Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Sep 17;2(3):100755.
doi: 10.1016/j.xpro.2021.100755. Epub 2021 Aug 2.

An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms

Rahul C Bhoyar  1 , Vigneshwar Senthivel  1   2 , Bani Jolly  1   2 , Mohamed Imran  1   2 , Abhinav Jain  1   2 , Mohit Kumar Divakar  1   2 , Vinod Scaria  1   2 , Sridhar Sivasubbu  1   2
Affiliations

An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms

Rahul C Bhoyar et al. STAR Protoc. .

Abstract

Sequencing of SARS-CoV-2 genomes is crucial for understanding the genetic epidemiology of the COVID-19 pandemic. It is also critical for understanding the evolution of the virus and also for the rapid development of diagnostic tools. The present protocol is a modification of the Illumina COVIDSeq test. We describe an amplicon-based next-generation sequencing approach with short turnaround time, adapted for bench-top sequencers like MiSeq, iSeq, and MiniSeq. For complete details on the use and execution of this protocol, please refer to Bhoyar et al. (2021).

Keywords: Bioinformatics; Clinical Protocol; Genomics; Immunology; Microbiology; Sequence analysis; Sequencing.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Layout of the sample plate to be used denoting the samples, PC and NC Up-to 94 samples can be processed at once. A positive control (CPC HT) and Negative Control (ELB HT)is included in every plate that is processed using the COVIDSeq protocol.
Figure 2
Figure 2
Quality of the final library pool was analyzed by agarose gel electrophoresis (2%), the expected fragment of ~300 bp size was observed
See this image and copyright information in PMC

References

    1. Bhoyar R.C., Jain A., Sehgal P., Divakar M.K., Sharma D., Imran M., Jolly B., Ranjan G., Rophina M., Sharma S. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. PLoS One. 2021;16:e0247115. - PMC - PubMed
    1. Poojary M., Shantaraman A., Jolly B., Scaria V. Computational protocol for assembly and analysis of SARS-nCoV-2 genomes. Res. Rep. 2020;4:e1–e14doi. doi: 10.9777/rr.2020.10001. - DOI
    1. Rambaut A., Holmes E.C., O’Toole Á., Hill V., McCrone J.T., Ruis C., du Plessis L., Pybus O.G. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 2020;5:1403–1407. doi: 10.1038/s41564-020-0770-5. - DOI - PMC - PubMed
    1. Hadfield J., Megill C., Bell S.M., Huddleston J., Potter B., Callender C., Sagulenko P., Bedford T., Neher R.A. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;1:4121–4123. doi: 10.1093/bioinformatics/bty407. - DOI - PMC - PubMed
    1. Jolly B., Scaria V. Computational analysis and phylogenetic clustering of SARS-CoV-2 genomes. Bio Protoc. 2021;11:e3999. doi: 10.21769/BioProtoc.3999. - DOI - PMC - PubMed

Publication types

MeSH terms