Genomic epidemiology of SARS-CoV-2 virus with a bioinformatics platform

Sebastian Iglesias-Osores, Percy Omar Tullume-Vergara, Johana Acosta-Quiroz, Johnny Leandro Saavedra-Camacho, Arturo Rafael-Heredia

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Introduction: viral epidemics have presented a risk to human health since they can turn into pandemics and affect a large part of the population, especially for poor developing countries. In 2020, the worldwide pandemic of COVID-19 is underway. Research is currently being carried out showing data that combines genetic and social information that can change our understanding of the dynamics of the epidemic.

Objective: to describe data science-based technology tool called Nextstrain that allows epidemics to be visualized with data as up to date as possible using academic databases.

Development: there are currently viral sequences from 57 countries on 6 continents. The common ancestor of the virus circulating in the world emerged in Wuhan, China, in late November or early December 2019, and from where it is supposed to have mutated towards humans, from bats and pangolins. Regarding monitoring, research work is already being carried out using this tool, such as in Taiwan, France, and Finland, which were able to determine where the SARS-CoV-2 strains that were causing outbreaks in their respective country originated. Besides, Nextstrain allows to freely share the phylogenetic analyzes of various authors from different countries and allows us to see the great work in the epidemiology of the virus.

Conclusions: Nextstrain is a tool based on big data that gives us a better view of the worldwide epidemiology of pathogens of interest. Its use is based on bioinformatic tools and it shows us this information through a pleasant and understandable ecosystem.

Palabras clave

Infecciones por Coronavirus, Síndrome Respiratorio Agudo Grave, Betacoronavirus; Genoma Viral; Web Semántica


Fong IW, Fong IW. Emerging Animal Coronaviruses: First SARS and Now MERS. In: Emerging Zoonoses [Internet]. Springer International Publishing; 2017 [cited 14/06/2020]. p. 63–80. Available from:

Chan JFW, Kok KH, Zhu Z, Chu H, To KKW, Yuan S, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect [Internet]. 2020 [cited 14/06/2020];9(1):221–36. Available from:

Kamel Boulos MN, Geraghty EM. Geographical tracking and mapping of coronavirus disease COVID-19/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic and associated events around the world: How 21st century GIS technologies are supporting the global fight against outbreaks and epidemics. Int J Health Geogr [Internet]. 2020 [cited 14/06/2020];19(1):8. Available from:

Burke RM, Midgley CM, Dratch A, Fenstersheib M, Haupt T, Holshue M, et al. Active Monitoring of Persons Exposed to Patients with Confirmed COVID-19 - United States, January-February 2020. MMWR Morb Mortal Wkly Rep [Internet]. 2020 [cited 14/06/2020];69(9):245–6. Available from:

Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, et al. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses [Internet].Trends Microbiol [Internet]. 2016 [cited 14/06/2020]. 24(6):490-502. Available from:

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet [Internet]. 2020 [cited 14/06/2020];395(10224):565–74. Available from:

Pybus OG, Fraser C, Rambaut A. Evolutionary epidemiology: preparing for an age of genomic plenty. Philos Trans R Soc B Biol Sci [Internet]. 2013 [cited 28/04/2020];368(1614):20120193. Available from:

Ladner JT, Grubaugh ND, Pybus OG, Andersen KG. Precision epidemiology for infectious disease control. Nat Med [Internet]. 2019 [cited 14/06/2020];25(2):206–11. Available from:

Von Bubnoff A. Next-Generation Sequencing: The Race Is On. Cell Press [Internet]; 2008 [cited 14/06/2020]. 132:721–3. Available from:

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics [Internet]. 2018 [cited 10/04/2020];34(23):4121–3. Available from:

Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, et al. Phylodynamic applications in 21st century global infectious disease research. Glob Heal Res Policy [Internet]. 2017 [cited 14/06/2020];2(1):1–10. Available from:

Sagulenko P, Puller V, Neher RA. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol [Internet]. 2018 [cited 14/06/2020]; 4(1):vex042. Available from:

Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet [Internet]. 2020 [cited 14/06/2020];395(10223):507–13. Available from:

Wang JT, Lin YY, Chang SY, Yeh SH, Hu BH, Chen PJ, et al. The role of phylogenetic analysis in clarifying the infection source of a COVID-19 patient. Journal of Infection [Internet]. 2020 [cited 14/06/2020]; 81(1): 147–178. Available from:

Bal A, Destras G, Gaymard A, Bouscambert-Duchamp M, Valette M, Escuret V, et al. Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del). Clinical microbiology and infection [Internet]. NLM (Medline); 2020 [cited 14/06/2020]; 26(7): 960–962. Available from:

Haveri A, Smura T, Kuivanen S, Österlund P, Hepojoki J, Ikonen N, et al. Serological and molecular findings during SARS-CoV-2 infection: the first case study in Finland, January to February 2020. Eurosurveillance [Internet]. 2020 [cited 28/04/2020];25(11):2000266. Available from:

Padilla-Rojas C, Lope-Pari P, Vega-Chozo K, Balbuena-Torres J, Caceres-Rey O, Bailon-Calderon H, et al. Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru. Microbiol Resour Announc [Internet]. 2020 [cited 14/06/2020];9(19):[aprox.10 p]. Available from:

Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Challenges [Internet]. 2017 [cited 14/06/2020];1(1):33–46. Available from:

Kamps R, Brandão RD, van den Bosch BJ, Paulussen ADC, Xanthoulea S, Blok MJ, et al. Next-generation sequencing in oncology: Genetic diagnosis, risk prediction and cancer classification. International Journal of Molecular Sciences [Internet]. 2017 [cited 14/06/2020]; 18(2): 308. Available from:

Kato K. Impact of the next generation DNA sequencers. Int J Clin Exp Med [Internet]. 2009 [cited 28/04/2020];2(2):193–202. Available from:

Chua EW, Ng PY. MinION: A novel tool for predicting drug hypersensitivity? Front Pharmacol [Internet]. 2016 [cited 14/06/2020];7(JUN):1–7. Available from:

Goodwin S, McPherson JD, McCombie WR. Coming of age: Ten years of next-generation sequencing technologies. Nat Rev Genet [Internet]. 2016 [cited 14/06/2020];17(6):333–51. Available from:

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