Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e
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Abstract
Seasonal coronaviruses (OC43, 229E, NL63, and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here we address the influence of antigenic drift on immune evasion of seasonal coronaviruses. We provide evidence that at least two of these viruses, OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein that are exposed to human humoral immunity. This suggests that reinfection may be due, in part, to positively selected genetic changes in these viruses that enable them to escape recognition by the immune system. It is possible that, as with seasonal influenza, these adaptive changes in antigenic regions of the virus would necessitate continual reformulation of a vaccine made against them.
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SciScore for 10.1101/2020.10.30.352914: (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 All analysis code is written in Python 3 (Python Programming Language, SCR_008394) in Jupyter notebooks (Jupyter-console, RRID:SRC_018414). Pythondetected: Python Programming Language ( RRID:SCR_008394)Pythonsuggested: (IPython, RRID:SCR_001658)Sequence data: All viral sequences are publicly accessible and were downloaded from ViPR (www.viprbrc.org) under the “Coronavirdiae” with host “human” (Pickett et al. ViPRsuggested: (vipR, RRID:SCR_010685)Phylogenetic inference: For each of the 4 HCoV datasets, full-length sequences were aligned to a reference genome using the augur align command … SciScore for 10.1101/2020.10.30.352914: (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 All analysis code is written in Python 3 (Python Programming Language, SCR_008394) in Jupyter notebooks (Jupyter-console, RRID:SRC_018414). Pythondetected: Python Programming Language ( RRID:SCR_008394)Pythonsuggested: (IPython, RRID:SCR_001658)Sequence data: All viral sequences are publicly accessible and were downloaded from ViPR (www.viprbrc.org) under the “Coronavirdiae” with host “human” (Pickett et al. ViPRsuggested: (vipR, RRID:SCR_010685)Phylogenetic inference: For each of the 4 HCoV datasets, full-length sequences were aligned to a reference genome using the augur align command (Hadfield et al. 2018) and MAFFT (Katoh et al. 2002). MAFFTsuggested: (MAFFT, RRID:SCR_011811)A Snakemake file (Köster and Rahmann 2012) within each HCoV directory follows the general outline of a Nextstrain build (Nextstrain, RRID:SCR_018223) and was used to align each gene to a reference strain and build a time-resolved phylogeny with IQ-Tree v1 (Nguyen et al. 2015) and TimeT ree (Sagulenko, Puller, and Neher 2018). of a Nextstraindetected: Nextstrain ( RRID:SCR_018223)IQ-Treesuggested: (IQ-TREE, RRID:SCR_017254)Kappa is the ratio of rates of transitions:transversions, and was calculated by averaging values from spike and RdRp trees built by BEAST 2.6.3 (Bouckaert et al. 2019) using the HKY+gamma4 model with 2 partitions and “coalescent constant population”. BEASTsuggested: (BEAST, RRID:SCR_010228)Results from OddPub: Thank you for sharing your 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.
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SciScore for 10.1101/2020.10.30.352914: (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 Phylogenetic inference For each of the 4 HCoV datasets, full-length sequences were aligned to a reference genome using the augur align command (Hadfield et al. 2018) and MAFFT (Katoh et al. 2002). MAFFTsuggested: (MAFFT, RRID:SCR_011811)All BEAST results are found in .log files in gene- and HCoV-specific subdirectories within beast/ . BEASTsuggested: (BEAST, RRID:SCR_010228)…SciScore for 10.1101/2020.10.30.352914: (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 Phylogenetic inference For each of the 4 HCoV datasets, full-length sequences were aligned to a reference genome using the augur align command (Hadfield et al. 2018) and MAFFT (Katoh et al. 2002). MAFFTsuggested: (MAFFT, RRID:SCR_011811)All BEAST results are found in .log files in gene- and HCoV-specific subdirectories within beast/ . BEASTsuggested: (BEAST, RRID:SCR_010228)Results from OddPub: Thank you for sharing your 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.
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