MOLECULAR EPIDEMIOLOGY TO UNDERSTAND THE SARS-CoV-2 EMERGENCE IN THE BRAZILIAN AMAZON REGION
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Abstract
The COVID-19 pandemic in Brazil has demonstrated an important public health impact, as has been observed in the world. In Brazil, the Amazon Region contributed with a large number of cases of COVID-19, especially in the beginning of the circulation of SARS-CoV-2 in the country. Thus, we describe the epidemiological profile of COVID-19 and the genetic diversity of SARS-CoV-2 strains circulating in the Amazon Region. We observe an extensive spread of virus in this Brazilian site. The data on sex, age and symptoms presented by the investigated individuals were similar to what has been observed worldwide. The genomic analysis of the viruses revealed important amino acid changes, including the D614G and the I33T in Spike and ORF6 proteins, respectively. The latter found in strains originating in Brazil. The phylogenetic analyzes demonstrated the circulation of the lineages B.1 and B.1.1, whose circulation in Brazil has already been previous reported. Our data reveals molecular epidemiology of SARS-CoV-2 in the Amazon Region. These findings also reinforce the importance of continuous genomic surveillance this virus with the aim of providing accurate and updated data to understand and map the transmission network of this agent in order to subsidize operational decisions in public health.
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SciScore for 10.1101/2020.09.04.20184523: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study was approved by Evandro Chagas Institute Ethical Committee ( Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Epidemiological analysis: Graphs of epidemiological data (age, sex, state, signs and symptoms) and circulation were performed with support by the LVR-IEC database and the Microsoft Office Excel program. Microsoft Office Excelsuggested: (Microsoft Excel, RRID:SCR_016137)The adapters sequences reads with a quality lower than Phred 20 and reads with less than 40 bp size, were removed using Trimmommatic53. Phredsuggested:…SciScore for 10.1101/2020.09.04.20184523: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study was approved by Evandro Chagas Institute Ethical Committee ( Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Epidemiological analysis: Graphs of epidemiological data (age, sex, state, signs and symptoms) and circulation were performed with support by the LVR-IEC database and the Microsoft Office Excel program. Microsoft Office Excelsuggested: (Microsoft Excel, RRID:SCR_016137)The adapters sequences reads with a quality lower than Phred 20 and reads with less than 40 bp size, were removed using Trimmommatic53. Phredsuggested: (Phred, RRID:SCR_001017)The processed reads were visualized with FastQC54. For Trimmomatic, we have used the following parameters: LEADING: 3 TRAILING:3 MINLEN:40 Genome Assembly (De Novo and Reference Mapping): For this step, the reads validated based on quality trimming were used to assembly the SARS-CoV-2 genomes. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)Taxonomic annotation and submission to GISAID: The generated de novo contigs were compared using the Blastx tool57 implemented in Diamond v. Blastxsuggested: (BLASTX, RRID:SCR_001653), against the RefSeq database (NCBI’s RefSeqsuggested: (RefSeq, RRID:SCR_003496)Phylogenetic Analysis and Mutation analysis: The genomes sequences were aligned with other genomes from all the world using the Mafft v.7.47159. Mafftsuggested: (MAFFT, RRID:SCR_011811)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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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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