Implementation of Hierarchical Clustering Method in Analyzing Genetic Relationship on DNA SARS-CoV-2 Sequences

Abstract

In mid-September of 2020, WHO released data starting that more than 28 million people worldwide have contracted coronavirus. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the full name coronavirus, specifically Covid-19. This virus attacks the human respiratory system and can cause infection in the human lungs and even death. WHO noted that more than 900 thousand people worldwide have died due to being infected with the coronavirus. In Indonesia, more than 210 thousand people have been infected by the coronavirus, and more than 8,5 thousand of them have died. Based on this data, it is necessary to analyze the coronavirus's kinship to reduce the spreading. This research uses The Euclidean distance in determining the distance matrix. This research will then use the Hierarchical Clustering method for analyzing the genetic relationship on DNA SARS-CoV-2 sequences. This research will take samples of SARS-CoV-2 DNA sequences from 20 countries infected. From the simulation result, the ancestors of SARS-CoV-2 coming from China. Besides, it also found that the SARS-CoV-2 DNA sequence from Indonesia has the closest ancestor from Pakistan.