ArticlePloS one2021
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 2 of them syntheses that pooled it.
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Who cites it
78 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection.The Cochrane database of systematic reviews · 2024Pooled it
- Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use.Reviews in medical virology · 2022Pooled it
- Advances on Sensors and Diagnostics of SARS-CoV-2 Biomarkers.Analytical chemistry · 2026Article
- Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population.Journal of virology · 2025Article
- Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification.Viruses · 2025Article
- Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- Development of a Targeted NGS Assay for the Detection of Respiratory Pathogens including SARS-CoV-2 in Felines.Pathogens (Basel, Switzerland) · 2024Article
- Article
- Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia.Pathogens (Basel, Switzerland) · 2024Article
- Quartz Crystal Microbalance Platform for SARS-CoV-2 Immuno-Diagnostics.International journal of molecular sciences · 2023Article
- Article
- SARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses.Nature communications · 2023Article
- Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variants BA.2, BA.5 and BQ.1.1 in critically ill patients with COVID-19: a prospective, multicenter cohort study.Intensive care medicine experimental · 2023Article
- Review
- Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives.Chemical science · 2023Review
- One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy.One health (Amsterdam, Netherlands) · 2023Article
- Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission.Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi · 2023Article
- Article
- SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater - a longitudinal study in Bengaluru, India.The Lancet regional health. Southeast Asia · 2023Article
- Emerging Landscape of SARS-CoV-2 Variants and Detection Technologies.Molecular diagnosis & therapy · 2023Review
18 more citing papers are in PubMed but not listed here.
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57 authors.
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Abstract
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.
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