Since its first appearance in China, in the end of 2019, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has mutated into several variants. The genome analysis of the spike of SARS-CoV-2 is necessary to identify the mutations in each variant. In this study, we obtained the whole genome sequences of SARS-CoV-2 Wild Type and variants from GenBank (National Center of Biotechnology Information, USA), and GISAID EpiCoV database (Germany). We analyzed the spike glycoprotein gene sequences using the Basic Local Alignment Search Tool (BLAST), and identified the changes in nucleotide and amino acid. Additionally, we also discuss the prevalence and correlation between the submission time of SARS-CoV-2 variants on the GISAID database with the outbreak timeline. The result of our analysis showed that there are 9 amino acid changes in SARS-CoV-2 alpha, beta and delta variants, and 3 amino acid changes in gamma variant. There were 8,861 submissions of Indonesian variants on the GISAID database per November 21, 2021. The correlation between submission time of SARS-CoV-2 variants and outbreak timeline showed that SARS-CoV-2 delta (B.1.617.2) variant potentially caused the sudden increase of COVID-19 confirmed cases from July to September 2021.