Next Generation Sequencing (NGS) of SARS-CoV-2
Paragon Genomics has developed PCR amplicon-based NGS panels for sequencing the whole genome of SARS-CoV-2 (the virus responsible for COVID-19) on both Illumina and MGI Tech Sequencing platforms. The panels are designed to obtain complete viral genomes even from samples with very low SARS-CoV-2 viral content.
CleanPlex SARS-CoV-2 Panel
CleanPlex for MGI SARS-CoV-2 Panel
|This amplicon-based SARS-CoV-2 NGS panel is designed for COVID-19 Coronavirus research and surveillance, enabling complete genome sequencing of the new SARS-CoV-2 virus responsible for the COVID-19 pandemic. This panel is specific for Illumina Sequencing platforms.||This amplicon-based SARS-CoV-2 NGS panel is designed for COVID-19 Coronavirus research and surveillance, enabling complete genome sequencing of the new SARS-CoV-2 virus responsible for the COVID-19 pandemic. This panel is specific for MGI Tech’s DNBSEQ platforms.|
Panel design is based on the SARS-CoV-2 sequence NC_045512.2. A total of 343 primer pairs, distributed in two pools, were selected by a proprietary panel design pipeline to cover the whole genome except for 92 bases at the ends. Primers were optimized to preferentially amplify the SARS-CoV-2 cDNA versus the background human cDNA or DNA. They were also optimized to uniformly amplify the covered genome. Amplicon sizes range from 116bp to 196bp, with a median size of 149 bp. This expertly designed panel allows for the interrogation of the entire viral sequence with as little as 200 thousand reads per samples. As the virus mutates, the panel contains sufficient targeted regions such that detection will not be affected. With sequencing, these mutations can also be tracked to study the path of infection and examine different strains.
To evaluate performance and sensitivity during our initial development phase, the panel was tested against reference plasmids: pUC backbone containing either the nucleic capsid (N) gene or the spike (S) gene, two surface proteins specific to SARS-CoV-2.Targets were spiked into cDNA converted from Human Total RNA (agilent), and serially diluted down to zero copies per sample and tested to determine LoD. Results show higher sensitivity than traditional qPCR methods (1).
(1). Victor M Corman et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR