Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
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Abstract
Epidemiological and genomic analyses uncover viral mutational dynamics and transmission bottleneck size during the early COVID-19 pandemic in Austria.
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SciScore for 10.1101/2020.07.15.204339: (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 Read pairs were mapped on the combined Hg38 and SARS-CoV-2 genome (GenBank: MN908947.3) using the BWA-MEM software package (v 0.7.17) (43). BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)From the viral reads BAM file, the consensus FASTA file was generated using the Samtools (v 1.9) (45), mpileup, Bcftools (v 1.9) (46), and SEQTK (https://github.com/lh3/seqtk). Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)For calling low frequency variants the viral read alignment file was realigned using the Viterbi method provided by LoFreq (v 2.1.2) (47). LoFreqsuggested: (LoFreq, RRID:SCR_013054)Annotation… SciScore for 10.1101/2020.07.15.204339: (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 Read pairs were mapped on the combined Hg38 and SARS-CoV-2 genome (GenBank: MN908947.3) using the BWA-MEM software package (v 0.7.17) (43). BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)From the viral reads BAM file, the consensus FASTA file was generated using the Samtools (v 1.9) (45), mpileup, Bcftools (v 1.9) (46), and SEQTK (https://github.com/lh3/seqtk). Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)For calling low frequency variants the viral read alignment file was realigned using the Viterbi method provided by LoFreq (v 2.1.2) (47). LoFreqsuggested: (LoFreq, RRID:SCR_013054)Annotations of the variants was performed with SnpEff (v 4.3) (49) and SnpSift (v 4.3) (50). SnpEffsuggested: (SnpEff, RRID:SCR_005191)SnpSiftsuggested: (SnpSift, RRID:SCR_015624)Phylogenetic analysis and inference of transmission lines: Phylogenetic analysis was conducted using the Augur package (version 7.0.2) (51). Augursuggested: NoneWe reconstructed the phylogeny with the augur pipeline using IQ-Tree (52) and further processed the resulting trees with treetime to infer ancestral traits of the nodes (53). IQ-Treesuggested: (IQ-TREE, RRID:SCR_017254)The consequence type of the mutations was annotated using a customized implementation of the Ensembl Variant Effect Predictor (VEP version 92) using the first SARS-CoV-2 sequenced genome (NCBI ID: NC_045512v2) as a reference. Ensembl Variant Effect Predictorsuggested: NoneVariantsuggested: (VARIANT, RRID:SCR_005194)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.
- 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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