دورية أكاديمية
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.
| العنوان: | High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. |
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| المؤلفون: | Bhoyar RC; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Jain A; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Sehgal P; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Divakar MK; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Sharma D; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Imran M; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Jolly B; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Ranjan G; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Rophina M; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Sharma S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Siwach S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Pandhare K; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Sahoo S; Institute of Medical Sciences and SUM Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India., Sahoo M; Institute of Medical Sciences and SUM Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India., Nayak A; Institute of Medical Sciences and SUM Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India., Mohanty JN; Institute of Medical Sciences and SUM Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India., Das J; Institute of Medical Sciences and SUM Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India., Bhandari S; Sawai Man Singh Medical College, Jaipur, Rajasthan, India., Mathur SK; Sawai Man Singh Medical College, Jaipur, Rajasthan, India., Kumar A; Sawai Man Singh Medical College, Jaipur, Rajasthan, India., Sahlot R; Sawai Man Singh Medical College, Jaipur, Rajasthan, India., Rojarani P; Kurnool Medical College, Kurnool, Andhra Pradesh, India., Lakshmi JV; Kurnool Medical College, Kurnool, Andhra Pradesh, India., Surekha A; Kurnool Medical College, Kurnool, Andhra Pradesh, India., Sekhar PC; Kurnool Medical College, Kurnool, Andhra Pradesh, India., Mahajan S; Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India., Masih S; Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India., Singh P; Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India., Kumar V; Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India., Jose B; Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India., Mahajan V; Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India., Gupta V; Government Institute of Medical Sciences, NOIDA, Uttar Pradesh, India., Gupta R; Government Institute of Medical Sciences, NOIDA, Uttar Pradesh, India., Arumugam P; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Singh A; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Nandy A; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., P V R; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Jha RM; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Kumari A; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Gandotra S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Rao V; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Faruq M; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Kumar S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Reshma G B; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Varma G N; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Roy SS; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Sengupta A; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Chattopadhyay S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Singhal K; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Pradhan S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India., Jha D; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Naushin S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Wadhwa S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Tyagi N; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Poojary M; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Scaria V; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India., Sivasubbu S; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.; Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India. |
| المصدر: | PloS one [PLoS One] 2021 Feb 17; Vol. 16 (2), pp. e0247115. Date of Electronic Publication: 2021 Feb 17 (Print Publication: 2021). |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: San Francisco, CA : Public Library of Science |
| مواضيع طبية MeSH: | COVID-19/*epidemiology , COVID-19/*virology , High-Throughput Nucleotide Sequencing/*methods , SARS-CoV-2/*genetics , SARS-CoV-2/*isolation & purification, COVID-19/genetics ; Genome, Viral/genetics ; Humans ; India/epidemiology ; Molecular Epidemiology/methods ; Multiplex Polymerase Chain Reaction/methods ; Pandemics ; Phylogeny ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Sensitivity and Specificity |
| مستخلص: | The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2. Competing Interests: The authors have declared that no competing interests exist. |
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| المشرفين على المادة: | 0 (RNA, Viral) |
| تواريخ الأحداث: | Date Created: 20210217 Date Completed: 20210316 Latest Revision: 20240330 |
| رمز التحديث: | 20240330 |
| مُعرف محوري في PubMed: | PMC7888613 |
| DOI: | 10.1371/journal.pone.0247115 |
| PMID: | 33596239 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1932-6203 |
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| DOI: | 10.1371/journal.pone.0247115 |