Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes

Background

Severe Acute Respiratory Syndrome- related coronaviruses (SARS-CoV) are one of the largest single-stranded RNA virus families known to date (Zhu et al., 2020). Recently, SARS-CoV-2, a novel strain of coronavirus, has been identified as the causal pathogen for the ongoing Coronavirus disease 2019 (COVID-19) pandemic (Huang et al., 2020). The infectious disease that first originated in Wuhan, China, spread to other nations at an alarmingly rapid pace. With 3,517,345 cases reported globally and a death toll of 243,401 (as of 5^th May 2020), the disease continues to be a public health concern and a potential threat to the socio-economic welfare of nations and healthcare systems worldwide (World Health Organization, 2020. Novel Coronavirus (2019-nCoV): situation report, 106).

Owing to the rapid advancement of next-generation sequencing (NGS) technology and analysis methods, sequencing the viral genome has been recognized as a viable tool to aid the diagnosis and treatment of COVID-19 and help to understand the disease epidemiology. As the disease evolves over time, more sequencing data for SARS-CoV-2 genomes is being made available in the public domain. To date, there are over 25,000 publicly available genomes of SARS-CoV-2 from different geographical origins. Phylogenetic principles have previously been successfully utilized to contain and diffuse recent pandemic events such as avian influenza, the Zika virus epidemic, and HIV (Salemi et al., 2008; Babakir-Mina et al., 2009; Angeletti et al., 2016). With the rapid accumulation of sequencing data, phylogenetic and phylodynamic analysis are potentially powerful tools for studying the evolutionary patterns of rapidly evolving RNA viruses, and therefore help to understand the epidemiology of the outbreak.

Visualizing evolutionary epidemiology can help to provide a deeper understanding of the global diversity of SARS-CoV-2. Nextstrain is an open-source project that aims to provide real-time interactive visualization of rapidly evolving pathogens coupled with additional data such as geographic information (Hadfield et al., 2018). Nextstrain utilizes Augur, a bioinformatics toolkit for the systematic analysis of genome sequences, and Auspice, an interactive web service for the visualization of analysis results. This protocol has been created to aid bioinformaticians in gaining an epidemiological understanding of the SARS-CoV-2 pathogen using the powerful phylogenetic analysis toolkit provided by Nextstrain. The data and parameters used in this protocol are specific to SARS-CoV-2 genomes; however, Nextstrain is a generalized toolkit for the analysis of pathogen phylogenies and can be customized using the appropriate data and parameters suited to the pathogen of interest. All software and datasets used in this protocol are available in the public domain.