Spread dynamics of SARS-CoV-2 epidemic in China: a phylogenetic analysis
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Abstract
Background
Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic and infected millions of people. As the first country proclaimed the SARS-CoV-2 outbreak, China implemented travel ban measure, and curbed the epidemic quickly. We performed a phylogenetic analysis to reveal the spread dynamics detail of SARS-CoV-2 in China and the impact of travel ban on SARS-CoV-2.
Method
Focusing on SARS-CoV-2 sequences collected from China in public database released as of March 31, 2020, we performed a Bayesian inference phylogenetic analyses to estimate the effective population size ( Ne ) curve of SARS-CoV-2 epidemic. Furthermore, we displayed the geographic spread mode of SARS-CoV-2 among different China regions by using Bayesian stochastic search variable selection (BSSVS) method.
Results
The most recent common ancestor (tMRCA) of SARS-CoV-2 in China was traced back to December 9, 2019. According the Ne estimation and geographic spread reconstruction, January 25, 2020 was considered as the crucial time point during the SARS-CoV-2 epidemic in China,which was 2 days after the travel ban implemented. On the point, the tendency of viral population size changed from ascending to decreasing, and the cross-regional spread paths were blocked.
Conclusions
Travel ban is an effective measure to intervene in the spread of SARS-CoV-2, It is necessary to continue efforts in research for prevention and control measures.
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SciScore for 10.1101/2020.05.20.20107854: (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 A multiple alignment was performed by CLUSTAL X program(7) and trimmed into full-length S gene with 3822nt. CLUSTAL Xsuggested: (Clustal X , RRID:SCR_017055)General Time Reversible (GTR) was selected as the nucleotide substitution model by calculated AIC score using jModeltest v1.9.1 program(10). jModeltestsuggested: (jModelTest, RRID:SCR_015244)The output files generated by bayesian computing were discarded the first 10% as burn-in and then combined by LogCombiner tool in BEAST v1.10.4 packages. BEASTsuggested: (BEAST, RRID:SCR_010228)Tracer software v1.7.1(17) was used to diagnose MCMCs … SciScore for 10.1101/2020.05.20.20107854: (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 A multiple alignment was performed by CLUSTAL X program(7) and trimmed into full-length S gene with 3822nt. CLUSTAL Xsuggested: (Clustal X , RRID:SCR_017055)General Time Reversible (GTR) was selected as the nucleotide substitution model by calculated AIC score using jModeltest v1.9.1 program(10). jModeltestsuggested: (jModelTest, RRID:SCR_015244)The output files generated by bayesian computing were discarded the first 10% as burn-in and then combined by LogCombiner tool in BEAST v1.10.4 packages. BEASTsuggested: (BEAST, RRID:SCR_010228)Tracer software v1.7.1(17) was used to diagnose MCMCs output and estimate Ne curve with additional 10% burn-in. Tracersuggested: (Tracer, RRID:SCR_019121)We displayed the discrete geographical phylogenetic MCC trees in FigTree v1.4.3 and generated a visual kml file by spreaD3 v0.9.7(19), which was viewed in Google Earth v7.1.8. FigTreesuggested: (FigTree, RRID:SCR_008515)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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