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17th International Symposium on Bioinformatics Research and Applications, ISBRA 2021 ; 13064 LNBI:165-175, 2021.
Article in English | Scopus | ID: covidwho-1565307

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.

2.
J Med Virol ; 92(10): 2221-2226, 2020 10.
Article in English | MEDLINE | ID: covidwho-505569

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.


Subject(s)
COVID-19/diagnosis , DNA Probes/metabolism , DNA, Single-Stranded/genetics , Genome, Viral , SARS-CoV-2/genetics , Whole Genome Sequencing/methods , Biotin/chemistry , COVID-19/pathology , COVID-19/virology , DNA Probes/chemical synthesis , DNA, Single-Stranded/metabolism , Genotype , Humans , Mutation , Nasopharynx/virology , Phylogeny , Reverse Transcriptase Polymerase Chain Reaction/standards , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , SARS-CoV-2/pathogenicity , Sensitivity and Specificity
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