Jurnal Internasional Medical Journal of Indonesia FKUI Vol. 30 No. 2 2021
Analysis of SARS-CoV-2 Nucleocapsid Protein Sequence Variations in ASEAN Countries
Dublin Core
Title
Jurnal Internasional Medical Journal of Indonesia FKUI Vol. 30 No. 2 2021
Analysis of SARS-CoV-2 Nucleocapsid Protein Sequence Variations in ASEAN Countries
Analysis of SARS-CoV-2 Nucleocapsid Protein Sequence Variations in ASEAN Countries
Subject
nucleocapsid proteins, phylogeny, SARS-CoV-2, sequence alignment
Description
BACKGROUND Nucleocapsid (N) protein is one of four structural proteins of SARS-CoV-2 which is known to be more conserved than spike protein and is highly immunogenic. This study aimed to analyze the variation of the SARS-CoV-2 N protein sequences in ASEAN countries, including Indonesia.
METHODS Complete sequences of SARS-CoV-2 N protein from each ASEAN country were obtained from Global Initiative on Sharing All Influenza Data (GISAID), while the reference sequence was obtained from GenBank. All sequences collected from December 2019 to March 2021 were grouped to the clade according to GISAID, and two
representative isolates were chosen from each clade for the analysis. The sequences were aligned by MUSCLE, and phylogenetic trees were built using MEGA-X software based on the nucleotide and translated AA sequences.
RESULTS 98 isolates of complete N protein genes from ASEAN countries were analyzed. The nucleotides of all isolates were 97.5% conserved. Of 31 nucleotide changes, 22 led to amino acid (AA) substitutions; thus, the AA sequences were 94.5% conserved. The phylogenetic tree of nucleotide and AA sequences shows similar branches. Nucleotide
variations in clade O (C28311T); clade GR (28881–28883 GGG>AAC); and clade GRY (28881–28883 GGG>AAC and C28977T) lead to specific branches corresponding to the clade within both trees.
CONCLUSIONS The N protein sequences of SARS-CoV-2 across ASEAN countries are highly conserved. Most isolates were closely related to the reference sequence originating from China, except the isolates representing clade O, GR, and GRY which formed specific branches in the phylogenetic tree.
METHODS Complete sequences of SARS-CoV-2 N protein from each ASEAN country were obtained from Global Initiative on Sharing All Influenza Data (GISAID), while the reference sequence was obtained from GenBank. All sequences collected from December 2019 to March 2021 were grouped to the clade according to GISAID, and two
representative isolates were chosen from each clade for the analysis. The sequences were aligned by MUSCLE, and phylogenetic trees were built using MEGA-X software based on the nucleotide and translated AA sequences.
RESULTS 98 isolates of complete N protein genes from ASEAN countries were analyzed. The nucleotides of all isolates were 97.5% conserved. Of 31 nucleotide changes, 22 led to amino acid (AA) substitutions; thus, the AA sequences were 94.5% conserved. The phylogenetic tree of nucleotide and AA sequences shows similar branches. Nucleotide
variations in clade O (C28311T); clade GR (28881–28883 GGG>AAC); and clade GRY (28881–28883 GGG>AAC and C28977T) lead to specific branches corresponding to the clade within both trees.
CONCLUSIONS The N protein sequences of SARS-CoV-2 across ASEAN countries are highly conserved. Most isolates were closely related to the reference sequence originating from China, except the isolates representing clade O, GR, and GRY which formed specific branches in the phylogenetic tree.
Creator
Mochammad Rajasa Mukti Negara, Ita Krissanti, Gita Widya Pradini
Publisher
Fakultas Kedokteran Universitas Indonesia
Date
2021-06-30
Contributor
Sri Wahyuni
Rights
ISSN : 0853-1773
Format
PDF
Language
English
Type
Text
Coverage
Jurnal Internasional Medical Journal of Indonesia FKUI Vol. 30 No. 2 2021
Files
Citation
Mochammad Rajasa Mukti Negara, Ita Krissanti, Gita Widya Pradini, “Jurnal Internasional Medical Journal of Indonesia FKUI Vol. 30 No. 2 2021
Analysis of SARS-CoV-2 Nucleocapsid Protein Sequence Variations in ASEAN Countries,” Repository Horizon University Indonesia, accessed February 6, 2025, https://repository.horizon.ac.id/items/show/1003.
Analysis of SARS-CoV-2 Nucleocapsid Protein Sequence Variations in ASEAN Countries,” Repository Horizon University Indonesia, accessed February 6, 2025, https://repository.horizon.ac.id/items/show/1003.