The SARS-CoV-2 early infections phylogeny as an example of the misinterpreting of phylogenies in epidemiology

Pablo Colunga-Salas, Daniela Segura-Trejo, Carlos Ismar Miranda-Caballero, Sokani Sánchez-Montes, Mario Arteaga-Vázquez, Ingeborg Becker


The use of phylogenies to study the geographic origin and traceability of infections caused by outbreaks of diseases has increased. However, the use of these phylogenetic tools is limited by the information available, as well as the results obtained by phylogenies. As an example, we analyzed the SARS-CoV-2 genomes available in GenBank up to August 2020, we performed a global alignment and, based on a phylogenetic analysis of Bayesian inference, we compared the information on the origin of the first cases of COVID-19 in Latin American countries represented at that date by their genomes of COVID-19 positive patients. The results show that of the six Latin American countries represented, only Puerto Rico, the information obtained through phylogenetic analysis corresponds to the clinical case study carried out by the Ministry of Health of that country. This shows that for outbreaks similar to the one produced by SARS-CoV-2, with incomplete information it is important to take the information obtained from these phylogenetic analyzes with caution when carrying out geographic epidemiology studies.


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