Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil

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1. Version published to 10.3390/v13102013

   Oct 7, 2021
2. 

   ScreenIT

   Jul 26, 2021

   SciScore for 10.1101/2021.07.20.21260890: (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

   Antibodies
   Sentences	Resources
   We evaluated the Spike protein against ACE2 protein and four types of antibodies anti-Spike extracted from CoV-AbDab database [26].	ACE2 suggested: None
   The human antibodies were selected based on their preferences for distinct binding locations in Spike: subunits S1, S2, S1-S2, S1-RBD, and S1-notRBD.	S1-RBD suggested: None S1-notRBD suggested: None
   Software and Algorithms
   Sentences	Resources
   We used the Symmetric trait substitution model with the Bayesian Stochastic Search Variable Selection approach for rate estimation in BEAST 1.10.4.	BEAST suggested: (BEAST, RRID:SCR_010228)
   We aligned these sequences to the …

   SciScore for 10.1101/2021.07.20.21260890: (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

   Antibodies
   Sentences	Resources
   We evaluated the Spike protein against ACE2 protein and four types of antibodies anti-Spike extracted from CoV-AbDab database [26].	ACE2 suggested: None
   The human antibodies were selected based on their preferences for distinct binding locations in Spike: subunits S1, S2, S1-S2, S1-RBD, and S1-notRBD.	S1-RBD suggested: None S1-notRBD suggested: None
   Software and Algorithms
   Sentences	Resources
   We used the Symmetric trait substitution model with the Bayesian Stochastic Search Variable Selection approach for rate estimation in BEAST 1.10.4.	BEAST suggested: (BEAST, RRID:SCR_010228)
   We aligned these sequences to the WH01 genome using MAFFT 7.475 with --auto and --addfragments options and trimmed the 3’ and 5’ untranslated regions.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The stability analysis was performed using the Stability function from FoldX tool [23]	FoldX suggested: (FoldX, RRID:SCR_008522)
   Visualization and structure manipulation was conducted using PyMol.	PyMol suggested: (PyMOL, RRID:SCR_000305)

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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:

   To overcome the limitation in the number of sequences available for the state, we generated 1,927 novel SARS-CoV-2 genomes sequenced biweekly between March and June 2021, sampled from residents of 91 out of the 92 cities of Rio de Janeiro. These sequences represent ∼50% of the genomes publicly available in GISAID from the state so far, notably reaching a sequencing ratio of ∼1:100 cases reported during April and May 2021. We then analyzed lineage dynamics in Rio de Janeiro as well as the emergence and dispersion of new variants. Three main phases defined the pandemic in the state of Rio de Janeiro, each of them represented by a different lineage. Remarkably, all phases occurred with distinct patterns of transmissibility and mortality. Whereas the daily number of cases increased during the second and third phase, more people died in the first and third ones. We hypothesized that lack of knowledge about the disease and resources to treat patients in early pandemic may explain such severity in the first phase [30–32]. After almost a year of pandemic, a significant amount of information had been already gathered about the virus and the disease, certainly improving patient care. We have observed a switch in the death profiles over the course of pandemic, while deaths were more restricted to old groups and people with comorbidities in the first phase, a substantial increase of young people was reported at the third wave. Prioritizing the vaccination of elderly people might have had...

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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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.07.20.21260890v1 on medRxiv

   Jul 22, 2021