Due to the high mutation rate of the virus, the COVID-19 pandemic evolved rapidly. Certain variants of the virus, such as Delta and Omicron emerged with altered viral properties leading to severe transmission and death rates. These variants burdened the medical systems worldwide with a major impact to travel, productivity, and the world economy. Unsupervised machine learning methods have the ability to compress, characterize, and visualize unlabelled data. This paper presents a framework that utilizes unsupervised machine learning methods to discriminate and visualize the associations between major COVID-19 variants based on their genome sequences. These methods comprise a combination of selected dimensionality reduction and clustering techniques. The framework processes the RNA sequences by performing a k-mer analysis on the data and further visualises and compares the results using selected dimensionality reduction methods that include principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation projection (UMAP). Our framework also employs agglomerative hierarchical clustering to visualize the mutational differences among major variants of concern and country-wise mutational differences for selected variants (Delta and Omicron) using dendrograms. We also provide country-wise mutational differences for selected variants via dendrograms. We find that the proposed framework can effectively distinguish between the major variants and has the potential to identify emerging variants in the future.

Due to the rapid evolution of the SARS-CoV-2 (COVID-19) virus, a number of mutations emerged with variants such as Alpha, Gamma, Delta and Omicron which created massive impact to the world economy. Unsupervised machine learning methods have the ability to compresses, characterize and visualises unlabelled data. In this paper, we present a framework that utilizes unsupervised machine learning methods that includes combination of selected dimensional reduction and clustering methods to discriminate and visualise the associations with the major COVID-19 variants based on genome sequences. The framework utilises k-mer analysis for processing the genome (RNA) sequences and compares different dimensional reduction methods, that include principal component analysis (PCA), and t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation projection (UMAP). Furthermore, the framework employs agglomerative hierarchical clustering methods and provides a visualisation using a dendogram. We find that the proposed framework can effectively distinguish the major variants and hence can be used for distinguishing emerging variants in the future.