SARS-COV-2 GENOME MUTATION PROFILE ANALYSIS IN TROPICAL AND TEMPERATE ZONE BETWEEN DECEMBER 2020 – JANUARY 2021

• Main Author: Wijayana, Sena
• Format: Final Project
• Language: Indonesia
• Subjects: Genetika dan evolusi
• Online Access: https://digilib.itb.ac.id/gdl/view/55280
• Institution: Institut Teknologi Bandung

mutation can impact viral infectioness and survivability at certain environment condition and host’s immune system. The spread of COVID-19 can be affacted by pathogen, host and environment factor. Eventhough there are various studies that shown a link between host and environmental factors with the spread of COVID-19, but these studies only reviewed the positive number cases. Analysis of the mutation profile in the virus can provide information regarding the ability of SARS-CoV-2 infection based on environmental and host factors and also provide an understanding the dynamics of the SARS-CoV-2 mutation. This study was conducted to determine the mutation profile of SARS-CoV-2 based on differences in tropical and temperate zones and to determine the SARS-CoV-2 mutation profiles that infect humans based on differences in gender and age of the patient. The method of this study consist of searching 4124 SARS-CoV-2 complete genome sequence and patient metadata through the GISAID database during collection date from December 1, 2020, to January 31, 2021, which were high coverage, then alignment and cutting of sequence on Highly mutation ORF/CDS (NSP2, NSP3, RdRp, and Spike) with Jalview and MAFFT. Sequence data obtained is inputted into Nextclade to determine mutations that occur in each sequence. The type and frequency of mutations were determined and grouped with the Jupyter program based on latitude (Northern Temperate, Tropic of Cancer, Tropic of Capricorn, and Southern Temperate) then visualized with a bar chart and analyzed by determining the similarity and dissimilarity value in the proximity matrix with Pearson correlation coefficient and Euclidean distance parameters, then visualized with PCoA (Principal Coordinate Analysis) on XLSTAT. Dominant mutations in each tropical and temperate zone were used to determined by the percentage of occurrence based on gender (male and female) and age group (<18, 18 – 60, and >60 years) with Jupyter and visualized with bar charts and analyzed for similarity of data on proximity matrix with parameters Pearson correlation coefficient on XLSTAT. Different types of dominant mutations were obtained in each tropical and temperate zone in NSP2, NSP3, RdRp and Spike. The similarity value of the tropical and temperate zone mutation profiles showed <0.95 with a difference value of >0.67. The visualization on PCoA shows that each zone is in a different quadrant. The results of the mutation profile in each tropical and temperate zone based on gender and age groups obtained a similarity value >0.95. Based on these results, the dominant mutation profile in the tropical and temperate zones has been obtained with significantly different dominant mutation profiles. The dominant mutation profile of SARSCoV- 2 that infects patients by gender and age group in each tropical zone and temperature is not significantly different.