NGS-SA: Publications and pre-prints of our genomics surveillance work

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq

Authors: Tshiabuila D, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Maharaj A, Anyaneji UJ, Naidoo Y, Tegally H, San EJ, Wilkinson E, Lessells R, de Oliveira T

Journal: Research Square, 2022. DOI:


Background: Over 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vaccines, and antivirals. Although several sequencing technologies have been employed, Illumina and Oxford Nanopore remain the two most commonly used platforms. The sequence quality between these two platforms warrants a comparison of the genomes produced by the two technologies. Here, we compared the sequence quality produced by the Oxford Nanopore Technology GridION and the Illumina MiSeq for 28 sequencing runs.

Results: Our results show that the MiSeq had a signi cantly higher number of sequences classi ed by Nextclade as good and mediocre compared to the GridION. The MiSeq also had a signi cantly higher sequence coverage and mutation counts than the GridION.

Conclusion: Due to the low sequence coverage, high number of indels, and sensitivity to viral load noted with the GridION when compared to MiSeq, we can conclude that the MiSeq is more favourable for genomic surveillance, as successful genomic surveillance is dependent on high quality, near-whole genome sequences.