Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
-
SciScore for 10.1101/2020.06.26.20135715: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization In sensitivity analysis and in order to measure the effect of the SARS-CoV-2 uneven genomic representativeness across the world, two down sampling strategies datasets were implemented where, based on location, the sequences were randomly resampled 100 times and the phylogenetic and migration inference was replicated. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Genomic library preparation and sequencing: Library preparation and sequencing were performed following the ARTIC network (real-time molecular epidemiology for outbreak … SciScore for 10.1101/2020.06.26.20135715: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization In sensitivity analysis and in order to measure the effect of the SARS-CoV-2 uneven genomic representativeness across the world, two down sampling strategies datasets were implemented where, based on location, the sequences were randomly resampled 100 times and the phylogenetic and migration inference was replicated. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Genomic library preparation and sequencing: Library preparation and sequencing were performed following the ARTIC network (real-time molecular epidemiology for outbreak response) protocol and using both Nanopore and Illumina technologies (22). Nanoporesuggested: NoneGenomic sequence assembly: Nanopore reads were basecalled using Guppy version 3.2.2 (Oxford Nanopore Technologies, Oxford, UK) and then demultiplexed and trimmed using Porechop version 0.3.2_pre (23). Porechopsuggested: (Porechop, RRID:SCR_016967)Single nucleotide variants were called with a depth of at least 200x and then polished consensus was generated using Nanopolish version 0.13.2 (25). Nanopolishsuggested: (Nanopolish, RRID:SCR_016157)MiSeq reads were demultiplexed and quality control was performed with a Q-score threshold of 30 using fastp (26). MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Processed reads were aligned against SARS-CoV-2 reference genome (GenBank NC_045512.2), single nucleotide variants were called with a depth of at least 100x and consensus genomes were generated using BWA-MEM version 0.7.17 (24) and BBMap (27). BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)BBMapsuggested: (BBmap, RRID:SCR_016965)The full genomic dataset was classified in lineages (29) using PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages) (30) and aligned with 10 iterative refinements using MAFFT (31). MAFFTsuggested: (MAFFT, RRID:SCR_011811)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:This study has some limitations. Firstly, the geographical sources of infection relied on people to self-report their own symptoms onset and travel history, which is subject to inaccuracies. Secondly, we use air travel data from important destinations in Colombia but other locations may also have fueled COVID-19 emergence and dissemination in the country; flight travel data was not available from March 9, 2020, onwards. Thirdly, the number of sequences sampled represented a tiny fraction of the documented number of imported cases into Colombia; the sample was selected to be a country-wide representative given limited resources for genome sequencing and consequently, the introduced viral diversity may also have been underestimated. Another limitation of this analysis is the inherent uncertainty stemming from global unsystematic sampling. Therefore, the inferences about the number of introductions and the corresponding geographical source need to be interpreted with caution. We attempted to overcome this by undertaking sensitivity analyses and contrasting the results with the available epidemiological data and our estimates from travel data. However, more sequence data from Colombia and undersampled countries together with information of sampling representativeness per country is needed in order to account for sampling uncertainty in a more statistically rigorous manner. Our study provided evidence that an important number of independent introductions occurred to Colombia with ...
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.
-