Publication Highlight: Viral Whole Genome Sequencing Using Illumina Microbial Amplicon Prep (iMAP) with ARTIC-Style Primer Schemes for RSV, SARS-CoV-2, and Dengue Virus (Serotypes 1–4)
In a new technical report, GenPath Africa colleagues Stepfan de Villiers, Kerwin Liedeman, Lucious Chabuka, Eduan Wilkinson, Cheryl Baxter, and Tulio De Oliveira from the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) describe an optimized workflow for sequencing the entire genomes of several major respiratory and mosquito-borne viruses. Their refined method makes it easier and more affordable for laboratories to monitor viral threats like COVID-19, RSV, and Dengue fever.
What is this publication about?
This publication provides a step-by-step technical protocol for performing viral whole genome sequencing (WGS). The researchers adapted the Illumina Microbial Amplicon Prep (iMAP) system to work with "ARTIC-style" primer schemes, which are specialized sets of DNA "keys" that allow scientists to piece together the entire genetic code of a virus. The protocol specifically covers Respiratory Syncytial Virus (RSV), SARS-CoV-2 (the virus that causes COVID-19), and all four serotypes of Dengue virus.
Why is this important?
Sequencing the entire genome of a virus is the gold standard for understanding viral evolution and identifying emerging variants. However, these high-tech methods can often be expensive and complex to implement in every laboratory. This new protocol has been specifically optimized to enhance sensitivity and reduce reagent costs by using "half-volume" reactions. By lowering the financial and technical barriers to entry, more labs can contribute to high-quality genomic epidemiology and variant analysis.
How can this make a difference?
By providing a reproducible and cost-effective framework, this protocol supports near real-time surveillance and outbreak detection. It allows public health officials to more accurately track how different viruses are moving through a population and to identify mutations that might make a virus more contagious or resistant to treatments. Ultimately, making these advanced tools more accessible strengthens the global ability to respond to seasonal epidemics and future pandemics.
Stepfan de Villiers, Kerwin Liedeman, Lucious Chabuka, Velda Wentzel, Tebogo Ramakutoane, Nondumiso Zakwe, Ottovan Dakurah, Eduan Wilkinson, Marije Hofstra, Lavanya Singh, Cheryl Baxter, Tulio De Oliveira, "Viral Whole Genome Sequencing Using Illumina Microbial Amplicon Prep (iMAP) with ARTIC-Style Primer Schemes for RSV, SARS-CoV-2, and Dengue Virus (Serotypes 1–4)." Protocols.io, 2026. doi:10.17504/protocols.io.36wgqxz4xlk5/v1.
