Genomic analysis reveals local transmission of SARS-CoV-2 in early pandemic phase in Peru
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Abstract
The dissemination of cases of the new SAR-COV-2 coronavirus represents a serious public health problem for Latin America and Peru. For this reason, it is important to characterize the genome of the isolates that circulate in Latin America. To characterize the complete genome of first samples of the virus circulating in Peru, we amplified seven overlapping segments of the viral genome by RT-PCR and sequenced using Miseq platform. The results indicate that the genomes of the Peruvian SARS-COV-2 samples belong to the genetic groups G and S. Likewise, a phylogenetic and MST analysis of the isolates confirm the introduction of multiple isolates from Europe and Asia that, after border closing, were transmitted locally in the capital and same regions of the country. These Peruvian samples (56%) grouped into two clusters inside G clade and share B.1.1.1 lineage. The characterization of these isolates must be considered for the use and design of diagnostic tools, and effective treatment and vaccine formulations.
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SciScore for 10.1101/2020.09.05.284604: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. 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 The fastq files generated were cleaned using Groomer and Trimmomatic (https://usegalaxy.org/). Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)The reads mapped to the Wuhan-Hu-1 reference genome available at the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/nuccore/?term=Severe+acute+respiratory+syndrome+coronavirus+2+AND+Wuhan) using BWA-ME (https://usegalaxy.org). BWA-MEsuggested: NoneFinally, the genomes were assembled using SPAdes and compared … SciScore for 10.1101/2020.09.05.284604: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. 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 The fastq files generated were cleaned using Groomer and Trimmomatic (https://usegalaxy.org/). Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)The reads mapped to the Wuhan-Hu-1 reference genome available at the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/nuccore/?term=Severe+acute+respiratory+syndrome+coronavirus+2+AND+Wuhan) using BWA-ME (https://usegalaxy.org). BWA-MEsuggested: NoneFinally, the genomes were assembled using SPAdes and compared to the reference genome using CONTIGuator (http://contiguator.sourceforge.net/). SPAdessuggested: (SPAdes, RRID:SCR_000131)Nucleotide and amino acid variations were detected using snpEff (http://snpeff.sourceforge.net/SnpEff_manual.html). snpEffsuggested: (SnpEff, RRID:SCR_005191)Likewise, a manual edition of the genomes was done using the Geneious Prime software (https://www.geneious.com/). https://www.geneious.com/suggested: (Geneious, RRID:SCR_010519)The MCC tree was visualized and edited using FigTree (http://tree.bio.ed.ac.uk/software/figtree/). FigTreesuggested: (FigTree, RRID:SCR_008515)Additionally, to detect local transmission of the virus we performed Maximum Likelihood analysis with 1000 bootstraps of confidence using MEGA X (https://www.megasoftware.net). MEGAsuggested: (Mega BLAST, RRID:SCR_011920)A minimum spanning tree (MST) analysis using BioNumerics version 7.6 ( BioNumericssuggested: NoneResults 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:An important limitation of our study is the uneven spatial and temporal sampling scheme, most SARS-CoV-2 sequences recovered in the present study were from Lima and a few samples of north and south regions of Peru. These sampling does not represent the viral diversity in other regions of Peru. More accurate reconstructions of the origin and regional spread of the clade B.1.1.1 will require a denser sampling from Peru and neighboring South American countries, particularly during the very early phase of the epidemic. It is crucial to analyze more cases by whole genome sequencing of the SARS-CoV-2 virus from different regions of the country, to better understand the spread and evolution of this new coronavirus in Perú. It is also important to integrate the information from the laboratory diagnosis and the genomic analysis of the virus with the clinical and epidemiological data to depict the clinical epidemiology and infection mechanisms of this coronavirus in Peru.
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.
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