Investigating the Global Spread of SARS-CoV-2 Leveraging Next-Gen Sequencing and Principal Component Analysis

Abstract

As COVID-19 has spread from the first reported cases into a global pandemic, there has been a number of efforts to understand the mutations and clusters of genetic lineages of the SARS-CoV-2 virus. The high mutation rate and rapid spread makes this analysis capable of tracking chains of infections as well as putting individual sequences in context. Whole genomes of the SARS-CoV-2 virus are being collected and shared from across the globe. With the advent of affordable and prolific Next Generation Sequencing, this is the first pandemic in which the genomic evolution of the pathogen can be tracked in near real-time. So far, phylogenetic analysis methods have recently found a broader application in this regard. Here we demonstrate that Principal Component Analysis (PCA), used heavily in population genetics, corroborates the existing findings while providing unique new capabilities to understand our public repositories of complete virus sequences. This novel application of PCA is demonstrated on all publicly available SARS-CoV-2 samples from GenBank and other open-access databases until mid-April. We show that PCA is a useful and easy-to-use tool to analyze SARS-CoV-2 genomes in addition to phylogenetic analytics. It offers a previously untapped opportunity to analyze the dynamics of the current SARS-CoV-2 pandemic in a new way.