RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis
Open accessAbstract
An important component of efforts to manage the ongoing COVID19 pandemic is the R apid A ssessment of how natural selection contributes to the emergence and proliferation of potentially dangerous S ARS-CoV-2 lineages and CL ades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations. Availability: RASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl . Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl . Contact: Dr. Sergei L Kosakovsky Pond ( spond@temple.edu ). Supplementary information: N/A
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Using the RASCL pipeline, no compelling evidence was found of imbalances between ratios of synonymous and non-synonymous substitutions indicative of positive or negative selection acting on any of the genes of viruses in either the BA.4 or BA.5 lineages.
“Using the RASCL pipeline7 (which employs a battery of tests that analyze ratios of synonymous and non-synonymous substitutions both at individual codon sites and entire protein-coding regions), we found no compelling evidence of imbalances between ratios of synonymous and non-synonymous substitutions such as would be indicative of positive”
From Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa (2022) · cites this paper as [7]
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- Authors
- Lucaci, A. G., Zehr, J. D., Shank, S. D., Bouvier, D., Mei, H., Nekrutenko, A., Martin, D. P., & Kosakovsky Pond, S. L.
- Affiliations
- Temple University (US)
- Pennsylvania State University (US)
- University of Cape Town (ZA)
- ORCID
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2022-01-18
- PMC
- PMC8786235
- OpenAlex
- W4205672035
- Cited by
- 2
- References
- 28
- Citations by year
- 2025: 1 · 2022: 1
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- TUScholarShare (Temple University) (submittedVersion, cc-by)
- Funders
- National Science Foundation (2027196)
- Wellcome Trust (222574, 222574/Z/21/Z)
- National Institutes of Health
- National Institute of Allergy and Infectious Diseases (AI134384, R01AI134384)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- SARS-CoV-2, COVID-19 pandemic, viral clades, natural selection, phylogenetic comparative analysis, genomic surveillance, variant emergence, codon alignment, selection tests, Galaxy workflow
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