest mutational frequency, followed by Nsp2, Nsp3 and Spike gene. We further focused on non-synonymous mutational distributions on four key viral proteins, spike with 75 mutations, RNA-dependent-RNA-polymerase with 41 mutations, 3C-like protease with 22 mutations and Papain-like protease with 10 mutations. Results show that non-synonymous mutations on critical sites of these four proteins pose great challenge for development of anti-viral drugs and other countering measures. Overall, this study provides more understanding of genetic diversity/variability of SARS-CoV-2 and insights for development of anti-viral therapeutics.
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Affiliation(s)
- Fangfeng Yuan
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois at Urbana ChampaignUrbanaIllinoisUSA
| | - Liping Wang
- Department of Diagnostic Medicine and PathobiologyCollege of Veterinary MedicineKansas State UniversityManhattanKansasUSA
| | - Ying Fang
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois at Urbana ChampaignUrbanaIllinoisUSA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical MedicineCollege of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
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20
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Zannoli S, Dirani G, Taddei F, Gatti G, Poggianti I, Denicolò A, Arfilli V, Manera M, Mancini A, Battisti A, Sambri V. A deletion in the N gene may cause diagnostic escape in SARS-CoV-2 samples. Diagn Microbiol Infect Dis 2021; 102:115540. [PMID: 34649189 PMCID: PMC8447549 DOI: 10.1016/j.diagmicrobio.2021.115540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 11/28/2022]
Abstract
Five SARS-CoV-2-positive samples showed N-gene drop-out with a RT-PCR multiplex test. WGS found all samples to harbor a deletion in the same region of the N gene, which is likely to impair the efficiency of amplification. This highlights the need for a continued surveillance of viral evolution and diagnostic test performance.
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Affiliation(s)
- Silvia Zannoli
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy.
| | - Giorgio Dirani
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Ilaria Poggianti
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Agnese Denicolò
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | | | - Martina Manera
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Andrea Mancini
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Arianna Battisti
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy; Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna
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21
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Karamese M, Ozgur D, Tutuncu EE. Molecular characterization, phylogenetic and variation analyses of SARS-CoV-2 strains in Turkey. Future Microbiol 2021; 16:1209-1214. [PMID: 34615381 PMCID: PMC8507978 DOI: 10.2217/fmb-2021-0118] [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] [Indexed: 01/01/2023] Open
Abstract
Aims: We present the sequence and single-nucleotide polymorphism (SNP) analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. Methods: The Illumina MiSeq platform was used for sequencing the libraries. The SNPs were detected by using Genome Analysis Toolkit – HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2. Results: All viral genome sequences of our isolates were located in lineage B under the different clusters, such as B.1 (n = 3), B.1.1 (n = 28) and B.1.9 (n = 16). According to the Global Initiative on Sharing All Influenza Data nomenclature, all of our complete genomes were placed in G, GR and GH clades. In our study, 549 total and 53 unique SNPs were detected. Conclusion: The results indicate that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences.
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Affiliation(s)
- Murat Karamese
- Department of Medical Microbiology, Kafkas University, Kars, 36100, Turkey
| | - Didem Ozgur
- Department of Medical Microbiology, Kafkas University, Kars, 36100, Turkey
| | - Emin E Tutuncu
- Department of Infectious Diseases & Clinical Microbiology, Kafkas University, Kars, 36100, Turkey
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22
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Han T, Cong H, Shen Y, Yu B. Recent advances in detection technologies for COVID-19. Talanta 2021; 233:122609. [PMID: 34215093 PMCID: PMC8196236 DOI: 10.1016/j.talanta.2021.122609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/10/2021] [Indexed: 12/16/2022]
Abstract
Corona Virus Disease 2019 (COVID-19) is a highly infectious respiratory illness that was caused by the SARS-CoV-2. It spread around the world in just a few months and became a worldwide pandemic. Quick and accurate diagnosis of infected patients is very important for controlling transmission. In addition to the commonly used Real-time reverse-transcription polymerase chain reaction (RT-PCR) detection techniques, other diagnostic techniques are also emerging endlessly. This article reviews the current diagnostic methods for COVID-19 and discusses their advantages and disadvantages. It provides an important reference for the diagnosis of COVID-19.
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Affiliation(s)
- Tingting Han
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Hailin Cong
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, China; State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, 266071, China
| | - Youqing Shen
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Bing Yu
- Institute of Biomedical Materials and Engineering, College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, China; State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao, 266071, China.
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23
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Zella D, Giovanetti M, Benedetti F, Unali F, Spoto S, Guarino M, Angeletti S, Ciccozzi M. The variants question: What is the problem? J Med Virol 2021; 93:6479-6485. [PMID: 34255352 PMCID: PMC8426965 DOI: 10.1002/jmv.27196] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/03/2021] [Accepted: 07/08/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China in early December 2019 has rapidly widespread worldwide. Over the course of the pandemic, due to the advance of whole-genome sequencing technologies, an unprecedented number of genomes have been generated, providing both invaluable insights into the ongoing evolution and epidemiology of the virus and allowing the identification of hundreds of circulating genetic variants during the pandemic. In recent months variants of SARS-CoV-2 that have an increased number of mutations on the Spike protein have brought concern all over the world. These have been called "variants of concerns" (VOCs), and/or "variants of interests" (VOIs) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. Tracking the spread of emerging SARS-CoV-2 variants is crucial to inform public health efforts and control the ongoing pandemic. In this review, a concise characterization of the SARS-CoV-2 mutational patterns of the main VOCs and VOIs circulating and cocirculating worldwide has been presented to determine the magnitude of the SARS-CoV-2 threat to better understand the virus genetic diversity and its potential impact on vaccination strategy.
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Affiliation(s)
- Davide Zella
- Department of Biochemistry and Molecular Biology, Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francesca Benedetti
- Department of Biochemistry and Molecular Biology, Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Francesco Unali
- Area Comunicazione e Brand Management, University Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Spoto
- Department of Diagnostic and Therapeutic Medicine, University Campus Bio-Medico of Rome, Rome, Italy
| | - Michele Guarino
- Department of Gastrointestinal Diseases, Campus Bio-Medico University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
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24
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Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19. Biomolecules 2021; 11:biom11060912. [PMID: 34207362 PMCID: PMC8233742 DOI: 10.3390/biom11060912] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons' A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% ± 5.84%) and the GC3 value (30.14% ± 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome's level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.
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25
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Kelta Wabalo E, Dukessa Dubiwak A, Welde Senbetu M, Sime Gizaw T. Effect of Genomic and Amino Acid Sequence Mutation on Virulence and Therapeutic Target of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS COV-2). Infect Drug Resist 2021; 14:2187-2192. [PMID: 34163183 PMCID: PMC8214021 DOI: 10.2147/idr.s307374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/26/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). It is one of the RNA coronaviruses which share the highest mutation rates of RNA viruses when compared with that of their hosts. The collective mutation rate of RNA viruses is up to a million times higher than their hosts and is correlated with enhanced virulence of viruses. The RNA, genomic material of SARS-CoV-2, has the capacity of showing amplified fast changes as the infection spreads. These changes were frequently observed in genes for spike glycoprotein, nucleocapsid, ORF1ab, and ORF8, together with RNA dependent RNA polymerase. In contrast, genes for envelope, membrane, ORF6, ORF7a and ORF7b showed no observable changes in terms of amino acid substitutions. Mutated SARS COV-2 at these particular sites has been associated with viral infectivity, false laboratory results and viral genome mutation and interferes with therapeutic targets. Interferences with therapeutic targets is frequently observed in genes for RdRp. Additionally, mutated viral genes for RdRp render slow fidelity of RdRp protein, resulting in a high mutation rate. Such a high mutation rate might allow new virulent forms of the virus to emerge and influence the disease profile. This review aimed to elaborate on the effect of genomic and amino acid sequence mutations on the virulence and therapeutic targets of SARS COV-2. To achieve this objective, multiple literatures have been reviewed.
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Affiliation(s)
- Endriyas Kelta Wabalo
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Abebe Dukessa Dubiwak
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Mengistu Welde Senbetu
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Tariku Sime Gizaw
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
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26
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Sakr MM, Elsayed NS, El-Housseiny GS. Latest updates on SARS-CoV-2 genomic characterization, drug, and vaccine development; a comprehensive bioinformatics review. Microb Pathog 2021; 154:104809. [PMID: 33647446 PMCID: PMC7910145 DOI: 10.1016/j.micpath.2021.104809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023]
Abstract
Amid the COVID-19 outbreak, several bioinformatic analyses have been conducted on SARS-CoV-2 virus genome. Numerous studies rushed to fill the gap about this novel virus. Comparison with other related sequences, structural predictions of the produced proteins, determination of variations in amino acid residues and depiction of possible drug and vaccine targets have been the focus of scientific research from the beginning of this year. In addition to discussing the viral taxonomy, clinical features, life cycle, and genome organization, this review will focus on the recent updates in genome and viral proteins characterization and potential therapeutic and vaccine candidates developed so far. Comparative studies with related genomes and proteins provide understanding for the viral molecular mechanisms and suggest targets for therapeutics and vaccinology trials to stop the escalation of this new virus. This pandemic, with its resulting social and economic afflictions, will definitely have significant marks on our lives in the following years.
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Affiliation(s)
- Masarra M Sakr
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt
| | - Noha S Elsayed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt.
| | - Ghadir S El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt
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Majumdar P, Niyogi S. SARS-CoV-2 mutations: the biological trackway towards viral fitness. Epidemiol Infect 2021; 149:e110. [PMID: 33928885 PMCID: PMC8134885 DOI: 10.1017/s0950268821001060] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/26/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023] Open
Abstract
The outbreak of pneumonia-like respiratory disorder at China and its rapid transmission world-wide resulted in public health emergency, which brought lineage B betacoronaviridae SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) into spotlight. The fairly high mutation rate, frequent recombination and interspecies transmission in betacoronaviridae are largely responsible for their temporal changes in infectivity and virulence. Investigation of global SARS-CoV-2 genotypes revealed considerable mutations in structural, non-structural, accessory proteins as well as untranslated regions. Among the various types of mutations, single-nucleotide substitutions are the predominant ones. In addition, insertion, deletion and frame-shift mutations are also reported, albeit at a lower frequency. Among the structural proteins, spike glycoprotein and nucleocapsid phosphoprotein accumulated a larger number of mutations whereas envelope and membrane proteins are mostly conserved. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. Divergent genetic variants created serious challenge towards the development of therapeutics and vaccines. This review will consolidate mutations in different SARS-CoV-2 proteins and their implications on viral fitness.
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Affiliation(s)
| | - Sougata Niyogi
- Dinabandhu Andrews Institute of Technology and Management, Block-S, 1/406A, Patuli, Kolkata, West Bengal700094, India
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28
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Lau BT, Pavlichin D, Hooker AC, Almeda A, Shin G, Chen J, Sahoo MK, Huang CH, Pinsky BA, Lee HJ, Ji HP. Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies. Genome Med 2021; 13:62. [PMID: 33875001 PMCID: PMC8054698 DOI: 10.1186/s13073-021-00882-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
Background The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Viral quasispecies emerge from de novo mutations that occur in individual patients. In combination, these sets of viral mutations provide distinct genetic fingerprints that reveal the patterns of transmission and have utility in contact tracing. Methods Leveraging thousands of sequenced SARS-CoV-2 genomes, we performed a viral pangenome analysis to identify conserved genomic sequences. We used a rapid and highly efficient computational approach that relies on k-mers, short tracts of sequence, instead of conventional sequence alignment. Using this method, we annotated viral mutation signatures that were associated with specific strains. Based on these highly conserved viral sequences, we developed a rapid and highly scalable targeted sequencing assay to identify mutations, detect quasispecies variants, and identify mutation signatures from patients. These results were compared to the pangenome genetic fingerprints. Results We built a k-mer index for thousands of SARS-CoV-2 genomes and identified conserved genomics regions and landscape of mutations across thousands of virus genomes. We delineated mutation profiles spanning common genetic fingerprints (the combination of mutations in a viral assembly) and a combination of mutations that appear in only a small number of patients. We developed a targeted sequencing assay by selecting primers from the conserved viral genome regions to flank frequent mutations. Using a cohort of 100 SARS-CoV-2 clinical samples, we identified genetic fingerprints consisting of strain-specific mutations seen across populations and de novo quasispecies mutations localized to individual infections. We compared the mutation profiles of viral samples undergoing analysis with the features of the pangenome. Conclusions We conducted an analysis for viral mutation profiles that provide the basis of genetic fingerprints. Our study linked pangenome analysis with targeted deep sequenced SARS-CoV-2 clinical samples. We identified quasispecies mutations occurring within individual patients and determined their general prevalence when compared to over 70,000 other strains. Analysis of these genetic fingerprints may provide a way of conducting molecular contact tracing.
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Affiliation(s)
- Billy T Lau
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA.,Stanford Genome Technology Center West, Stanford University, Palo Alto, CA, 94304, USA
| | - Dmitri Pavlichin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA
| | - Anna C Hooker
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA
| | - Alison Almeda
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA
| | - Giwon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA
| | - Jiamin Chen
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chun Hong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ho Joon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA.
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, CCSR 1120, Stanford, CA, 94305-5151, USA. .,Stanford Genome Technology Center West, Stanford University, Palo Alto, CA, 94304, USA.
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29
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Genotyping of the Major SARS-CoV-2 Clade by Short-Amplicon High-Resolution Melting (SA-HRM) Analysis. Genes (Basel) 2021; 12:genes12040531. [PMID: 33916492 PMCID: PMC8067340 DOI: 10.3390/genes12040531] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/17/2022] Open
Abstract
The genome of the SARS-CoV-2 virus, the causal agent of the COVID-19 pandemic, has diverged due to multiple mutations since its emergence as a human pathogen in December 2019. Some mutations have defined several SARS-CoV-2 clades that seem to behave differently in terms of regional distribution and other biological features. Next-generation sequencing (NGS) approaches are used to classify the sequence variants in viruses from individual human patients. However, the cost and relative scarcity of NGS equipment and expertise in developing countries prevent studies aimed to associate specific clades and variants to clinical features and outcomes in such territories. As of March 2021, the GR clade and its derivatives, including the B.1.1.7 and B.1.1.28 variants, predominate worldwide. We implemented the post-PCR small-amplicon high-resolution melting analysis to genotype SARS-CoV-2 viruses isolated from the saliva of individual patients. This procedure was able to clearly distinguish two groups of samples of SARS-CoV-2-positive samples predicted, according to their melting profiles, to contain GR and non-GR viruses. This grouping of the samples was validated by means of amplification-refractory mutation system (ARMS) assay as well as Sanger sequencing.
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30
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Gaudart J, Landier J, Huiart L, Legendre E, Lehot L, Bendiane MK, Chiche L, Petitjean A, Mosnier E, Kirakoya-Samadoulougou F, Demongeot J, Piarroux R, Rebaudet S. Factors associated with the spatial heterogeneity of the first wave of COVID-19 in France: a nationwide geo-epidemiological study. Lancet Public Health 2021; 6:e222-e231. [PMID: 33556327 PMCID: PMC7864788 DOI: 10.1016/s2468-2667(21)00006-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND The objective of this study was to better understand the factors associated with the heterogeneity of in-hospital COVID-19 morbidity and mortality across France, one of the countries most affected by COVID-19 in the early months of the pandemic. METHODS This geo-epidemiological analysis was based on data publicly available on government and administration websites for the 96 administrative departments of metropolitan France between March 19 and May 11, 2020, including Public Health France, the Regional Health Agencies, the French national statistics institute, and the Ministry of Health. Using hierarchical ascendant classification on principal component analysis of multidimensional variables, and multivariate analyses with generalised additive models, we assessed the associations between several factors (spatiotemporal spread of the epidemic between Feb 7 and March 17, 2020, the national lockdown, demographic population structure, baseline intensive care capacities, baseline population health and health-care services, new chloroquine and hydroxychloroquine dispensations, economic indicators, degree of urbanisation, and climate profile) and in-hospital COVID-19 incidence, mortality, and case fatality rates. Incidence rate was defined as the cumulative number of in-hospital COVID-19 cases per 100 000 inhabitants, mortality rate as the cumulative number of in-hospital COVID-19 deaths per 100 000, and case fatality rate as the cumulative number of in-hospital COVID-19 deaths per cumulative number of in-hospital COVID-19 cases. FINDINGS From March 19 to May 11, 2020, hospitals in metropolitan France notified a total of 100 988 COVID-19 cases, including 16 597 people who were admitted to intensive care and 17 062 deaths. There was an overall cumulative in-hospital incidence rate of 155·6 cases per 100 000 inhabitants (range 19·4-489·5), in-hospital mortality rate of 26·3 deaths per 100 000 (1·1-119·2), and in-hospital case fatality rate of 16·9% (4·8-26·2). We found clear spatial heterogeneity of in-hospital COVID-19 incidence and mortality rates, following the spread of the epidemic. After multivariate adjustment, the delay between the first COVID-19-associated death and the onset of the national lockdown was positively associated with in-hospital incidence (adjusted standardised incidence ratio 1·02, 95% CI 1·01-1·04), mortality (adjusted standardised mortality ratio 1·04, 1·02-1·06), and case fatality rates (adjusted standardised fatality ratio 1·01, 1·01-1·02). Mortality and case fatality rates were higher in departments with older populations (adjusted standardised ratio for populations with a high proportion older than aged >85 years 2·17 [95% CI 1·20-3·90] for mortality and 1·43 [1·08-1·88] for case fatality rate). Mortality rate was also associated with incidence rate (1·0004, 1·0002-1·001), but mortality and case fatality rates did not appear to be associated with baseline intensive care capacities. We found no association between climate and in-hospital COVID-19 incidence, or between economic indicators and in-hospital COVID-19 incidence or mortality rates. INTERPRETATION This ecological study highlights the impact of the epidemic spread, national lockdown, and reactive adaptation of intensive care capacities on the spatial distribution of COVID-19 morbidity and mortality. It provides information for future geo-epidemiological analyses and has implications for preparedness and response policies to current and future epidemic waves in France and elsewhere. FUNDING None.
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Affiliation(s)
- Jean Gaudart
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France; Public Assistance Marseille Hospitals (APHM), Biostatistics and Information and Communication Technologies Service (BioSTIC), Marseille, France.
| | - Jordi Landier
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France
| | | | - Eva Legendre
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France
| | - Laurent Lehot
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France
| | - Marc Karim Bendiane
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France
| | - Laurent Chiche
- Internal Medicine and Clinical Research Unit, European Hospital Marseille, Marseille, France
| | - Aliette Petitjean
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France
| | - Emilie Mosnier
- Aix Marseille University, National Institute of Health and Medical Research (INSERM), Institute of Research for Development (IRD), Economic and Social Sciences for Health and Medical Information Processing (SESSTIM), UMR1252, Marseille, France
| | - Fati Kirakoya-Samadoulougou
- Research Centre for Epidemiology, Biostatistics, and Research Clinic, School of Public Health, Free University of Brussels, Brussels, Belgium
| | | | - Renaud Piarroux
- Sorbonne University, INSERM, Pierre-Louis Institute of Epidemiology and Public Health (IPLESP), AP-HP, Laboratory of Parasitology and Mycologie, Pitié-Salpêtrière Hospital, Paris, France
| | - Stanislas Rebaudet
- European Hospital Marseille, Aix-Marseille University, INSERM, IRD, SESSTIM, IPLESP, Marseille, France
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31
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Younis NK, Zareef RO, Maktabi MAN, Mahfouz R. The Era of the Coronavirus Disease 2019 Pandemic: A Review on Dynamics, Clinical Symptoms and Complications, Diagnosis, and Treatment. Genet Test Mol Biomarkers 2021; 25:85-101. [PMID: 33596144 DOI: 10.1089/gtmb.2020.0227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) displays a broad spectrum of clinical presentations ranging from lack of symptoms to severe multiorgan system complications and death. Various laboratory assays have been employed in the diagnosis of COVID-19, including: nucleic acid-based tests; antigen tests; and serum testing for anti-severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antibodies. The disease can also be diagnosed based on suggestive clinical features and radiological findings. Until now, remdesivir is the only medication approved for the treatment of COVID-19 by the U.S. Food and Drug Administration (FDA); however, it is anticipated that several anti-SARS-CoV-2 monoclonal antibodies will gain soon approval. Other methods of treatment include supportive care directed toward treating the symptoms. Nevertheless, many studies have recently emerged, showing controversial preliminary results with the off-label medication hydroxychloroquine. Given that all results are still preliminary, including those seen by remdesivir, additional evidence and research are required to identify effective medications that are broadly effective and well tolerated. Importantly, two RNA-based vaccines have recently gained approval from Pfizer and Moderna, with many others still in clinical trials. This article reviews various aspects of COVID-19, including its epidemiology; its evolution and mutational spectrum; and its clinical dynamics, symptoms and complications, diagnosis, and treatment.
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Affiliation(s)
- Nour K Younis
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rana O Zareef
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mohammad Ali N Maktabi
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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32
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Giovanetti M, Benedetti F, Campisi G, Ciccozzi A, Fabris S, Ceccarelli G, Tambone V, Caruso A, Angeletti S, Zella D, Ciccozzi M. Evolution patterns of SARS-CoV-2: Snapshot on its genome variants. Biochem Biophys Res Commun 2021; 538:88-91. [PMID: 33199021 PMCID: PMC7836704 DOI: 10.1016/j.bbrc.2020.10.102] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
An acute respiratory syndrome (COVID-19), caused by a novel coronavirus (SARS-CoV-2) with a high rate of morbidity and elevate mortality, has emerged as one of the most important threats to humankind in the last centuries. Rigorous determination of SARS-CoV-2 infectivity is very difficult owing to the continuous evolution of the virus, with its single nucleotide polymorphism (SNP) variants and many lineages. However, it is urgently necessary to study the virus in depth, to understand the mechanism of its pathogenicity and virulence, and to develop effective therapeutic strategies. The present contribution summarizes in a succinct way the current knowledge on the evolutionary and structural features of the virus, with the aim of clarifying its mutational pattern and its possible role in the ongoing pandemic.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil,Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland Baltimore, USA
| | - Giovanni Campisi
- Department of Molecular and Translational Medicine, Section of Microbiology, Universityof Brescia, Brescia, Italy
| | - Alessandra Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Silvia Fabris
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Giancarlo Ceccarelli
- Dipartimento di Salute Pubblica e Malattie Infettive, Policlinico Umberto I Università‘Sapienza’, Rome, Italy
| | | | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, Universityof Brescia, Brescia, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland Baltimore, USA,Corresponding author
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy,Corresponding author
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33
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Panzera Y, Ramos N, Frabasile S, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Fuques E, Goñi N, Ramas V, Coppola L, Chiparelli H, Sorhouet C, Mogdasy C, Arbiza J, Delfraro A, Pérez R. A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay. Transbound Emerg Dis 2021; 68:3075-3082. [PMID: 33501730 PMCID: PMC8014828 DOI: 10.1111/tbed.14002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 01/20/2023]
Abstract
The analysis of genetic diversity in SARS‐CoV‐2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS‐CoV‐2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12‐nucleotide deletion in ORF7a, resulting in a 4‐amino acid in‐frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS‐CoV‐2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.
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Affiliation(s)
- Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sandra Frabasile
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Eddie Fuques
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Goñi
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Viviana Ramas
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Leticia Coppola
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Héctor Chiparelli
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Laboratorio de Biología Molecular, Mutualista Médica Uruguaya, Montevideo, Uruguay
| | - Cristina Mogdasy
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Adriana Delfraro
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Shahrajabian MH, Sun W, Cheng Q. Product of natural evolution (SARS, MERS, and SARS-CoV-2); deadly diseases, from SARS to SARS-CoV-2. Hum Vaccin Immunother 2021; 17:62-83. [PMID: 32783700 PMCID: PMC7872062 DOI: 10.1080/21645515.2020.1797369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2, the virus causing COVID-19, is a single-stranded RNA virus belonging to the order Nidovirales, family Coronaviridae, and subfamily Coronavirinae. SARS-CoV-2 entry to cellsis initiated by the binding of the viral spike protein (S) to its cellular receptor. The roles of S protein in receptor binding and membrane fusion makes it a prominent target for vaccine development. SARS-CoV-2 genome sequence analysis has shown that this virus belongs to the beta-coronavirus genus, which includes Bat SARS-like coronavirus, SARS-CoV and MERS-CoV. A vaccine should induce a balanced immune response to elicit protective immunity. In this review, we compare and contrast these three important CoV diseases and how they inform on vaccine development.
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Affiliation(s)
| | - Wenli Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- Global Alliance of HeBAU-CLS&HeQiS for BioAl-Manufacturing, Baoding, Hebei, China
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35
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Bal A, Destras G, Gaymard A, Stefic K, Marlet J, Eymieux S, Regue H, Semanas Q, d'Aubarede C, Billaud G, Laurent F, Gonzalez C, Mekki Y, Valette M, Bouscambert M, Gaudy-Graffin C, Lina B, Morfin F, Josset L. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. Euro Surveill 2021. [PMID: 33478625 DOI: 10.2807/1560-7917.es.2021.26.9.210013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69-V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.
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Affiliation(s)
- Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- These authors contributed equally to this article
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Gregory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- These authors contributed equally to this article
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Alexandre Gaymard
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- These authors contributed equally to this article
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Karl Stefic
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Julien Marlet
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Sébastien Eymieux
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Quentin Semanas
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Constance d'Aubarede
- Occupational Health and Medicine Department, Hospices Civils de Lyon, Lyon, France
| | - Geneviève Billaud
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- CIRI - Centre International de Recherche en Infectiologie, Team Pathogenesis of staphylococcal infections Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Claudia Gonzalez
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Yahia Mekki
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Maude Bouscambert
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Catherine Gaudy-Graffin
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
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Bal A, Destras G, Gaymard A, Stefic K, Marlet J, Eymieux S, Regue H, Semanas Q, d'Aubarede C, Billaud G, Laurent F, Gonzalez C, Mekki Y, Valette M, Bouscambert M, Gaudy-Graffin C, Lina B, Morfin F, Josset L. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. Euro Surveill 2021; 26:2100008. [PMID: 33478625 PMCID: PMC7848679 DOI: 10.2807/1560-7917.es.2021.26.3.2100008] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 12/19/2022] Open
Abstract
We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69-V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.
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Affiliation(s)
- Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- These authors contributed equally to this article
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Gregory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- These authors contributed equally to this article
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Alexandre Gaymard
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- These authors contributed equally to this article
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Karl Stefic
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Julien Marlet
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Sébastien Eymieux
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Quentin Semanas
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Constance d'Aubarede
- Occupational Health and Medicine Department, Hospices Civils de Lyon, Lyon, France
| | - Geneviève Billaud
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- CIRI - Centre International de Recherche en Infectiologie, Team Pathogenesis of staphylococcal infections Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Claudia Gonzalez
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Yahia Mekki
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Maude Bouscambert
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Catherine Gaudy-Graffin
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm
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Rahman MS, Hoque MN, Islam MR, Islam I, Mishu ID, Rahaman MM, Sultana M, Hossain MA. Mutational insights into the envelope protein of SARS-CoV-2. GENE REPORTS 2020; 22:100997. [PMID: 33319124 PMCID: PMC7723457 DOI: 10.1016/j.genrep.2020.100997] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023]
Abstract
The ongoing mutations in the structural proteins of SARS-CoV-2 are the major impediment for prevention and control of the COVID-19 disease. Presently we focused on evolution of the envelope (E) protein, one of the most enigmatic and less studied protein among the four structural proteins (S, E, M and N) associated with multitude of immunopathological functions of SARS-CoV-2. In the present study, we comprehensively analyzed 81,818 high quality E protein sequences of SARS-CoV-2 globally available in the GISAID database as of 20 August 2020. Compared to Wuhan reference strain, our mutational analysis explored only 1.2 % (982/81818) mutant strains undergoing a total of 115 unique amino acid (aa) substitutions in the E protein, highlighting the fact that most (98.8 %) of the E protein of SARS-CoV-2 strains are highly conserved. Moreover, we found 58.77 % (134 of 228) nucleotides (nt) positions of SARS-CoV-2 E gene encountering a total of 176 unique nt-level mutations globally, which may affect the efficacy of real time RT-PCR-based molecular detection of COVID-19. Importantly, higher aa variations observed in the C-terminal domain (CTD) of the E protein, particularly at Ser55-Phe56, Arg69 and the C-terminal end (DLLV: 72–75) may alter the binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 and thus could play a key role in COVID-19 pathogenesis. Furthermore, this study revealed the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. Our analysis also observed a triple cysteine motif harboring mutation (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. These results therefore suggest the continuous monitoring of the structural proteins including the envelope protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.
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Key Words
- CTD, C-terminal domain
- E, envelope
- Envelope protein
- M, membrane
- Mutations
- N, nucleocapsid
- NC, negatively charged
- NP, non-polar
- PC, positively charged
- S, spike
- SARS-CoV-2
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus-2
- TMD, transmembrane domain
- Transmembrane domain
- Triple cysteine motif
- aa, amino acid
- nt, nucleotide
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Affiliation(s)
- M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | | | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
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Zekri ARN, Easa Amer K, Hafez MM, Hassan ZK, Ahmed OS, Soliman HK, Bahnasy AA, Abdel Hamid W, Gad A, Ali M, Ali Hassan W, Samir Madboly M, Abdel Raouf A, Khattab AA, Salah El Din Hamdy M, Sherif Soliman M, Hamdi El Sissy M, Mohamed El Khateeb S, Hosny Ezzelarab M, Fathalla LA, Abouelhoda M. Genomic characterization of SARS-CoV-2 in Egypt. J Adv Res 2020; 30:123-132. [PMID: 33262895 PMCID: PMC7688418 DOI: 10.1016/j.jare.2020.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Introduction The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.
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Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Khaled Easa Amer
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Mohammed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Abeer A Bahnasy
- Surgical Pathology Department National Cancer Institute, Cairo University, 11796, Egypt
| | | | - Ahmad Gad
- Military Central Laboratories, Egypt
| | - Mahmoud Ali
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Wael Ali Hassan
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | | | - Ayman A Khattab
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | - May Sherif Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Maha Hamdi El Sissy
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | | | | | - Lamiaa A Fathalla
- Clinical Pathology Department, National Cancer Institute, Cairo University 11796, Egypt
| | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
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Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. Stability of SARS-CoV-2 phylogenies. PLoS Genet 2020; 16:e1009175. [PMID: 33206635 PMCID: PMC7721162 DOI: 10.1371/journal.pgen.1009175] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/07/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors associated with lab-or protocol-specific practices affect some sequences in the repositories. We find that some recurrent mutations in reported SARS-CoV-2 genome sequences have been observed predominantly or exclusively by single labs, co-localize with commonly used primer binding sites and are more likely to affect the protein-coding sequences than other similarly recurrent mutations. We show that their inclusion can affect phylogenetic inference on scales relevant to local lineage tracing, and make it appear as though there has been an excess of recurrent mutation or recombination among viral lineages. We suggest how samples can be screened and problematic variants removed, and we plan to regularly inform the scientific community with our updated results as more SARS-CoV-2 genome sequences are shared (https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473 and https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480). We also develop tools for comparing and visualizing differences among very large phylogenies and we show that consistent clade- and tree-based comparisons can be made between phylogenies produced by different groups. These will facilitate evolutionary inferences and comparisons among phylogenies produced for a wide array of purposes. Building on the SARS-CoV-2 Genome Browser at UCSC, we present a toolkit to compare, analyze and combine SARS-CoV-2 phylogenies, find and remove potential sequencing errors and establish a widely shared, stable clade structure for a more accurate scientific inference and discourse.
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Affiliation(s)
- Yatish Turakhia
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Landen Gozashti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Conor R. Walker
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Angie S. Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - Jason D. Fernandes
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States of America
| | - Rui Borges
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Greg Slodkowicz
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Lukas Weilguny
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, United States of America
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States of America
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40
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Rahman MS, Islam MR, Hoque MN, Alam ASMRU, Akther M, Puspo JA, Akter S, Anwar A, Sultana M, Hossain MA. Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Transbound Emerg Dis 2020; 68:1625-1638. [PMID: 32954666 PMCID: PMC7646266 DOI: 10.1111/tbed.13834] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/12/2020] [Accepted: 09/08/2020] [Indexed: 01/06/2023]
Abstract
Infecting millions of people, the SARS‐CoV‐2 is evolving at an unprecedented rate, demanding advanced and specified analytic pipeline to capture the mutational spectra. In order to explore mutations and deletions in the spike (S) protein — the most‐discussed protein of SARS‐CoV‐2 — we comprehensively analyzed 35,750 complete S protein‐coding sequences through a custom Python‐based pipeline. This GISAID‐collected dataset of until 24 June 2020 covered six continents and five major climate zones. We identified 27,801 (77.77% sequences) mutated strains compared to reference Wuhan‐Hu‐1 wherein 84.40% of these strains mutated by only a single amino acid (aa). An outlier strain (EPI_ISL_463893) from Bosnia and Herzegovina possessed six aa substitutions. We also identified 11 residues with high aa mutation frequency, and each contains four types of aa variations. The infamous D614G variant has spread worldwide with ever‐rising dominance and across regions with different climatic conditions alongside L5F and D936Y mutants, which have been documented throughout all regions and climate zones, respectively. We also found 988 unique aa substitutions spanned across 660 residues, which differed significantly among different continents (p = .003) and climatic zones (p = .021) as inferred with the Kruskal–Wallis test. Besides, 17 in‐frame deletions at four sites adjacent to receptor‐binding‐domain were determined that may have a possible impact on attenuation. This study provides a fast and accurate pipeline for identifying mutations and deletions from the large dataset for coding and also non‐coding sequences as evidenced by the representative analysis on existing S protein data. By using separate multi‐sequence alignment, removing ambiguous sequences and in‐frame stop codons, and utilizing pairwise alignment, this method can derive both synonymous and non‐synonymous mutations (strain_ID reference aa:mutation position:strain aa). We suggest that the pipeline will aid in the evolutionary surveillance of any SARS‐CoV‐2 encoded proteins and will prove to be crucial in tracking the ever‐increasing variation of many other divergent RNA viruses in the future. The code is available at https://github.com/SShaminur/Mutation-Analysis.
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Affiliation(s)
| | | | - Mohammad Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.,Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | | | - Masuda Akther
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Joynob Akter Puspo
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Salma Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.,Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
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41
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Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, Burfin G, Scholtes C, Morfin F, Valette M, Lina B, Bal A, Josset L. Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation. Virus Evol 2020; 6:veaa075. [PMID: 33318859 PMCID: PMC7665770 DOI: 10.1093/ve/veaa075] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (n = 8), with mNGS and RVOP producing the most complete genomes. For mid viral loads (Ct 20–25), amplicon-based enrichment methods led to genome coverage >99 per cent for all samples while 1/8 sample sequenced with RVOP and 2/8 samples sequenced with mNGS had a genome coverage below 99 per cent. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34nt-deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a loss of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer-annealing or probe-hybridizing regions and would require further validation using unbiased metagenomic sequencing.
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Affiliation(s)
- Caroline Charre
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Christophe Ginevra
- CIRI, Centre International de Recherche en Infectiologie, (Team pathogenesis of Legionella), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon 69007, France.,Hospices Civils de Lyon, Centre National de Référence des Légionelles, Lyon, France
| | - Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Solenne Brun
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Gwendolyne Burfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Caroline Scholtes
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Centre de recherche en cancérologie (CRCL), INSERM U1052- 69008, Lyon, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France.,Université de Lyon, Université Claude Bernard Lyon 1 (UCBL1), Lyon, France.,Université de Lyon, Virpath, CIRI, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, Lyon cedex 4, France
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Karamitros T, Papadopoulou G, Bousali M, Mexias A, Tsiodras S, Mentis A. SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies. J Clin Virol 2020; 131:104585. [PMID: 32818852 PMCID: PMC7418792 DOI: 10.1016/j.jcv.2020.104585] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 12/19/2022]
Abstract
In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, as well as in the design of accurate diagnostics. We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small- and large-scale intra-host variations in the viral genome. We identified tens of low- or higher- frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs (72/104) corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host as well as strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene. Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.
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Affiliation(s)
- Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece.
| | - Gethsimani Papadopoulou
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Anastasios Mexias
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Sotirios Tsiodras
- 4(th) Academic Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Andreas Mentis
- Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece
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Xiao B, Zhou Q, Lei T, He Y, Li L. [Application of laboratory diagnostic technologies for SARS-CoV-2: current progress and prospect]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:601-605. [PMID: 32895122 DOI: 10.12122/j.issn.1673-4254.2020.04.24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Since the outbreak of COVID-19 pandemic, the detection capability has been improving and the detection techniques have been evolving with innovations. qRT- PCR and mNGS, which represent the current mainstay diagnostic technologies, play key roles in disease diagnosis and monitoring of virus variation. The detection technologies based on serum and plasma IgM and IgG antibodies are important for auxiliary diagnosis. RT-LAMP is highly specific for a diagnostic purpose. Digital PCR could quantitatively detect nucleic acid and SHERLOCK has a higher sensitivity. These techniques all have great potential for future development and application for pathogen detection. In this review the authors summarize the basic rationales, technical characteristics and the current application of the SARS-CoV-2 detection techniques.
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Affiliation(s)
- Bin Xiao
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Quan Zhou
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Ting Lei
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Yongyin He
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
| | - Linhai Li
- Department of Laboratory Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, China
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Hoque MN, Chaudhury A, Akanda MAM, Hossain MA, Islam MT. Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease. PeerJ 2020; 8:e9689. [PMID: 33005486 PMCID: PMC7510477 DOI: 10.7717/peerj.9689] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by a novel evolutionarily divergent RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus first emerged in Wuhan, China in December 2019, and subsequently spreaded around the world. Genomic analyses revealed that this zoonotic virus may be evolved naturally but not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Comprehensive annotations of the whole-genomes revealed hundreds of nucleotides, and amino acids mutations, substitutions and/or deletions at different positions of the ever changing SARS-CoV-2 genome. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, cheap, rapid, and specific diagnostic tools targeting antigens or CRISPR-Cas-mediated method or a newly developed plug and play method should be available for the resource-poor developing countries. A large number of candidate drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools, and the preventive or therapeutic remedies of the COVID-19. We also discussed the future scopes for research, effective management, and surveillance of the newly emerged COVID-19 disease.
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Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md Abdul Mannan Akanda
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
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Benedetti F, Snyder GA, Giovanetti M, Angeletti S, Gallo RC, Ciccozzi M, Zella D. Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. J Transl Med 2020; 18:329. [PMID: 32867854 PMCID: PMC7457216 DOI: 10.1186/s12967-020-02507-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 08/26/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼ 30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by (a) the presence of specific amino acid residues of nsp1 and (b) the interaction between the protein and the host's small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects. METHODS A total of 17,928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER. RESULTS We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure. CONCLUSIONS Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host's gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: (i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and (ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA.,Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, USA
| | - Greg A Snyder
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA.,Department of Microbiology and Immunology, University of Maryland, Baltimore, USA
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Silvia Angeletti
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Robert C Gallo
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA.,Department of Medicine, University of Biomedical Campus, Rome, Italy.,Global Virus Network, Baltimore, USA
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.
| | - Davide Zella
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA. .,Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, USA. .,Global Virus Network, Baltimore, USA.
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Islam MR, Hoque MN, Rahman MS, Alam ASMRU, Akther M, Puspo JA, Akter S, Sultana M, Crandall KA, Hossain MA. Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity. Sci Rep 2020; 10:14004. [PMID: 32814791 PMCID: PMC7438523 DOI: 10.1038/s41598-020-70812-6] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionary divergent RNA virus, is responsible for the present devastating COVID-19 pandemic. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,516 nucleotide-level variations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide (nt) deletion analysis found twelve deletion sites throughout the genome other than previously reported deletions at coding sequence of the ORF8 (open reading frame), spike, and ORF7a proteins, specifically in polyprotein ORF1ab (n = 9), ORF10 (n = 1), and 3´-UTR (n = 2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n = 744), demonstrating the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) showing crucial interactions with angiotensin-converting enzyme 2 (ACE2) and cross-reacting neutralizing antibody were found to be conserved among the analyzed virus strains, except for replacement of lysine with arginine at 378th position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Furthermore, our results of the preliminary epidemiological data on SARS-CoV-2 infections revealed that frequency of aa mutations were relatively higher in the SARS-CoV-2 genome sequences of Europe (43.07%) followed by Asia (38.09%), and North America (29.64%) while case fatality rates remained higher in the European temperate countries, such as Italy, Spain, Netherlands, France, England and Belgium. Thus, the present method of genome annotation employed at this early pandemic stage could be a promising tool for monitoring and tracking the continuously evolving pandemic situation, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategies.
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Affiliation(s)
- M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Masuda Akther
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - J Akter Puspo
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Salma Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, USA
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
- Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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Surleac M, Banica L, Casangiu C, Cotic M, Florea D, Sandulescu O, Milu P, Streinu-Cercel A, Vlaicu O, Paraskevis D, Paraschiv S, Otelea D. Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. Life (Basel) 2020; 10:life10080152. [PMID: 32823907 PMCID: PMC7460100 DOI: 10.3390/life10080152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The spread of SARS-CoV-2 generated an unprecedented global public health crisis. Soon after Asia, Europe was seriously affected. Many countries, including Romania, adopted lockdown measures to limit the outbreak. AIM We performed a molecular epidemiology analysis of SARS-CoV-2 viral strains circulating in Romania during the first two months of the epidemic in order to detect mutation profiles and phylogenetic relatedness. METHODS Respiratory samples were directly used for shotgun sequencing. RESULTS All Romanian sequences belonged to lineage B, with a different subtype distribution between northern and southern regions (subtype B.1.5 and B.1.1). Phylogenetic analysis suggested that the Romanian epidemic started with multiple introduction events from other European countries followed by local transmission. Phylogenetic links between northern Romania and Spain, Austria, Scotland and Russia were observed, as well as between southern Romania and Switzerland, Italy, France and Turkey. One viral strain presented a previously unreported mutation in the Nsp2 gene, namely K489E. Epidemiologically-defined clusters displayed specific mutations, suggesting molecular signatures for strains coming from areas that were isolated during the lockdown. CONCLUSIONS Romanian epidemic was initiated by multiple introductions from European countries followed by local transmissions. Different subtype distribution between northern and southern Romania was observed after two months of the pandemic.
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Affiliation(s)
- Marius Surleac
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
- Institute of Biochemistry, Romanian Academy, 060031 Bucharest, Romania
| | - Leontina Banica
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
| | - Corina Casangiu
- “Marie Curie” Emergency Clinical Hospital, 077120 Bucharest, Romania;
| | - Marius Cotic
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
| | - Dragos Florea
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
- “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Oana Sandulescu
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
- “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Petre Milu
- “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Anca Streinu-Cercel
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
- “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Ovidiu Vlaicu
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
| | - Dimitrios Paraskevis
- National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Faculty of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Simona Paraschiv
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
- “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania;
- Correspondence: ; Tel.: +40-212010980 (ext. 3085); Fax: +40-213186090
| | - Dan Otelea
- “Prof. Dr. Matei Bals” National Institute for Infectious Diseases, 021105 Bucharest, Romania; (M.S.); (L.B.); (M.C.); (D.F.); (O.S.); (A.S.-C.); (O.V.); (D.O.)
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Tabibzadeh A, Zamani F, Laali A, Esghaei M, Safarnezhad Tameshkel F, Keyvani H, Jamshidi Makiani M, Panahi M, Motamed N, Perumal D, Khoonsari M, Ajdarkosh H, Sohrabi M, Ghanbari B, Savaj S, Mosavi-Jarrahi A, Karbalaie Niya MH. SARS-CoV-2 Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran. INFECTION GENETICS AND EVOLUTION 2020; 84:104387. [PMID: 32485332 PMCID: PMC7832360 DOI: 10.1016/j.meegid.2020.104387] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022]
Abstract
Background The aim of the current study was to investigate and track the SARS-CoV-2 in Iranian Coronavirus Disease 2019 (COVID-19) patients using molecular and phylogenetic methods. Methods We enrolled seven confirmed cases of COVID-19 patients for the phylogenetic assessment of the SARS-CoV-2 in Iran. The nsp-2, nsp-12, and S genes were amplified using one-step RT-PCR and sequenced using Sanger sequencing method. Popular bioinformatics software were used for sequences alignment and analysis as well as phylogenetic construction. Results The mean age of the patients in the present study was 60.42 ± 9.94 years and 57.1% (4/7) were male. The results indicated high similarity between Iranian and Chinese strains. We could not find any particular polymorphisms in the assessed regions of the three genes. Phylogenetic trees by neighbor-joining and maximum likelihood method of nsp-2, nsp-12, and S genes showed that there are not any differences between Iranian isolates and those of other countries. Conclusion As a preliminary phylogenetic study in Iranian SARS-CoV-2 isolates, we found that these isolates are closely related to the Chinese and reference sequences. Also, no sensible differences were observed between Iranian isolates and those of other countries. Further investigations are recommended using more comprehensive methods and larger sample sizes. SARS-2 genome showed one genetic pattern. Iran has the same sequence of SARS-2 like other countries isolates. SNPs in nsp-2 did not show any polymorphisms between this study isolates and other countries.
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Affiliation(s)
- Alireza Tabibzadeh
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Farhad Zamani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Azadeh Laali
- Antimicrobial Resistant Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Esghaei
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Keyvani
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran; Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahin Jamshidi Makiani
- Antimicrobial Resistant Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mahshid Panahi
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Pathology, Iran University of Medical Sciences, Tehran, Iran
| | - Nima Motamed
- Department of Social Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Dhayaneethie Perumal
- Faculty of Science, Engineering and Computing, Kingston University, Kingston, United Kingdom
| | - Mahmoodreza Khoonsari
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Ajdarkosh
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Masuodreza Sohrabi
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Behrooz Ghanbari
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Shokoufeh Savaj
- Department of Nephrology, Firoozgar Hospital, Iran University of Medical Science, Tehran, Iran
| | | | - Mohammad Hadi Karbalaie Niya
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran; Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
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