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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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2
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Djorwé S, Bousfiha A, Nzoyikorera N, Nkurunziza V, Ait Mouss K, Kawthar B, Malki A. Epidemiology, clinical characteristics and risk factors of coronavirus disease 2019 (COVID-19) in Casablanca. Access Microbiol 2023; 5:acmi000400. [PMID: 37223059 PMCID: PMC10202397 DOI: 10.1099/acmi.0.000400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/20/2023] [Indexed: 05/25/2023] Open
Abstract
This is an analytical cross-sectional study of coronavirus disease 2019 (COVID-19) based on data collected between 1 November 2020 and 31 March 2021 in Casablanca focusing on the disease's epidemiological status and risk factors. A total of 4569 samples were collected and analysed by reverse-transcription polymerase chain reaction (RT-PCR); 967 patients were positive, representing a prevalence of 21.2 % for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The mean age was 47.5±18 years, and infection was more common in young adults (<60 years). However, all age groups were at risk of COVID-19, and in terms of disease severity, the elderly were at greater risk because of potential underlying health problems. Among the clinical signs reported in this study, loss of taste and/or smell, fever, cough and fatigue were highly significant predictors of a positive COVID-19 test result (P<0.001). An assessment of the reported symptoms revealed that 27 % of COVID-19-positive patients (n=261) experienced loss of taste and/or smell, whereas only 2 % (n=72) of COVID-19-negative patients did (P<0.001). This result was consistent between univariate (OR=18.125) and multivariate (adjusted OR=10.484) logistic regression analyses, indicating that loss of taste and/or smell is associated with a more than 10-fold higher multivariate adjusted probability of a positive COVID-19 test (adjusted OR=10.48; P<0.001). Binary logistic regression model analysis based on clinical signs revealed that loss of taste and/or smell had a performance index of 0.846 with a P<0.001, confirming the diagnostic utility of this symptom for the prediction of COVID-19-positive status. In conclusion, symptom evaluation and a RT-PCR [taking into account cycle threshold (C t) values of the PCR proxy] test remain the most useful screening tools for diagnosing COVID-19. However, loss of taste/smell, fatigue, fever and cough remain the strongest independent predictors of a positive COVID-19 result.
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Affiliation(s)
- Soulandi Djorwé
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, PB 7955 Sidi Othman Casablanca, Morocco
- Bourgogne Laboratory of Medical and Scientific Analysis, 136, Residence Belhcen, Bd Bourgogne, Casablanca, Morocco
| | - Amale Bousfiha
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, PB 7955 Sidi Othman Casablanca, Morocco
| | - Néhémie Nzoyikorera
- National Reference Laboratory, National Institute of Public Health, Bujumbura, Burundi
- Higher Institute of Biosciences and Biotechnology, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
- Laboratory of Microbial Biotechnology and Infectiology Research, Mohammed VI Center for Research & Innovation, Rabat, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Victor Nkurunziza
- Laboratory of Hematology, University Hospital Centre Ibn Rochd, 1, Rue des Hôpitaux, 20100, Casablanca, Morocco
| | - Khadija Ait Mouss
- Department of Microbiology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, 19 rue Tarik Bnou Zyad, 20360, Casablanca, Morocco
| | - Bellamine Kawthar
- Bourgogne Laboratory of Medical and Scientific Analysis, 136, Residence Belhcen, Bd Bourgogne, Casablanca, Morocco
| | - Abderrahim Malki
- Laboratory of Physiopathology and Molecular Genetics, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca (Morocco), Avenue Cdt Driss El Harti, PB 7955 Sidi Othman Casablanca, Morocco
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De R, Dutta S. Role of the Microbiome in the Pathogenesis of COVID-19. Front Cell Infect Microbiol 2022; 12:736397. [PMID: 35433495 PMCID: PMC9009446 DOI: 10.3389/fcimb.2022.736397] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
The ongoing pandemic coronavirus disease COVID-19 is caused by the highly contagious single-stranded RNA virus, SARS-coronavirus 2 (SARS-CoV-2), which has a high rate of evolution like other RNA viruses. The first genome sequences of SARS-CoV-2 were available in early 2020. Subsequent whole-genome sequencing revealed that the virus had accumulated several mutations in genes associated with viral replication and pathogenesis. These variants showed enhanced transmissibility and infectivity. Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide. Thereafter, several variants emerged, which were found to harbor mutations in essential viral genes encoding proteins that could act as drug and vaccine targets. Numerous vaccines have been successfully developed to assuage the burden of COVID-19. These have different rates of efficacy, including, although rarely, a number of vaccinated individuals exhibiting side effects like thrombosis. However, the recent emergence of the Britain strain with 70% more transmissibility and South African variants with higher resistance to vaccines at a time when several countries have approved these for mass immunization has raised tremendous concern regarding the long-lasting impact of currently available prophylaxis. Apart from studies addressing the pathophysiology, pathogenesis, and therapeutic targets of SARS-CoV-2, analysis of the gut, oral, nasopharyngeal, and lung microbiome dysbiosis has also been undertaken to find a link between the microbiome and the pathogenesis of COVID-19. Therefore, in the current scenario of skepticism regarding vaccine efficacy and challenges over the direct effects of currently available drugs looming large, investigation of alternative therapeutic avenues based on the microbiome can be a rewarding finding. This review presents the currently available understanding of microbiome dysbiosis and its association with cause and consequence of COVID-19. Taking cues from other inflammatory diseases, we propose a hypothesis of how the microbiome may be influencing homeostasis, pro-inflammatory condition, and the onset of inflammation. This accentuates the importance of a healthy microbiome as a protective element to prevent the onset of COVID-19. Finally, the review attempts to identify areas where the application of microbiome research can help in reducing the burden of the disease.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkota, India
- Division of Immunology, National Institute of Cholera and Enteric Diseases, Kolkota, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkota, India
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A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients. Life (Basel) 2021; 11:life11111224. [PMID: 34833100 PMCID: PMC8620851 DOI: 10.3390/life11111224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Since its first detection in December 2019, more than 232 million cases of COVID-19, including 4.7 million deaths, have been reported by the WHO. The SARS-CoV-2 viral genomes have evolved rapidly worldwide, causing the emergence of new variants. This systematic review and meta-analysis was conducted to provide a global mutational profile of SARS-CoV-2 from December 2019 to October 2020. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA), and a study protocol was lodged with PROSPERO. Data from 62 eligible studies involving 368,316 SARS-CoV-2 genomes were analyzed. The mutational data analyzed showed most studies detected mutations in the Spike protein (n = 50), Nucleocapsid phosphoprotein (n = 34), ORF1ab gene (n = 29), 5′-UTR (n = 28) and ORF3a (n = 25). Under the random-effects model, pooled prevalence of SARS-CoV-2 variants was estimated at 95.1% (95% CI; 93.3–96.4%; I2 = 98.952%; p = 0.000) while subgroup meta-analysis by country showed majority of the studies were conducted ‘Worldwide’ (n = 10), followed by ‘Multiple countries’ (n = 6) and the USA (n = 5). The estimated prevalence indicated a need to continuously monitor the prevalence of new mutations due to their potential influence on disease severity, transmissibility and vaccine effectiveness.
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Yang S, Pan X, Yuan D, Zeng P, Jia P. Cross-disciplinary approaches to assist with nucleic acid testing for SARS-CoV-2. Appl Microbiol Biotechnol 2021; 105:6291-6299. [PMID: 34423408 PMCID: PMC8380513 DOI: 10.1007/s00253-021-11498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/28/2022]
Abstract
Improving the capacity of detecting positive severe acute respiratory syndrome coronavirus 2 is critical for identifying the infection of coronavirus disease 2019 (COVID-19) precisely and thereby curbing the pandemic. Cross-disciplinary approaches may improve the efficiency of COVID-19 diagnosis by compensating to some extent the limitations encountered by traditional test methods during the COVID-19 pandemic. Combining computed tomography (CT), serum-specific antibody detection, and nanopore sequencing with nucleic acid testing for individual testing may improve the accuracy of identifying COVID-19 patients. At community or even regional/national levels, the combination of pooled screening and spatial epidemiological strategies may enable the detection of early transmission of epidemics in a cost-effective way, which is also less affected by restricted access to diagnostic tests and kit supplies. This would significantly advance our capacity of curbing epidemics as soon as possible, and better prepare us for entering a new era of high-impact and high-frequency epidemics.
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Affiliation(s)
- Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China
| | - Xiongfeng Pan
- International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China
- Xiangya School of Public Health, Central South University, Changsha, China
| | - Dan Yuan
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Peibin Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
| | - Peng Jia
- International Institute of Spatial Lifecourse Epidemiology (ISLE), Wuhan University, Wuhan, China.
- School of Resources and Environmental Science, Wuhan University, Wuhan, China.
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Ouadghiri M, Aanniz T, Essabbar A, Seffar M, Kabbaj H, El Amin G, Zouaki A, Amzazi S, Belyamani L, Ibrahimi A. Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. Microbiol Resour Announc 2021; 10:e00240-21. [PMID: 33888505 PMCID: PMC8063648 DOI: 10.1128/mra.00240-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022] Open
Abstract
Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.
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Affiliation(s)
- Mouna Ouadghiri
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelomunim Essabbar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Myriam Seffar
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Hakima Kabbaj
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Ghizlane El Amin
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Amal Zouaki
- Laboratoire Central de Virologie, Centre Hospitalo-Universitaire Ibn Sina, Hôpital des Spécialités, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
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First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. Microbiol Resour Announc 2021; 10:10/11/e00027-21. [PMID: 33737349 PMCID: PMC7975867 DOI: 10.1128/mra.00027-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys). We report the nearly complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) collected from a nasopharyngeal swab specimen from a male patient from Harhoura-Rabat, Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys).
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