Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.
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Date
2022
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Abstract
Corona Virus Disease 2019 (COVID-19) is an ongoing pandemic that has spread rapidly around the
world and has seen over 431 000 000 identified cases and 5 930 000 deaths caused by this disease by
the end of January 2022. Many viral lineages have arisen from Severe Acute Respiratory Syndrome
Corona Virus 2 (SARS-CoV-2) as public health measures from numerous countries have failed to
contain the spread of the virus. Sequencing of SARS-CoV-2 has enabled the identification and
classification of the viral lineages, while real-time tracking of the emergence and spread of these
lineages has been facilitated by the open sharing of genomic surveillance data and collaborative online
platforms. Several studies have suggested that various mutations may have a functional effect on the
virus, such as a substitution in the spike protein (D614G) may result in increased transmissibility whilst
an N439K substitution in the receptor-binding domain (RBD) may assist in neutralizing monoclonal
antibodies. It is therefore necessary that a fast and reliable sequencing technology be used to rapidly
and correctly produce SARS-CoV-2 genomes that can be used to identify viral lineages. Many
sequencing laboratories have begun using Nanopore sequencing as it promises high throughput, realtime
sequencing, at an affordable cost and many of their sequencing platforms allow for portability.
The sequencing technology has, however, not been verified to produce consensus SARS-CoV-2
genomes that are comparable to Illumina Sequencing which is currently the gold standard Next
Generation Sequencing (NGS) technology for SARS-CoV-2 sequencing. In this study, we compared
the Illumina and Nanopore sequencing platforms by comparing the SARS-CoV-2 genomes produced
by the Illumina MiSeq and Oxford Nanopore Technology (ONT) GridION X5. The results show that
the GridION is currently unsuitable for SARS-CoV-2 genomic surveillance as consensus genomes
produced by the platform have a lower quality than those produced by the MiSeq which reduces the
reliability of the data obtained from the genomes. These results can be used to better understand the
Nanopore sequencing technology and how it differs from the Illumina technology which will help in
updating the Nanopore technology to produce consensus genomes at a faster rate than the Illumina
technology whilst still having a similar quality.
Description
Masters Degree. University of KwaZulu-Natal, Durban.