Abstract
In this study, we designed a set of SARS-CoV-2 enrichment probes to increase the capacity for sequence-based virus detection and obtain the comprehensive genome sequence at the same time. This universal SARS-CoV-2 enrichment probe set contains 502 120 nt single-stranded DNA biotin-labeled probes designed based on all available SARS-CoV-2 viral sequences and it can be used to enrich for SARS-CoV-2 sequences without prior knowledge of type or subtype. Following the CDC health and safety guidelines, marked enrichment was demonstrated in a virus strain sample from cell culture, three nasopharyngeal swab samples (cycle threshold [C t ] values: 32.36, 36.72, and 38.44) from patients diagnosed with COVID-19 (positive control) and four throat swab samples from patients without COVID-19 (negative controls), respectively. Moreover, based on these high-quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication and its phylogenetic relationship with other selected high-quality samples from the Genome Variation Map. Therefore, this universal SARS-CoV-2 enrichment probe system can capture and enrich SARS-CoV-2 viral sequences selectively and effectively in different samples, especially clinical swab samples with a relatively low concentration of viral particles.
Keywords: SARS coronavirus; gene expression; genetic networks; genetic variability; mutation.
【저자키워드】 Mutation, Gene Expression, genetic variability, SARS Coronavirus, genetic networks, 【초록키워드】 SARS-CoV-2, coronavirus, Mutation, Gene Expression, knowledge, Genetic, Nasopharyngeal swab, Health, Viral, CDC, cycle threshold, Cell culture, Patient, virus detection, genetic variability, SARS Coronavirus, expression, Biotin, Concentration, Coronavirus replication, genome sequence, Phylogenetic relationship, Viral particles, capture, negative controls, SARS-CoV-2 sequences, sequence, SARS-CoV-2 sequence, positive control, throat swab, nasopharyngeal swab sample, heterozygosity, subtype, single-stranded DNA, virus strain, probe, SARS-CoV-2 viral, swab sample, selected, can be used, demonstrated, Map, diagnosed with COVID-19, patients without COVID-19, 【제목키워드】 capture, SARS-CoV-2 genome sequence, capture sequencing,