Timing the SARS-CoV-2 index case in Hubei province
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may have had a history of abortive human infections before a variant established a productive enough infection to create a transmission chain with pandemic potential. Therefore, the Wuhan cluster of infections identified in late December of 2019 may not have represented the initiating event. Pekar et al. used genome data collected from the early cases of the COVID-19 pandemic combined with molecular clock inference and epidemiological simulation to estimate when the most successful variant gained a foothold in humans. This analysis pushes human-to-human transmission back to mid-October to mid-November of 2019 in Hubei Province, China, with a likely short interval before epidemic transmission was initiated.
Science , this issue p. 412
Article activity feed
-
-
SciScore for 10.1101/2020.11.20.392126: (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 To facilitate convergence, (i) a hard lower bound of 1×10-5 substitutions/site/year was placed on the clock rate and (ii) we initiated the MCMC using the maximum likelihood phylogeny that had been transformed into a chronogram via TempEst v1.5.3 (38). TempEstsuggested: (TempEst, RRID:SCR_017304)Convergence and mixing was assessed in Tracer v1.7.1 (39) and chains were combined in LogCombiner, such that all ESS values were >200. Tracersuggested: (Tracer, RRID:SCR_019121)Epidemic Simulation: To explore the evolutionary dynamics at play during the beginning of the COVID-19 pandemic, we … SciScore for 10.1101/2020.11.20.392126: (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 To facilitate convergence, (i) a hard lower bound of 1×10-5 substitutions/site/year was placed on the clock rate and (ii) we initiated the MCMC using the maximum likelihood phylogeny that had been transformed into a chronogram via TempEst v1.5.3 (38). TempEstsuggested: (TempEst, RRID:SCR_017304)Convergence and mixing was assessed in Tracer v1.7.1 (39) and chains were combined in LogCombiner, such that all ESS values were >200. Tracersuggested: (Tracer, RRID:SCR_019121)Epidemic Simulation: To explore the evolutionary dynamics at play during the beginning of the COVID-19 pandemic, we performed a series of epidemic simulations using FAVITES v1.2.6 (21) First, we generated static contact networks in FAVITES under a preferential-attachment model using the Barabási-Albert algorithm (40). FAVITESsuggested: NoneMutation analysis: To approximate the number of mutations that separated the index case virus from that represented by the most recent common ancestor of all 583 analyzed SARS-CoV-2 genomes, we calculated the time between the date of index case and the tMRCA after rejection sampling (Fig. 3) and multiplied that time (in years) by the corresponding mean substitution rate from the posterior sample from BEAST. BEASTsuggested: (BEAST, RRID:SCR_010228)Results from OddPub: Thank you for sharing your code.
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.
-
SciScore for 10.1101/2020.11.20.392126: (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 To facilitate convergence, (i) a hard lower bound of 1x10-5 substitutions/site/year was placed on the clock rate and (ii) we initiated the MCMC using the maximum likelihood phylogeny that had been transformed into a chronogram via TempEst v1.5.3 (38) . TempEstsuggested: (TempEst, RRID:SCR_017304)Convergence and mixing was assessed in Tracer v1.7.1 (39) and chains were combined in LogCombiner, such that all ESS values were >200. …SciScore for 10.1101/2020.11.20.392126: (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 To facilitate convergence, (i) a hard lower bound of 1x10-5 substitutions/site/year was placed on the clock rate and (ii) we initiated the MCMC using the maximum likelihood phylogeny that had been transformed into a chronogram via TempEst v1.5.3 (38) . TempEstsuggested: (TempEst, RRID:SCR_017304)Convergence and mixing was assessed in Tracer v1.7.1 (39) and chains were combined in LogCombiner, such that all ESS values were >200. Tracersuggested: (Tracer, RRID:SCR_019121)W e explored the sensitivity of the rejection sampling approach to different molecular clocks in the BEAST inference. 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.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
-
