Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source DOI Creative Commons
Josip Rudar, Peter Kruczkiewicz, Oksana Vernygora

и другие.

Microbiology Spectrum, Год журнала: 2024, Номер 12(4)

Опубликована: Март 4, 2024

ABSTRACT We conducted an in silico analysis to better understand the potential factors impacting host adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) white-tailed deer, humans, and mink due strong evidence sustained transmission within these hosts. Classification models trained on single nucleotide amino acid differences between samples effectively identified deer-, human-, mink-derived SARS-CoV-2. For example, balanced accuracy score Extremely Randomized Trees classifiers was 0.984 ± 0.006. Eighty-eight commonly predictive mutations are found at sites under positive negative selective pressure. A large fraction selection (86.9%) or by machine learning (87.1%) genes other than spike. Some locations encoded gene regions predicted be B- T-cell epitopes implicated modulating immune response suggesting that may involve evasion system, modulation class-I major-histocompatibility complex, diminished recognition CD8+ T cells. Our also silent mutations, such as C7303T C9430T, play important role discriminating deer-derived across multiple clades. Finally, our investigation into origin B.1.641 lineage from deer Canada discovered additional human sequence Michigan related sampled near emergence this lineage. These findings demonstrate machine-learning approaches can used combination with evolutionary genomics identify possibly involved cross-species viruses novel viral lineages. IMPORTANCE Severe is a highly transmissible virus capable infecting establishing itself wildlife populations, deer. This fact highlights importance developing ways genetic contribute its spread new species. especially since populations serve reservoirs potentially facilitate re-introduction variants populations. In study, we apply phylogenetic methods uncover biomarkers SARS-CoV-2 find demonstrating both non-synonymous differentiate animal-derived sequences human-derived ones each other. suggests involves system suppression antigen presentation. developed here general investigate

Язык: Английский

Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source DOI Creative Commons
Josip Rudar, Peter Kruczkiewicz, Oksana Vernygora

и другие.

Microbiology Spectrum, Год журнала: 2024, Номер 12(4)

Опубликована: Март 4, 2024

ABSTRACT We conducted an in silico analysis to better understand the potential factors impacting host adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) white-tailed deer, humans, and mink due strong evidence sustained transmission within these hosts. Classification models trained on single nucleotide amino acid differences between samples effectively identified deer-, human-, mink-derived SARS-CoV-2. For example, balanced accuracy score Extremely Randomized Trees classifiers was 0.984 ± 0.006. Eighty-eight commonly predictive mutations are found at sites under positive negative selective pressure. A large fraction selection (86.9%) or by machine learning (87.1%) genes other than spike. Some locations encoded gene regions predicted be B- T-cell epitopes implicated modulating immune response suggesting that may involve evasion system, modulation class-I major-histocompatibility complex, diminished recognition CD8+ T cells. Our also silent mutations, such as C7303T C9430T, play important role discriminating deer-derived across multiple clades. Finally, our investigation into origin B.1.641 lineage from deer Canada discovered additional human sequence Michigan related sampled near emergence this lineage. These findings demonstrate machine-learning approaches can used combination with evolutionary genomics identify possibly involved cross-species viruses novel viral lineages. IMPORTANCE Severe is a highly transmissible virus capable infecting establishing itself wildlife populations, deer. This fact highlights importance developing ways genetic contribute its spread new species. especially since populations serve reservoirs potentially facilitate re-introduction variants populations. In study, we apply phylogenetic methods uncover biomarkers SARS-CoV-2 find demonstrating both non-synonymous differentiate animal-derived sequences human-derived ones each other. suggests involves system suppression antigen presentation. developed here general investigate

Язык: Английский

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