Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Single Nucleotide Polymorphisms-SNPs

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Validation of polymerase chain reaction-indexed next-generation sequencing assay on the Illumina iSeq 100 platform for MPL exon 10 mutation detection: a robust alternative to Sanger sequencing.

Journal of clinical pathology·2026

Same author

Ubiquitination Defect of XIAP as Novel Susceptibility to Invasive Fungal Pneumonia.

The Journal of infectious diseases·2026

Same author

Self-Assembly of Stimuli-Responsive Peptide Enhances Therapeutics by Specifically Disrupting Hepatocellular Carcinoma Lysosomes In Vivo.

Advanced materials (Deerfield Beach, Fla.)·2026

Same author

Border measures may delay but rarely prevent early dominance of local transmission: imported-to-local patterns across public health emergencies of international concern.

Journal of travel medicine·2026

Same author

A comparison of Epstein-Barr virus digital PCR and quantitative PCR for identifying nasopharyngeal cancer.

Annals of the Academy of Medicine, Singapore·2026

Same author

A Comparative Evaluation of Four Bioinformatic Tools for Identifying HIV-1 <i>pol</i> Drug Resistance Mutations Using Illumina MiSeq Data.

Biology·2026

Search research articles

Related Experiment Video

Updated: Aug 7, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing.

Lian Chye Winston Koh^1,2, Yiqi Seow^2,3, Kiat Whye Kong³

¹Bioinformatics Institute, Agency for Science Technology and Research, Singapore.

Frontiers in Genetics

|March 13, 2023

Summary

This study presents a new sequencing workflow for COVID-19 genetic characterization. The method efficiently identifies subgenomic RNA, aiding in tracking viral load during outbreaks.

Keywords:

SARS-CoV-2 genomics subgenomic RNA temporal transcriptome

More Related Videos

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Published on: June 30, 2023

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

Related Experiment Videos

Last Updated: Aug 7, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Published on: June 30, 2023

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

Area of Science:

Virology
Genomics
Public Health

Background:

The COVID-19 pandemic presents a significant global health challenge.
Accurate and rapid genetic characterization of SARS-CoV-2 is crucial for outbreak management.
Existing sequencing workflows may not be suitable for decentralized or rapid deployment.

Purpose of the Study:

To develop and validate a modified sequencing workflow for COVID-19 genetic analysis.
To demonstrate the workflow's capability in identifying subgenomic RNA characteristics.
To enable comprehensive genetic characterization during public health emergencies.

Main Methods:

Utilized a short tiling amplicon library preparation method (280bp).
Paired the method with Illumina's iSeq100 desktop sequencer.
Developed Taqman assays based on sequencing data to quantify subgenomic RNA.

Main Results:

Successfully identified gapped reads indicative of subgenomic RNA junctions in patient samples.
The workflow proved versatile, small-footprint, and suitable for decentralized use.
Taqman assays accurately quantified subgenomic ORF5 and ORF7a RNA.
Combined approach effectively tracked subgenomic RNA titres alongside standard qRT-PCR.

Conclusions:

The modified sequencing workflow offers a versatile solution for decentralized COVID-19 genetic characterization.
The ability to identify and track subgenomic RNA is valuable for understanding viral dynamics.
This approach enhances capabilities for comprehensive genetic analysis during infectious disease outbreaks.