henhaobio
Sign in

bioRxivMolecular BiologyPreprint

SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms

Paola Cristina ResendeiD, Fernando Couto MottaiD, Sunando RoyiD, Luciana AppolinarioiD, Allison de Araújo FabriiD, Joilson XavieriD, Kathryn HarrisiD, Aline da Rocha MatosiD, Bráulia Costa CaetanoiD, Maria OgrzewalskaiD, Milene Dias MirandaiD, Cristiana Couto GarciaiD, André AbreuiD, Rachel J. WilliamsiD, Judith BreueriD, Marilda Mendonça SiqueiraiD

PDFDOI
Structured summary available · Jump to summary ↓

Abstract

Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger.

Abstract summary

Claude Opus 5.5 · xhigh effort · 2 Nov 2026 · from the abstract · CC BY-NC 4.0

Three multiplex tiling protocols using a single primer set recover long amplicons of SARS-CoV-2 directly from clinical sample total RNA for sequencing on Nanopore, Illumina, or Sanger platforms.

Assembling complete and accurate viral genomes directly from clinical samples remains challenging for genomic surveillance of viral pathogenicity, origin, and spread. To address this, the work introduces three protocols based on a single long-amplicon primer set adaptable across laboratories using Nanopore, Illumina, or Sanger sequencing.

Key results

  1. ClaimedA single primer set paired with three protocols recovers long SARS-CoV-2 amplicon reads from clinical-sample total RNA for sequencing on three distinct platforms.

    The protocols are designed for compatibility with Nanopore, Illumina, and Sanger sequencing methods; however, the abstract reports no sample counts, amplicon lengths, or genome coverage metrics. · Abstract

Methods, data and reproducibility

Three multiplex tiling amplicon protocols were designed around one shared primer set to amplify long SARS-CoV-2 fragments starting from total RNA isolated from clinical specimens. The resulting amplicons are compatible with Nanopore, Illumina, or Sanger sequencing.

  • Clinical sample total RNA extracts containing SARS-CoV-2 · SARS-CoV-2
Methods & tools
Nanopore sequencing, Illumina sequencing, Sanger sequencing
Reproducibility gaps
Primer sequences, protocol links, clinical sample counts, and sequencing data accessions are not included in the abstract.
Limitations (1)
  • The abstract provides no quantitative validation data, such as number of clinical samples tested, amplicon sizes, sequencing depth, or genome assembly completeness. · noted in this summary

Read this if you are conducting SARS-CoV-2 genomic surveillance and need a long-amplicon multiplex tiling protocol compatible with Nanopore, Illumina, or Sanger sequencing.

Citations
68

Reproducibility ledger

Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.

Sign in to file a reproducibility report.

Related papers

Similarity Map
SelectedSame fieldCross-field
THISPaden '20Brandt '21Gohl '20Pater '21Speranskaya '20Freed '20
77% semantic matchGenomics
Clinton R. Paden, Ying Tao, Krista J. Queen+4 more·Emerging infectious diseases·Jul 1, 2020· 135 citations