BernardoGG/SARS-CoV-2_Genomic_lineages_Ecuador: Identification and analysis of the early transmission dynamics, importations and local circulation of SARS-CoV-2 in Ecuador inferred from genomic data.

Identification and analysis of the early transmission dynamics, importations and local circulation of SARS-CoV-2 in Ecuador inferred from genomic data.

Bernardo Gutierrez1,2, Sully Márquez3, Belén Prado-Vivar3, Mónica Becerra-Wong3, Juan José Guadalupe4, Darlan da Silva Candido1, Juan Carlos Fernandez-Cadena5, Gabriel Morey-Leon6, Rubén Armas-Gonzalez7, Derly Madeleiny Andrade-Molina5, Alfredo Bruno8,9, Domenica de Mora8, Maritza Olmedo8, Denisse Portugal8, Manuel Gonzalez8, Alberto Orlando8, Jan Felix Drexler10, Andres Moreira10, Anna-Lena Sander10, Nina Krause10, Leandro Patiño8, Andres Carrasco8, Orson Mestanza8, Jeannette Zurita11,12, Gabriela Sevillano12, Louis du Plessis1, John T. McCrone13, Josefina Coloma14, Gabriel Trueba3, Veronica Barragan3, Patricio Rojas-Silva3, Michelle Grunauer15, Moritz U.G. Kraemer1, Nuno R. Faria1,16, Marina Escalera-Zamudio1, Oliver G. Pybus1,17*, Paul Cárdenas3*

1Department of Zoology, University of Oxford, Oxford, UK.
2Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.
3Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador.
4Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador.
5Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador.
6Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil, Ecuador.
7Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador.
8Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador.
9Universidad Agraria del Ecuador.
10Charité – Universitätsmedizin Berlin, Berlin, Germany.
11Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.
12Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador.
13Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
14School of Public Health, University of California, Berkeley, USA.
15Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador.
16MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
17Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.

Repository usage and structure

The structure of this repository is shown below. It highlights the location of individual R scripts used to generate plots or analyses and input data files. Input and output data from the phylogenetic analyses, plot and supplementary files and supplementary files are not listed in their entirety.

SARS-CoV-2_Genomic_lineages_Ecuador/
├── Data
│   ├── MSP_epi_data
│   └── genetic_data
│       ├── GISAID_complete_highcoverage_20210107
│       └── metadata
├── Analyses
│   └── phylogenetics
│       ├── ML_SARS2_EC
│       └── BEAST_SARS2_EC
|           ├── BEAST_rate_estimation
|           └── DTA
├── Plots
└── README.md

Input data

All input data that we are able to share publicly are stored in the Data directory. Epidemiological data was collected and made public by the National Service of Risk Management and Emergencies of Ecuador (Servicio Nacional de Gestión de Riesgos y Emergencias del Ecuador, SNGRE), the Ministry of Public Health of Ecuador (Ministerio de Salud Pública del Ecuador, MSP), and the Civil Registry of Ecuador (Registro Civil del Ecuador). The data sets used in this study have been collated by the Ecuacovid repository (github.com/andrab/ecuacovid). The following sub-directories are included:

  • Ministry of Health epidemiological data contained in the MSP_epi_data directory.

  • SARS-CoV-2 viral genome sequence data generated by the Microbiology Institute at Universidad San Francisco de Quito, the Omics Science Laboratory at Universidad de Especialidades Espíritu Santo, the Instituto Nacional de Investigación en Salud Pública on-site and in collaboration with Charité – Universitätsmedizin Berlin, and the Unit for Biomedical Investigations at Zurita & Zurita Laboratorios contained in the genetic_data directory. This directory also includes alignments with sequences downloaded from the GISAID repository and subsampled for our analyses.

Analyses

The Analyses directory contains supplementary files and the phylogenetics sub-directory which includes:

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