SEQUENCE ANALYSIS OF THE NUCLEOCAPSID PROTEIN GENE OF SARS-COV-2 IN COVID-19 PATIENTS IN WEST JAVA, INDONESIA

• Main Author: Annisa Evitayani, Irin
• Format: Final Project
• Language: Indonesia
• Subjects: Ilmu hayati ; Biologi
• Online Access: https://digilib.itb.ac.id/gdl/view/53835
• Institution: Institut Teknologi Bandung

The coronavirus disease 2019 (COVID-19) pandemic has taken a lot of lives in almost every country on earth. The disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known as a contagious infection with high virus transmissibility. Its genome encodes structural protesins such as surface (S), membrane (M), envelope (E), dan nucleocapsid (N) proteins. According to various journal articles, SARS-CoV-2 N gene has one of the highest mutation number among SARS-CoV-2 genes. N protein functions to bind RNA in a process called packaging. An antiviral drug that targets this process could hinder viral replication However, studies regarding N gene variant analysis in Indonesia are still limited. Therefore, this research aims to analyze the variants of SARS-CoV-2 nucleocapsid genes in COVID-19 patients in West Java, Indonesia, by observing phylogenetic and protein secondary structure analysis. Oropharyngealnasopharyngeal swab samples were obtained from Laboratorium Kesehatan Provinsi Jawa Barat, then amplified with PCR method. N gene sequence was read by Sanger sequencing. The results found three different mutations on two samples, R203K/G204R and A211S on the the first sample and S193I on the second sample, with one degenerate base found. Looking at Indonesian samples from GISAID, the mutation R203K/G204R is a mutation that occurs most often in N gene, while S193I has the third highest occurance. A211S is a novel mutation that hasn’t been reported, but is found on GISAID data sequence with very low frequency. Phylogenetic analysis shows the first sample grouped with 11 Indonesian samples that also have R203K/G204R mutation, while the second sample grouped with 8 Indonesian samples that also have S193I mutation. A total of 178 sequences used in this analysis does not appear to have A211S mutation. Nucleocapsid proteins, each with R203K/G204R and another with S193I mutation, are shown to have an increased number of beta strands than wild-type protein. Beta strands are known to be more rigid than other secondary structures.