ABSTRACT
The unprecedented level of genome sequencing during the SARS-CoV-2 pandemic brought about the challenge of processing this genomic data. However, the state-of-the-art phylogenetic methods were mostly designed for analyzing data that are significantly sparser and require extensive subsampling of strains. We present (ε, τ) -MSN, a novel tool that reconstructs a viral genetic relatedness network based on genetic distances, that can process hundreds of thousands of sequences in under several hours. We applied (ε, τ) -MSN to the global COVID-19 outbreak data and were able to build a genetic network on more than 100,000 SARS-CoV-2 sequences. We show that (ε, τ) -MSN can accurately detect transmission events and build a genetic network with significantly higher assortativity with respect to continent and country attributes of SARS-CoV-2 samples. The source code for this software suite is available at https://github.com/Sergey-Knyazev/eMST. © 2021, Springer Nature Switzerland AG.
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 [Ct ] 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.