Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa

Next-generation sequencing (NGS) is a powerful high-throughput tool for virological genomic surveillance. While Illumina and Ion Torrent sequencing platforms have been extensively used for generating viral RNA genome sequences, there is limited information comparing the quality of data generated by these platforms for whole-genome sequencing of SARS-CoV-2 as part of a genomic surveillance program. We compare performance metrics of data generated by Illumina MiSeq and Ion Torrent GeneStudio S5 systems. 183 routine SARS-CoV-2 genomic surveillance samples collected from the Eastern Cape were sequenced by both platforms and analyzed using the same analysis pipeline. All sequence assemblies, alignments, mutational calling, and clade classification were performed using the Genome Detective Virus tool and Nextclade software. Using the same analysis pipeline, our results indicate that the Ion torrent S5 and Illumina Miseq had similar sequence success rates with 175 (95,6%) samples successfully sequenced on the Ion Torrent S5 followed by 172 (94%) on Illumina Miseq. Additionally, the overall sequence quality was significantly higher on the Ion torrent S5 resulting in 99,4% sequences having greater than 80% genomic coverage compared to 79,7% on the Illumina Miseq. The Ion torrent displays a lower sensitivity to viral loads (Ct score range 14,1 – 44,1) in comparison to the Illumina Miseq, which prefers samples with higher viral loads (lower Ct scores).

Both platforms successfully identified key spike mutations specific to Beta and Delta VOC's. A disparity in clade classification was observed in 17 (<10%) sequences across the two platforms, however, these were a result of low coverage attributed to poor primer coverage obtained on the Illumina Miseq. Manual library preparation finds both methods compatible regarding sample processing and turnaround times, sequence quality, large sample quantities, identification of variant-specific mutations, and clade calling. The Illumina Miseq and the Ion torrent S5 coupled with the IonChef are reliable platforms capable of performing targeted sequencing with amplicons, providing specific, accurate, and high throughput analysis of the SARS-CoV-2 whole viral genomes. These findings suggest that the Ion Torrent Genestudio S5 system and Illumina MiSeq platforms are viable options for the genomic surveillance of SARS-CoV-2, each with specific advantages and trade-offs.