Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic
Abstract
We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern, but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of two months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7’s set of mutations.
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Review 1: "Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic"
This preprint analyzes all complete UK SARS-CoV-2 genomes that were from the B.1.1.7 lineage to identify putative SARS-CoV-2 recombinant viruses. The reviewer deems the data as potentially informative but empathize limitations in methodological protocol.
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Matteo Chiara
Review for "Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic"
Graziano Pesole & Matteo Chiara (University of Bari) 📗📗📗📗◻️
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SciScore for 10.1101/2021.06.18.21258689: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources 1.1.7 regions at the junction of genetic regions according to the mosaic structure detected by the custom Python script described above (https://github.com/cov-ert/type_variants; Supplementary Table S1). Pythonsuggested: (IPython, RRID:SCR_001658)We used samtools (Li et al. 2009), with default filters for mapping and base quality, to extract allele calls from the read data using its mpileup subroutine, and to calculate mean read depth per genome using its depth subroutine. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Results from OddPub: Thank you for sharing your code and data.
Results …SciScore for 10.1101/2021.06.18.21258689: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources 1.1.7 regions at the junction of genetic regions according to the mosaic structure detected by the custom Python script described above (https://github.com/cov-ert/type_variants; Supplementary Table S1). Pythonsuggested: (IPython, RRID:SCR_001658)We used samtools (Li et al. 2009), with default filters for mapping and base quality, to extract allele calls from the read data using its mpileup subroutine, and to calculate mean read depth per genome using its depth subroutine. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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