ArticleGenomics2021
ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections.
Article in Genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Immune signature in vaccinated versus non-vaccinated aged people with COVID-19 pneumonia.Journal of translational medicine · 2024Article
- The Renin-Angiotensin System (RAS) in COVID-19 Disease: Where We Are 3 Years after the Beginning of the Pandemic.Microorganisms · 2024Review
- Article
- Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs.Life science alliance · 2023Article
- Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing.Pathogens (Basel, Switzerland) · 2022Article
- Cellular Landscaping of COVID-19 and Gynaecological Cancers: An Infrequent Correlation.Journal of oncology · 2022Review
- STArS (STrain-Amplicon-Seq), a targeted nanopore sequencing workflow for SARS-CoV-2 diagnostics and genotyping.Biology methods & protocols · 2022Article
- Genomic Snapshot of SARS-CoV-2 in Migrants Entering Through Mediterranean Sea Routes.Frontiers in public health · 2022Article
- Regulatory T Cells as Predictors of Clinical Course in Hospitalised COVID-19 Patients.Frontiers in immunology · 2021Article
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.
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