Lineage Tree: Visualization Platform for Exploring SARS-CoV-2 Pango Lineage Networks and Lineage-Defining Mutations

Abstract

Public health surveillance plays a pivotal role in ending the COVID-19 emergency, especially monitoring the emergence of new lineages. A dynamic SARS-CoV-2 lineage naming system, known as the Pango nomenclature system currently being used to assist genomic epidemiology. Currently, researchers manually draw charts to visualize mutations found in major pango lineages that shape the evolutionary paths of SARS-CoV-2 and there is no automated pipeline to produce these visualizations. This study proposes a system to strengthen the monitoring and tracking of SARS-CoV-2 by utilizing datasets from Pango-lineage designations and the GISAID EpiCoV database that eliminates the tedious and manual methodology. In addition, information regarding the mutations that uniquely define the lineage and mutations that are shared with the immediate lineage parent could benefit researchers such as those interested in designing new vaccines against the newly mutated SARS -CoV-2 viruses.