Projecting the impact of behaviour and isolation interventions and super spreader events from mass gatherings and international travel on Malaysia’s COVID-19 epidemic trajectories using an augmented SEIR model

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1. 

   ScreenIT

   Oct 30, 2020

   SciScore for 10.1101/2020.10.29.20222224: (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
   2.2 Model features and key assumptions: This study uses an SEIR model (Figure 1), built using System Dynamics on Vensim by Ventana Systems, adopted from a basic model built by Tom Fiddaman of Ventana Systems [16].	Vensim by Ventana Systems suggested: None

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   One caveat, however, is the fact that IIE and BIE are treated as …

   SciScore for 10.1101/2020.10.29.20222224: (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
   2.2 Model features and key assumptions: This study uses an SEIR model (Figure 1), built using System Dynamics on Vensim by Ventana Systems, adopted from a basic model built by Tom Fiddaman of Ventana Systems [16].	Vensim by Ventana Systems suggested: None

   ---

   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:

   One caveat, however, is the fact that IIE and BIE are treated as separate parameters in the model. This neglects the reality that restrictions in civilian movement likely influence the effectiveness of contact tracing and isolation. Additionally, although BIE was likely not constant, we deduced it reached 50% once compliance to lockdown was reportedly 95%, based on model calibration exercises [33], and was maintained at 50% until the end of strict lockdown. And although IIE was likely not constant and much lower than 50% at the beginning of lockdown compared to its end, we tried to account for this by having testing capacity scaled over time to reach max capacity from 6,210 tests – 36,812 tests. Highlighting a clear limitation of the homogeneity assumption in SEIR modelling, the model was unable to sufficiently project the effects of a second lower peak on 6 June 2020, which arose from outbreaks among mainly undocumented foreign workers at a number of immigration detention depots in the country. As the outbreaks occurred in populations that were significantly isolated from the larger community, it is likely that the rapid rise in new transmissions was able to be controlled much faster using intensified targeted approaches, resulting in the rapid drop to less than 1000 active cases by 14 June 2020 [34]. Additionally, the model was unable to account for a change in patient discharge criteria, based on an updated WHO recommendation to release patients from isolation without requ...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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   Read the original source
2. 

   Version published to 10.1101/2020.10.29.20222224 on medRxiv

   Oct 30, 2020