An Analysis of SARS-CoV-2 Using ViReport
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Abstract
The ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of cases and hundreds of thousands of deaths. Given the current lack of treatments or vaccines available, it may be useful to trace the evolu-tion and spread of the virus to better develop methods of preventative intervention. In this study, we analyzed over 4,000 full genome sequences of human SARS-CoV-2 using novel tool ViReport [13], an automated workflow for performing phylogenetic analyses on viral sequences and generating comprehensive molecular epidemiologi-cal reports. The complete ViReport output can be found at https://github.com/mirandajsong/ViReport-SARS-CoV-2 .
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SciScore for 10.1101/2020.06.20.163162: (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
No key resources detected.
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: We detected the following sentences addressing limitations in the study:Some considerations of the limitations of this analysis include the dataset used; given that there are well over 8 million confirmed cases of SARS-CoV-2 in the world (as of June 2020) but the sample only included around 4500 sequences, the sample is evidently a very small subset that may not be representative of current events both in …
SciScore for 10.1101/2020.06.20.163162: (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
No key resources detected.
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: We detected the following sentences addressing limitations in the study:Some considerations of the limitations of this analysis include the dataset used; given that there are well over 8 million confirmed cases of SARS-CoV-2 in the world (as of June 2020) but the sample only included around 4500 sequences, the sample is evidently a very small subset that may not be representative of current events both in geographical distribution and time. For example, the UK has the fifth most cases in the world [3] but is not listed as one of the categories represented by the sample. As the viral sequence database updates with new sequences or sequences from other sources are pooled together, the analysis may become more representative. Future directions for this work include additional analysis of the generated statistics; a topic of interest is how the sequences are distributed by date for each country, as this may be indicative of how successful policies in place are in terms of managing the ongoing epi-demic. Another topic is exploring the distribution of pairwise distances over time, which may lead to conclusions regarding the mutation rate of the SARS-CoV-2 virus. With regard to ViReport, additional work is being done to analyze potential differences in results based on which tools are selected at each step.
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.
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