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Structural Variants in SARS-CoV-2 Occur at Template-Switching Hotspots

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-59745-251-9_3openalex-snapshot
Multiple Alignment of DNA Sequences with MAFFT
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Random nature of coronavirus RNA recombination in the absence of selection pressure
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Assessing the performance of the Oxford Nanopore Technologies MinION
inferredcites →https://doi.org/10.1016/j.cell.2020.04.011openalex-snapshot
The Architecture of SARS-CoV-2 Transcriptome
inferredcites →https://doi.org/10.1016/j.cell.2020.06.043openalex-snapshot
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus
inferredcites →https://doi.org/10.1016/j.cub.2020.03.022openalex-snapshot
Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak
inferredcites →https://doi.org/10.1016/j.cub.2020.03.063openalex-snapshot
Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak
inferredcites →https://doi.org/10.1038/nrmicro2614openalex-snapshot
Why do RNA viruses recombine?
inferredcites →https://doi.org/10.1038/s41564-020-0771-4openalex-snapshot
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic
inferredcites →https://doi.org/10.1038/s41586-020-2012-7openalex-snapshot
A pneumonia outbreak associated with a new coronavirus of probable bat origin
inferredcites →https://doi.org/10.1038/s41586-020-2169-0openalex-snapshot
Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
inferredcites →https://doi.org/10.1038/s41591-020-0820-9openalex-snapshot
The proximal origin of SARS-CoV-2
inferredcites →https://doi.org/10.1093/bioinformatics/btp250openalex-snapshot
VARNA: Interactive drawing and editing of the RNA secondary structure
inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot
fastp: an ultra-fast all-in-one FASTQ preprocessor
inferredcites →https://doi.org/10.1093/cid/ciaa219openalex-snapshot
2019 Novel Coronavirus Is Undergoing Active Recombination
inferredcites →https://doi.org/10.1093/nar/16.24.11705openalex-snapshot
Preferred sites of recombination in poliovirus RNA: an analysis of 40 intertypic cross-over sequences
inferredcites →https://doi.org/10.1093/nar/23.11.1870openalex-snapshot
A model for rearrangements in RNA genomes
inferredcites →https://doi.org/10.1093/nar/28.8.1714openalex-snapshot
Role of RNA structure in non-homologous recombination between genomic molecules of brome mosaic virus
inferredcites →https://doi.org/10.1093/nar/gks918openalex-snapshot
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
inferredcites →https://doi.org/10.1093/nsr/nwaa036openalex-snapshot
On the origin and continuing evolution of SARS-CoV-2
inferredcites →https://doi.org/10.1111/mec.15066openalex-snapshot
Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification
inferredcites →https://doi.org/10.1126/science.aac8608openalex-snapshot
Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia
inferredcites →https://doi.org/10.1128/jvi.01048-15openalex-snapshot
Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination
inferredcites →https://doi.org/10.1128/jvi.01358-06openalex-snapshot
A Contemporary View of Coronavirus Transcription
inferredcites →https://doi.org/10.1128/jvi.01926-07openalex-snapshot
Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-Like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus
inferredcites →https://doi.org/10.1128/jvi.71.8.6183-6190.1997openalex-snapshot
Generation of coronavirus spike deletion variants by high-frequency recombination at regions of predicted RNA secondary structure
inferredcites →https://doi.org/10.1128/jvi.77.22.12033-12047.2003openalex-snapshot
Mechanism of RNA Recombination in Carmo- and Tombusviruses: Evidence for Template Switching by the RNA-Dependent RNA Polymerase In Vitro
inferredcites →https://doi.org/10.1186/1471-2148-7-40openalex-snapshot
Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
inferredcites →https://doi.org/10.1186/1748-7188-6-26openalex-snapshot
ViennaRNA Package 2.0
inferredcites →https://doi.org/10.18632/oncotarget.18339openalex-snapshot
Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination
inferredcites →https://doi.org/10.2807/1560-7917.es.2017.22.13.30494openalex-snapshot
GISAID: Global initiative on sharing all influenza data – from vision to reality
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1128/spectrum.02191-21openalex-snapshot
Conserved Pattern and Potential Role of Recurrent Deletions in SARS-CoV-2 Evolution
inferred← citeshttps://doi.org/10.21203/rs.3.rs-456574/v1openalex-snapshot
Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern
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