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Chen J, Xu F. Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections. Mol Diagn Ther 2023; 27:685-701. [PMID: 37563539 PMCID: PMC10590290 DOI: 10.1007/s40291-023-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
This review provides an in-depth discussion of the development, principles and utility of nanopore sequencing technology and its diverse applications in the identification of various pulmonary pathogens. We examined the emergence and advancements of nanopore sequencing as a significant player in this field. We illustrate the challenges faced in diagnosing mixed infections and further scrutinize the use of nanopore sequencing in the identification of single pathogens, including viruses (with a focus on its use in epidemiology, outbreak investigation, and viral resistance), bacteria (emphasizing 16S targeted sequencing, rare bacterial lung infections, and antimicrobial resistance studies), fungi (employing internal transcribed spacer sequencing), tuberculosis, and atypical pathogens. Furthermore, we discuss the role of nanopore sequencing in metagenomics and its potential for unbiased detection of all pathogens in a clinical setting, emphasizing its advantages in sequencing genome repeat areas and structural variant regions. We discuss the limitations in dealing with host DNA removal, the inherent high error rate of nanopore sequencing technology, along with the complexity of operation and processing, while acknowledging the possibilities provided by recent technological improvements. We compared nanopore sequencing with the BioFire system, a rapid molecular diagnostic system based on polymerase chain reaction. Although the BioFire system serves well for the rapid screening of known and common pathogens, it falls short in the identification of unknown or rare pathogens and in providing comprehensive genome analysis. As technological advancements continue, it is anticipated that the role of nanopore sequencing technology in diagnosing and treating lung infections will become increasingly significant.
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Affiliation(s)
- Jie Chen
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
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2
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de Lima TM, Martins RB, Miura CS, Souza MVO, Cassiano MHA, Rodrigues TS, Veras FP, Sousa JDF, Gomes R, de Almeida GM, Melo SR, da Silva GC, Dias M, Capato CF, Silva ML, Luiz VEDDB, Carenzi LR, Zamboni DS, Jorge DMDM, Cunha FDQ, Tamashiro E, Anselmo-Lima WT, Valera FCP, Arruda E. Tonsils are major sites of persistence of SARS-CoV-2 in children. Microbiol Spectr 2023; 11:e0134723. [PMID: 37737615 PMCID: PMC10581087 DOI: 10.1128/spectrum.01347-23] [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: 04/01/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
In the present study, we show that SARS-CoV-2 can infect palatine tonsils, adenoids, and secretions in children without symptoms of COVID-19, with no history of recent upper airway infection. We studied 48 children undergoing tonsillectomy due to snoring/OSA or recurrent tonsillitis between October 2020 and September 2021. Nasal cytobrushes, nasal washes, and tonsillar tissue fragments obtained at surgery were tested by RT-qPCR, immunohistochemistry (IHC), flow cytometry, and neutralization assay. We detected the presence of SARS-CoV-2 in at least one specimen tested in 27% of patients. IHC revealed the presence of the viral nucleoprotein in epithelial surface and in lymphoid cells in both extrafollicular and follicular regions, in adenoids and palatine tonsils. Also, IHC for the SARS-CoV-2 non-structural protein NSP-16 indicated the presence of viral replication in 53.8% of the SARS-CoV-2-infected tissues. Flow cytometry showed that CD20+ B lymphocytes were the most infected phenotypes, followed by CD4+ lymphocytes and CD123 dendritic cells, CD8+ T lymphocytes, and CD14+ macrophages. Additionally, IF indicated that infected tonsillar tissues had increased expression of ACE2 and TMPRSS2. NGS sequencing demonstrated the presence of different SARS-CoV-2 variants in tonsils from different tissues. SARS-CoV-2 antigen detection was not restricted to tonsils but was also detected in nasal cells from the olfactory region. Palatine tonsils and adenoids are sites of prolonged RNA presence by SARS-CoV-2 in children, even without COVID-19 symptoms. IMPORTANCE This study shows that SRS-CoV-2 of different lineages can infect tonsils and adenoids in one quarter of children undergoing tonsillectomy. These findings bring advancement to the area of SARS-CoV-2 pathogenesis, by showing that tonsils may be sites of prolonged infection, even without evidence of recent COVID-19 symptoms. SARS-CoV-2 infection of B and T lymphocytes, macrophages, and dendritic cells may interfere with the mounting of immune responses in these secondary lymphoid organs. Moreover, the shedding of SARS-CoV-2 RNA in respiratory secretions from silently infected children raises concern about possible diagnostic confusion in the presence of symptoms of acute respiratory infections caused by other etiologies.
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Affiliation(s)
- Thais Melquiades de Lima
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Ronaldo Bragança Martins
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
- Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo School of Pharmaceutical Sciences, Ribeirão Preto, São Paulo, Brazil
| | - Carolina Sponchiado Miura
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Maria Vitória Oliveira Souza
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Murilo Henrique Anzolini Cassiano
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Tamara Silva Rodrigues
- Department of Biochemistry and Immunology, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Flávio Protásio Veras
- Department of BioMolecular Sciences, University of São Paulo School of Pharmaceutical Sciences, Ribeirão Preto, São Paulo, Brazil
| | - Josane de Freitas Sousa
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Rogério Gomes
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Glaucia Maria de Almeida
- Department of Biochemistry and Immunology, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Stella Rezende Melo
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Gabriela Condé da Silva
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Matheus Dias
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Carlos Fabiano Capato
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Maria Lúcia Silva
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Veridiana Ester Dias de Barros Luiz
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Lucas Rodrigues Carenzi
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Dario Simões Zamboni
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
- Department of Biochemistry and Immunology, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Macedo de Melo Jorge
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Fernando de Queiroz Cunha
- Department of Pharmacology, University of Sao Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Edwin Tamashiro
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Wilma Terezinha Anselmo-Lima
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Fabiana Cardoso Pereira Valera
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
| | - Eurico Arruda
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, University of São Paulo School of Medicine, Ribeirão Preto, São Paulo, Brazil
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3
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Tomar SS, Khairnar K. Challenges of SARS-CoV-2 genomic surveillance in India during low positivity rate scenario. Front Public Health 2023; 11:1117602. [PMID: 37441634 PMCID: PMC10335399 DOI: 10.3389/fpubh.2023.1117602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Being the second most populous country in the world, India presents valuable lessons for the world about dealing with the SARS-CoV-2 pandemic. From this perspective, we attempted a retrospective evaluation of India's SARS-CoV-2 genomic surveillance strategy and also gave some recommendations for undertaking effective genomic surveillance. The dynamics of the COVID-19 pandemic are continuously evolving, and there is a dire need to modulate the genomic surveillance strategy accordingly. The pandemic is now settling towards a low positivity rate scenario, so it is required to revise the practices and policies formulated for a high positivity rate scenario. The perspective also recommends adopting a decentralised approach for SARS-CoV-2 genomic surveillance with a focus on optimising the workflow of SARS-CoV-2 genomic surveillance to ensure early detection of emerging variants, especially in the low positivity rate scenario. The perspective emphasises a key observation that the SARS-CoV-2 genomic surveillance is an important mitigation effort during the pandemic, the guards of such mitigation efforts should not be lowered during the low positivity rate scenario. We attempt to highlight the limitations faced by the Indian healthcare administration during the SARS-CoV-2 genomic surveillance and, simultaneously, suggest policy interventions derived from our first-hand experience, which may be implementable in a vast, populated country like India.
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Affiliation(s)
- Siddharth Singh Tomar
- Environmental Virology Cell (EVC), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Krishna Khairnar
- Environmental Virology Cell (EVC), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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4
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Bosmeny MS, White AA, Pater AA, Crew J, Geltz J, Gagnon KT. Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing. Virol J 2023; 20:90. [PMID: 37149667 PMCID: PMC10163848 DOI: 10.1186/s12985-023-02059-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 05/08/2023] Open
Abstract
Insufficient tracking of virus introduction, spread, and new lineage emergence for the human monkeypox (mpox) virus 1 (hMPXV1) outbreak of 2022 hindered epidemiological studies and public health response. hMPXV1 mutations accumulated unexpectedly faster than predicted. Thus, new variants with altered pathogenicity could emerge and spread without early detection. Whole genome sequencing addresses this gap when implemented but requires widely accessible and standardized methodologies to be effective both regionally and globally. Here we developed a rapid nanopore whole genome sequencing method complete with working protocols, from DNA extraction to phylogenetic analysis tools. Using this method, we sequenced 84 complete hMPXV1 genomes from Illinois, a Midwestern region of the United States, spanning the first few months of the outbreak. The resulting five-fold increase in hMPXV1 genomes from this region established two previously unnamed global lineages, several mutational profiles not seen elsewhere, multiple separate introductions of the virus into the region, and the likely emergence and spread of new lineages from within this region. These results demonstrate that a dearth of genomic sequencing of hMPXV1 slowed our understanding and response to the mpox outbreak. This accessible nanopore sequencing approach makes near real-time mpox tracking and rapid lineage discovery straightforward and creates a blueprint for how to deploy nanopore sequencing for genomic surveillance of diverse viruses and future outbreaks.
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Affiliation(s)
- Michael S Bosmeny
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Adam A White
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA
| | - Jennifer Crew
- Illinois Department of Public Health, Springfield, IL, USA
| | - Joshua Geltz
- Illinois Department of Public Health, Springfield, IL, USA
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, USA.
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL, USA.
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Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Front Bioeng Biotechnol 2022; 10:1052436. [PMID: 36507266 PMCID: PMC9732709 DOI: 10.3389/fbioe.2022.1052436] [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: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.
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Affiliation(s)
- Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Romina Cabrera-Rodriguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Silvia Perez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Judith Estevez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- Departamento de Análisis Matemático, Facultad de Ciencias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Helena Gil-Campesino
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Oscar Díez-Gil
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Jonay Garcia-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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6
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Madi N, Sadeq M, Essa S, Safar HA, Al-Adwani A, Al-Khabbaz M. Strain Variation Based on Spike Glycoprotein Gene of SARS-CoV-2 in Kuwait from 2020 to 2021. Pathogens 2022; 11:pathogens11090985. [PMID: 36145416 PMCID: PMC9505955 DOI: 10.3390/pathogens11090985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), which was first identified in Wuhan, China, in December 2019. With the global transmission of the virus, many SARS-CoV-2 variants have emerged due to the alterations of the spike glycoprotein. Therefore, the S glycoprotein encoding gene has widely been used for the molecular analysis of SARS-Co-2 due to its features affecting antigenicity and immunogenicity. We analyzed the S gene sequences of 35 SARS-CoV-2 isolates in Kuwait from March 2020 to February 2021 using the Sanger method and MinION nanopore technology to confirm novel nucleotide alterations. Our results show that the Kuwaiti strains from clade 19A and B were the dominant variants early in the pandemic, while clade 20I (Alpha, V1) was the dominant variant from February 2021 onward. Besides the known mutations, 21 nucleotide deletions in the S glycoprotein in one Kuwaiti strain were detected, which might reveal a recombinant SARS-CoV-2 with the defective viral genome (DVG). This study emphasizes the importance of closely perceiving the emerging clades with these mutations during this continuous pandemic as some may influence the specificity of diagnostic tests, such as RT-PCR and even vaccine design directing these positions.
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Affiliation(s)
- Nada Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
- Correspondence: ; Tel.: +965-99736265; Fax: +965-25332719
| | - Mohammad Sadeq
- Jaber Al-Ahmad Armed Forces Hospital, Sabhan 91710, Kuwait
| | - Sahar Essa
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Hussain A. Safar
- Research Core Facility and OMICS Research Unit, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Anfal Al-Adwani
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
| | - Marwa Al-Khabbaz
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
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Madi N, Safar HA, Mustafa AS, Chehadeh W, Asadzadeh M, Sadeq M, Alawadhi E, Al-Muhaini A, Benthani FA. Molecular epidemiology and genetic characterization of SARS-CoV-2 in Kuwait: A descriptive study. Front Microbiol 2022; 13:858770. [PMID: 36090111 PMCID: PMC9459148 DOI: 10.3389/fmicb.2022.858770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been fatal to human health, affecting almost the entire world. Here we reported, for the first time, characterization of the genetic variants of SARS-CoV-2 circulating in Kuwait to understand their genetic diversity and monitor the accumulation of mutations over time. This study randomly enrolled 209 COVID-19 patients whose nasopharyngeal swabs were positive for SARS-CoV-2 between February 2020 and June 2021 using RT-PCR. The whole genomes of SARS-CoV-2 from the nasopharyngeal swabs were sequenced using the Oxford Nanopore sequencing technology following the ARTIC network protocol. Whole-genome sequencing has identified different clades/sub-clades circulating in Kuwait, mimicking the virus’s global spread. Clade 20A was dominant from February 2020 until January 2021, and then clade 20I (Alpha, V1) emerged and dominated. In June 2021, the number of cases infected with clades 21I, 21A, and 21 J (Delta) increased and dominated. We detected several known clade-defining missense and synonymous mutations and other missense mutations in the genes encoding important viral proteins, including ORF1a, S, ORF3a, ORF8 regions and a novel mutation in the N region. ORF1ab region harbored more mutations and deletions (n = 62, 49.2%) compared to the other 12 gene regions, and the most prevalent missense mutations were P314L (97%) in ORF1b and D614G (97%) in the S glycoprotein regions. Detecting and analyzing mutations and monitoring the evolution of SARS-CoV-2 over time is essential to help better understand the spread of various clades/strains of SARS-CoV-2 and their implications for pathogenesis. In addition, knowledge of the circulating variants and genome sequence variability of SARS-CoV-2 may potentially influence the development of vaccines and antiviral drugs to control the COVID-19 pandemic.
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Affiliation(s)
- Nada Madi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
- *Correspondence: Nada Madi,
| | - Hussain A. Safar
- OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | - Mohammad Asadzadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait, Kuwait
| | | | - Ebaa Alawadhi
- Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Ali Al-Muhaini
- Jaber Al-Ahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Fahad A. Benthani
- Research Institute for Developmental Medicine, Johannes Kepler University of Linz, Linz, Austria
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8
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Barbé L, Schaeffer J, Besnard A, Jousse S, Wurtzer S, Moulin L, Le Guyader FS, Desdouits M. SARS-CoV-2 Whole-Genome Sequencing Using Oxford Nanopore Technology for Variant Monitoring in Wastewaters. Front Microbiol 2022; 13:889811. [PMID: 35756003 PMCID: PMC9218694 DOI: 10.3389/fmicb.2022.889811] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 01/21/2023] Open
Abstract
Since the beginning of the Coronavirus Disease-19 (COVID-19) pandemic, multiple Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mutations have been reported and led to the emergence of variants of concern (VOC) with increased transmissibility, virulence or immune escape. In parallel, the observation of viral fecal shedding led to the quantification of SARS-CoV-2 genomes in wastewater, providing information about the dynamics of SARS-CoV-2 infections within a population including symptomatic and asymptomatic individuals. Here, we aimed to adapt a sequencing technique initially designed for clinical samples to apply it to the challenging and mixed wastewater matrix, and hence identify the circulation of VOC at the community level. Composite raw sewage sampled over 24 h in two wastewater-treatment plants (WWTPs) from a city in western France were collected weekly and SARS-CoV-2 quantified by RT-PCR. Samples collected between October 2020 and May 2021 were submitted to whole-genome sequencing (WGS) using the primers and protocol published by the ARTIC Network and a MinION Mk1C sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom). The protocol was adapted to allow near-full genome coverage from sewage samples, starting from ∼5% to reach ∼90% at depth 30. This enabled us to detect multiple single-nucleotide variant (SNV) and assess the circulation of the SARS-CoV-2 VOC Alpha, Beta, Gamma, and Delta. Retrospective analysis of sewage samples shed light on the emergence of the Alpha VOC with detection of first co-occurring signature mutations in mid-November 2020 to reach predominance of this variant in early February 2021. In parallel, a mutation-specific qRT-PCR assay confirmed the spread of the Alpha VOC but detected it later than WGS. Altogether, these data show that SARS-CoV-2 sequencing in sewage can be used for early detection of an emerging VOC in a population and confirm its ability to track shifts in variant predominance.
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Affiliation(s)
- Laure Barbé
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | - Sarah Jousse
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
| | | | - Laurent Moulin
- R&D Laboratory, DRDQE, Eau de Paris, Ivry-sur-Seine, France
| | | | | | - Marion Desdouits
- Laboratoire de Microbiologie (LSEM, Unité MASAE), IFREMER, Nantes, France
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9
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Wang Y, Chen D, Zhu C, Zhao Z, Gao S, Gou J, Guo Y, Kong X. Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing. Front Immunol 2022; 13:814806. [PMID: 35444655 PMCID: PMC9013895 DOI: 10.3389/fimmu.2022.814806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread and poses a major threat to public health worldwide. The whole genome sequencing plays a crucial role in virus surveillance and evolutionary analysis. In this study, five genome sequences of SARS-CoV-2 were obtained from nasopharyngeal swab samples from Zhengzhou, China. Following RNA extraction and cDNA synthesis, multiplex PCR was performed with two primer pools to produce the overlapped amplicons of ~1,200 bp. The viral genomes were obtained with 96% coverage using nanopore sequencing. Forty-five missense nucleotide mutations were identified; out of these, 5 mutations located at Nsp2, Nsp3, Nsp14, and ORF10 genes occurred with a <0.1% frequency in the global dataset. On the basis of mutation profiles, five genomes were clustered into two sublineages (B.1.617.2 and AY.31) or subclades (21A and 21I). The phylogenetic analysis of viral genomes from several regions of China and Myanmar revealed that five patients had different viral transmission chains. Taken together, we established a nanopore sequencing platform for genetic surveillance of SARS-CoV-2 and identified the variants circulating in Zhengzhou during August 2021. Our study provided crucial support for government policymaking and prevention and control of COVID-19.
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Affiliation(s)
- Yanan Wang
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duo Chen
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chaofeng Zhu
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshan Gao
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianjun Gou
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongjun Guo
- Department of Pathology, Henan Academy of Medical Sciences, Zhengzhou, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Prasetyoputri A, Dharmayanthi AB, Iryanto SB, Andriani A, Nuryana I, Wardiana A, Ridwanuloh AM, Swasthikawati S, Hariyatun H, Nugroho HA, Idris I, Indriawati I, Noviana Z, Oktavia L, Yuliawati Y, Masrukhin M, Hasrianda EF, Sukmarini L, Fahrurrozi F, Yanthi ND, Fathurahman AT, Wulandari AS, Setiawan R, Rizal S, Fathoni A, Kusharyoto W, Lisdiyanti P, Ningrum RA, Saputra S. The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. PeerJ 2022; 10:e13132. [PMID: 35341058 PMCID: PMC8953504 DOI: 10.7717/peerj.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/26/2022] [Indexed: 01/12/2023] Open
Abstract
Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.
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Affiliation(s)
- Anggia Prasetyoputri
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Anik B. Dharmayanthi
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Syam B. Iryanto
- Research Center for Informatics, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ade Andriani
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Isa Nuryana
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Andri Wardiana
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Asep M. Ridwanuloh
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Sri Swasthikawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Hariyatun Hariyatun
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Herjuno A. Nugroho
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Idris Idris
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Indriawati Indriawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Zahra Noviana
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Listiana Oktavia
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Yuliawati Yuliawati
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Masrukhin Masrukhin
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Erwin F. Hasrianda
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Linda Sukmarini
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Fahrurrozi Fahrurrozi
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Nova Dilla Yanthi
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Alfi T. Fathurahman
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ari S. Wulandari
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ruby Setiawan
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Syaiful Rizal
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ahmad Fathoni
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Wien Kusharyoto
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Ratih A. Ningrum
- Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia
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11
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Gagnon KT, Huang V. Special issue editorial: Methods to facilitate SARS-CoV-2 and COVID-19 research. J Biol Methods 2022; 8:e157. [PMID: 35036458 PMCID: PMC8753996 DOI: 10.14440/jbm.2021.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Keith T Gagnon
- Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Vera Huang
- Deputy Editor of JBM, San Francisco, CA 94131, USA
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