A new preprint by Tegally et al.1 describes the rapid expansion of Africa’s SARS-CoV-2 genomic surveillance network, which has generated over 100,000 full-genome sequences since 2020 and identified two major variants of concern, Alpha and Omicron. This extensive study, authored by over 400 researchers across Africa, includes a wealth of information on the impact of local sequencing capacity on turnaround time and provides the first real-world data on SARS-CoV-2 sequencing performance across next-generation sequencing (NGS) platforms using genome gap analysis.
Localized surveillance led to faster turnaround times
Turnaround time is critical in genomic surveillance, as rapid variant detection can enable swift public health responses. One potential barrier to fast turnaround times is limited local sequencing capacity. The study found that over two years, Africa’s surveillance network grew to include 39 out of 55 countries with on-site sequencing centers. Some centers also served as regional surveillance hubs, creating additional sequencing capacity for neighboring countries. Between local, regional, and outside-of-Africa surveillance sites, 52 African countries (95%) were ultimately represented in the 100,000 analyzed genomes. When the authors further examined the impact of sequencing site location on turnaround time, local sequencing centers had a significantly faster turnaround time than regional or outside-of-Africa sites, supporting investment in local genomic surveillance networks for timely data generation.
Ion Torrent NGS showed fewer gaps in SARS-CoV-2 genome sequencing
Another challenge in SARS-CoV-2 surveillance has been generating high-quality sequencing data on an ever-evolving virus. SARS-CoV-2 full-genome sequencing involves reverse transcription from RNA into DNA followed by amplification with sequence-specific primers. But as SARS-CoV-2 continues to evolve, its genome mutates, resulting in potential mismatches between primers and their targeted sequences. For example, the ARTIC primer set has required several updates and is currently in version 4.1. In comparison, Ion Torrent’s AmpliSeq primer set, which was originally available as an NGS panel and now as a complete SARS-CoV-2 genome sequencing assay with reagents, features an intelligent design with variant-tolerant primers for robust coverage of emerging mutations.
The superior coverage of Ion Torrent NGS was evident in a head-to-head comparison of median N count per genome across NGS platforms. While it was comparable to Sanger and MGI sequencing, Ion Torrent sequencing had noticeably fewer gaps (<250 mean N per genome) than the Illumina and Oxford Nanopore Technology platforms (>1250 mean N per genome) in this survey of 100,000 SARS-CoV-2 genomes, demonstrating the key role of primer design and sequencing technology in variant coverage during full-genome SARS-CoV-2 sequencing.
As SARS-CoV-2 continues to evolve, surveillance methods must be leveraged to detect and potentially respond to emerging variants. This large-scale analysis of 100,000 SARS-CoV-2 genomes demonstrates that full-genome SARS-CoV-2 sequencing with Ion Torrent NGS resulted in fewer mean gaps per genome than Illumina or Oxford Nanopore NGS platforms. The Ion AmpliSeq SARS-CoV-2 Insight Research Assay is proving to be robust to natural variation, enabling a wide array of genomic research applications with a diversity of sample types such as nasopharyngeal swabs, saliva, wastewater, and post-mortem FFPE tissue.
For Research Use Only. Not for use in diagnostic procedures.
1. Houriiyah Tegally, James E. San, Matthew Cotten, et al. (2022). The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. medRxiv 2022.04.17.22273906; doi: https://doi.org/10.1101/2022.04.17.22273906