Detecting SARS-CoV-2 and its variant strains with a full genome tiling array

Abstract

Coronavirus disease 2019 pandemic is the most damaging pandemic in recent human history. Rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and variant strains is paramount for recovery from this pandemic. Conventional SARS-CoV-2 tests interrogate only limited regions of the whole SARS-CoV-2 genome, which are subjected to low specificity and miss the opportunity of detecting variant strains. In this work, we developed the first SARS-CoV-2 tiling array that captures the entire SARS-CoV-2 genome at single nucleotide resolution and offers the opportunity to detect point mutations. A thorough bioinformatics protocol of two base calling methods has been developed to accompany this array. To demonstrate the effectiveness of the tiling array, we genotyped all genomic positions of eight SARS-CoV-2 samples. Using high-throughput sequencing as the benchmark, we show that the tiling array had a genome-wide accuracy of at least 99.5%. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. With around $5 per array, supreme accuracy, and an ultrafast bioinformatics protocol, the SARS-CoV-2 tiling array makes an invaluable toolkit for combating current and future pandemics. Our SARS-CoV-2 tilting array is currently utilized by Molecular Vision, a CLIA-certified lab for SARS-CoV-2 diagnosis.

A full genome tiling array enhanced the inspection and quarantine of SARS-CoV-2

“…For the tiling array, the processing duration from RNA virus to sequencing data is controlled within one day. Whole genome FASTA and FASTQ files are output using customized software based on a bioinformatics protocol of two base calling methods [ 12 ]. According to the Sanger sequencing results in this study and the previous reports, this assay accompany the base calling algorithms has ability to discover mutations with a genome-wide accuracy of at least 99.5% [ 12 ].…”

“…Whole genome FASTA and FASTQ files are output using customized software based on a bioinformatics protocol of two base calling methods [ 12 ]. According to the Sanger sequencing results in this study and the previous reports, this assay accompany the base calling algorithms has ability to discover mutations with a genome-wide accuracy of at least 99.5% [ 12 ]. More importantly, this method is highly cost-efficient with $30 per sample and high throughput with 96 parallel testing abilities.…”

“…1 ). The specified data analysis software generated the candidate consensus sequences as FASTA files based on the scanned fluorescence intensity value from the image [ 11 , 12 ]. By uploading the FASTA file onto a web application called Pangolin (Phylogenetic Assignment of Named Global Outbreak Lineages) [ 13 ], the most likely lineage to the query sequences can be assigned, and variants can be defined.…”

Biosensors for Point Mutation Detection

“…Biosensors based on SPR, CRISPR/Cas, LAMP and aptamers have been also proposed for the detection of other SARS-CoV-2 point mutations ( Xi et al, 2021 ). Other approaches developed recently for detecting SARS-CoV-2 point mutations include a toolset for qPCR-based SNP detection ( Noerz et al, 2021 ) and full genome tiling array that can analyze the whole SARS-CoV-2 genome at single nucleotide resolution ( Jiang et al, 2021 ). Dual synthetic mismatches CRISPR/Cas12a (dsmCRISPR) method for the detection of D614G mutation with high specificity and sensitivity has been presented recently ( Huang et al, 2021 ).…”

The Built Environment Assessment of Residential Areas in Wuhan during the Coronavirus Disease (COVID-19) Outbreak

“…There are over 255.1 million confirmed cases worldwide and over 5.12 million deaths, involving more than 200 countries and regions [1]. Variant strains have been found in many countries and regions [2,3], such as India, the United States, France, and Germany, and more studies have shown that variant strains are associated with higher mortality [4]. Many countries have begun encouraging vaccinations, promoting education, and strengthening food cold-chain testing [5][6][7][8].…”