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Chandy S, Kumar H, Pearl S, Basu S, M G, Sankar J, Manoharan A, Ramaiah S, Anbarasu A. Whole genome analysis reveals unique traits of SARS-CoV-2 in pediatric patients. Gene 2024; 919:148508. [PMID: 38670399 DOI: 10.1016/j.gene.2024.148508] [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: 02/27/2024] [Revised: 04/10/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to challenge the global healthcare with emerging variants and higher infectivity as well as morbidities. This study investigated potential age-related variations through genomic characterization of the virus under common clinical settings. A cohort comprising 71 SARS-CoV-2 strains from both infected infants and accompanying adults, diagnosed via RT-PCR at a tertiary pediatric hospital and research center, underwent Illumina paired-end sequencing. The subsequent analysis involved standard genomic screening, phylogeny construction, and mutational analyses. The analyzed SARSCoV- 2 strains were compared with globally circulating variants. The overall distribution revealed 67.61 % Delta, 25.7 % Omicron, and 1 % either Kappa or Alpha variants. In 2021, Delta predominated at ∼ 94 %, with Alpha/Kappa accounting for around 5 %. However, in 2022, over 94 % of the samples were Omicron variants, signifying a substantial shift from Delta dominance. Delta variants constituted 69.5 % of infections in adults and 78.5 % in infants, while Omicron variants were responsible for 31 % of cases in infants and 18 % in adults. The Spike region harbored the majority of mutations, with T19R being the most prevalent mutation in the Delta lineage. Notably, the frequencies of this mutation varied between infants and adults. In Omicron samples, G142D emerged as the most prevalent mutation. Our dataset predominantly featured clade 21A and lineage B.1.617.2. This study underscores the differential clinical presentations and genomic characteristics of SARS-CoV-2 in pediatric patients and accompanying adults. Understanding the dynamic evolution of the SARS- CoV-2 in both pediatric and adults can help in strengthening prophylactic measures.
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Affiliation(s)
- Sara Chandy
- The CHILDS Trust Medical Research Foundation (CTMRF), 12-A, Nageswara Road, Nungambakkam, Chennai 600034, Tamil Nadu, India
| | - Hithesh Kumar
- Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India; Medical and Biological Computing Laboratory, SBST, VIT, Vellore 632014, India
| | - Sara Pearl
- Medical and Biological Computing Laboratory, SBST, VIT, Vellore 632014, India; Department of Integrative Biology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Soumya Basu
- Medical and Biological Computing Laboratory, SBST, VIT, Vellore 632014, India; Department of Biotechnology, NIST University, Berhampore 761008, India
| | - Gurumoorthy M
- The CHILDS Trust Medical Research Foundation (CTMRF), 12-A, Nageswara Road, Nungambakkam, Chennai 600034, Tamil Nadu, India
| | - Janani Sankar
- The CHILDS Trust Medical Research Foundation (CTMRF), 12-A, Nageswara Road, Nungambakkam, Chennai 600034, Tamil Nadu, India
| | - Anand Manoharan
- Kanchi Kamakoti CHILDS Trust Hospital (KKCTH), 12-A, Nageswara Road, Nungambakkam, Chennai 600034, Tamil Nadu, India
| | - Sudha Ramaiah
- Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India; Medical and Biological Computing Laboratory, SBST, VIT, Vellore 632014, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, SBST, VIT, Vellore 632014, India; Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India.
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Tran DH, Do HDK, Tran HT, Pham TNM, Nguyen HD, Linh HT, Cuong HQ, Vu MT, Phung HTT. Rapid identification of SARS-CoV-2 strains via isothermal enzymatic recombinase amplification and nanopore sequencing. Arch Virol 2024; 169:87. [PMID: 38565796 DOI: 10.1007/s00705-024-06012-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/28/2024] [Indexed: 04/04/2024]
Abstract
Surveillance of the SARS-CoV-2 genome has become a crucial technique in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole-genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent need to develop rapid and cost-effective tools for precise on-site detection and identification of SARS-CoV-2 strains. In this study, we demonstrate the rapid diagnosis of COVID-19 and identification of SARS-CoV-2 variants by amplification and sequencing of the entire SARS-CoV-2 S gene using isothermal enzymatic recombinase amplification combined with the advanced Oxford nanopore sequencing technique. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing the effect of mutations on diagnostic approaches, antiviral treatments, and vaccines.
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Affiliation(s)
- Diem Hong Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hau Thi Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | | | - Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Thuy Linh
- Medical Device Testing Center, Pasteur Institute, Ho Chi Minh City, Vietnam
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Hoang Quoc Cuong
- Directorial Board, Pasteur Institute, Ho Chi Minh City, Vietnam
- Department of Health, Can Tho City, Vietnam
| | - Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam.
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Dostálková A, Zdeňková K, Bartáčková J, Čermáková E, Kapisheva M, Lopez Marin MA, Kouba V, Sýkora P, Chmel M, Bartoš O, Dresler J, Demnerová K, Rumlová M, Bartáček J. Prevalence of SARS-CoV-2 variants in Prague wastewater determined by nanopore-based sequencing. CHEMOSPHERE 2024; 351:141162. [PMID: 38218235 DOI: 10.1016/j.chemosphere.2024.141162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The early detection of upcoming disease outbreaks is essential to avoid both health and economic damage. The last four years of COVID-19 pandemic have proven wastewater-based epidemiology is a reliable system for monitoring the spread of SARS-CoV-2, a causative agent of COVID-19, in an urban population. As this monitoring enables the identification of the prevalence of spreading variants of SARS-CoV-2, it could provide a critical tool in the fight against this viral disease. In this study, we evaluated the presence of variants and subvariants of SARS-CoV-2 in Prague wastewater using nanopore-based sequencing. During August 2021, the data clearly showed that the number of identified SARS-CoV-2 RNA copies increased in the wastewater earlier than in clinical samples indicating the upcoming wave of the Delta variant. New SARS-CoV-2 variants consistently prevailed in wastewater samples around a month after they already prevailed in clinical samples. We also analyzed wastewater samples from smaller sub-sewersheds of Prague and detected significant differences in SARS-CoV-2 lineage progression dynamics among individual localities studied, e.g., suggesting faster prevalence of new variants among the sites with highest population density and mobility.
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Affiliation(s)
- Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Kamila Zdeňková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic.
| | - Jana Bartáčková
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Eliška Čermáková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Marina Kapisheva
- National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Marco A Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Vojtěch Kouba
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
| | - Petr Sýkora
- PVK a.s., Prague Water Supply and Sewerage Company, Czech Republic
| | - Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic; Military Health Institute, Military Medical Agency, Czech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Czech Republic
| | - Kateřina Demnerová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology Prague, Czech Republic; National Institute of Virology and Bacteriology, University of Chemistry and Technology Prague, Czech Republic
| | - Jan Bartáček
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czech Republic
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Isabel S, Eshaghi A, Duvvuri VR, Gubbay JB, Cronin K, Li A, Hasso M, Clark ST, Hopkins JP, Patel SN, Braukmann TWA. Targeted amplification-based whole genome sequencing of Monkeypox virus in clinical specimens. Microbiol Spectr 2024; 12:e0297923. [PMID: 38047694 PMCID: PMC10783113 DOI: 10.1128/spectrum.02979-23] [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] [Received: 09/05/2023] [Accepted: 10/29/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE We present a protocol to efficiently sequence genomes of the MPXV-causing mpox. This enables researchers and public health agencies to acquire high-quality genomic data using a rapid and cost-effective approach. Genomic data can be used to conduct surveillance and investigate mpox outbreaks. We present 91 mpox genomes that show the diversity of the 2022 mpox outbreak in Ontario, Canada.
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Affiliation(s)
- S. Isabel
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - A. Eshaghi
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - V. R. Duvvuri
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - J. B. Gubbay
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - K. Cronin
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - Aimin Li
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - M. Hasso
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - S. T. Clark
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
| | - J. P. Hopkins
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - S. N. Patel
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - T. W. A. Braukmann
- Public Health Ontario Laboratory, Public Health Ontario, Toronto, Ontario, Canada
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Haars J, Palanisamy N, Wallin F, Mölling P, Lindh J, Sundqvist M, Ellström P, Kaden R, Lennerstrand J. Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022-2023. Microorganisms 2023; 11:2417. [PMID: 37894075 PMCID: PMC10609123 DOI: 10.3390/microorganisms11102417] [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: 09/08/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to mutations in the SARS-CoV-2 genome, mainly in the receptor binding domain (RBD) of the spike (S) protein. In the present study, 7950 SARS-CoV-2 positive samples from the Uppsala and Örebro regions of central Sweden, collected between March 2022 and May 2023, were whole-genome sequenced using amplicon-based sequencing methods on Oxford Nanopore GridION, Illumina MiSeq, Illumina HiSeq, or MGI DNBSEQ-G400 instruments. Pango lineages were determined and all single nucleotide polymorphism (SNP) mutations that occurred in these samples were identified. We found that the dominant sublineages changed over time, and mutations conferring resistance to currently available mAbs became common. Notable ones are R346T and K444T mutations in the RBD that confer significant resistance against tixagevimab and cilgavimab mAbs. Further, mutations conferring a high-fold resistance to bebtelovimab, such as the K444T and V445P mutations, were also observed in the samples. This study highlights that resistance mutations have over time rendered currently available mAbs ineffective against SARS-CoV-2 in most patients. Therefore, there is a need for continued surveillance of resistance mutations and the development of new mAbs that target more conserved regions of the RBD.
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Affiliation(s)
- Jonathan Haars
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene Uppsala University, Akademiska Sjukhuset Entrance 40 Floor 5, 751 85 Uppsala, Sweden; (J.H.); (J.L.); (P.E.); (R.K.)
| | | | - Frans Wallin
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Södra Grev Rosengatan, 701 85 Örebro, Sweden;
| | - Paula Mölling
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden; (P.M.); (M.S.)
| | - Johan Lindh
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene Uppsala University, Akademiska Sjukhuset Entrance 40 Floor 5, 751 85 Uppsala, Sweden; (J.H.); (J.L.); (P.E.); (R.K.)
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden; (P.M.); (M.S.)
| | - Patrik Ellström
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene Uppsala University, Akademiska Sjukhuset Entrance 40 Floor 5, 751 85 Uppsala, Sweden; (J.H.); (J.L.); (P.E.); (R.K.)
| | - René Kaden
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene Uppsala University, Akademiska Sjukhuset Entrance 40 Floor 5, 751 85 Uppsala, Sweden; (J.H.); (J.L.); (P.E.); (R.K.)
- SciLifeLab, Clinical Genomics Uppsala, Husargatan 3, 752 37 Uppsala, Sweden
| | - Johan Lennerstrand
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene Uppsala University, Akademiska Sjukhuset Entrance 40 Floor 5, 751 85 Uppsala, Sweden; (J.H.); (J.L.); (P.E.); (R.K.)
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