Phylogenetic analysis of human parainfluenza type 3 virus strains responsible for the outbreak during the COVID-19 pandemic in Seoul, South Korea
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SciScore for 10.1101/2022.03.15.484550: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the Institutional Review Board (IRB) of the Korea University Guro Hospital (IRB number: Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Multiple sequence alignment was performed using the nucleotide sequences of the HN gene obtained in this study with those of the reference strains, using the MUSCLE algorithm (16) implemented in MEGA X software (17). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)MEGA Xsuggested: NoneThe best-fit substitution model was determined using ModelFinder with TIM+F+I+G4 based on the minimum Bayesian information … SciScore for 10.1101/2022.03.15.484550: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the Institutional Review Board (IRB) of the Korea University Guro Hospital (IRB number: Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Multiple sequence alignment was performed using the nucleotide sequences of the HN gene obtained in this study with those of the reference strains, using the MUSCLE algorithm (16) implemented in MEGA X software (17). MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)MEGA Xsuggested: NoneThe best-fit substitution model was determined using ModelFinder with TIM+F+I+G4 based on the minimum Bayesian information criterion value (19). ModelFindersuggested: NoneThe best model among the six clock-tree model combinations, the relaxed clock log-normal and constant coalescent population, was chosen by path sampling and stepping stone, using the model-selection package implemented in BEAST. BEASTsuggested: (BEAST, RRID:SCR_010228)The Tracer program v1.7.1 (20) was used to ensure that the effective sample size was greater than 200 for all the parameters. Tracersuggested: (Tracer, RRID:SCR_019121)The maximum clade credibility tree information was summarized using TreeAnnotator v2.6.6 (21) after burning in 10% of the trees. TreeAnnotatorsuggested: (BEAST2, RRID:SCR_017307)The Bayesian MCMC phylogenetic tree was visualized using FigTree v1.4.4 (22). FigTreesuggested: (FigTree, RRID:SCR_008515)Amino acid sequence analysis: The amino acid sequences were obtained by translating the nucleotide sequences of the partial nucleotide sequence of the HN gene using the standard genetic code in MEGA X. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)The crystal structure of HN protein was visualized using PyMOL 2.0 (24), based on the previously published crystal structure of HN (PDB ID: 1V3B). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Entropy analysis by Shannon entropy plot was performed using BioEdit, with a threshold value of 0.2 (25). 2.5. BioEditsuggested: (BioEdit, RRID:SCR_007361)Selection pressure analysis: The selection pressure on the HN gene of HPIV3 was estimated using the Datamonkey server (http://www.datamonky.org/). Datamonkey serversuggested: (DataMonkey, RRID:SCR_010278)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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