Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials & Methods

Clinical sample collections

Full-genome sequencing

Genome annotation and phylogenetic analysis

Mutation visualization

Ethical approval

Results

Demographics and clinical severity of COVID-19 patients

Full genome characterization of SARS-CoV-2 isolated from Makassar, South Sulawesi

Mutation analysis of the S protein

Mutation analysis of other SARS-CoV-2 genome regions

Discussion

Conclusion

Supplemental Information

The acknowledgment table for GISAID

DOI: 10.7717/peerj.13522/supp-1

The amino acid variations of 50 SARS-CoV-2 isolates collected from Makassar, South Sulawesi, Indonesia

The positions referred to the reference sequence NC_045512.2. The frequencies of each mutation are depicted in the lowest rows.

DOI: 10.7717/peerj.13522/supp-2

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests

Author Contributions

Muhammad Nasrum Massi conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Rufika Shari Abidin conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Abd-ElAziem Farouk performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Handayani Halik analyzed the data, prepared figures and/or tables, and approved the final draft.

Gita Vita Soraya conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Najdah Hidayah conceived and designed the experiments, prepared figures and/or tables, and approved the final draft.

Rizalinda Sjahril conceived and designed the experiments, prepared figures and/or tables, and approved the final draft.

Irda Handayani performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Mohamad Saifudin Hakim conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Faris Muhammad Gazali performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Vivi Setiawaty conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Tri Wibawa conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The study has obtained ethical approval from the Health Research Ethical Committee of Faculty of Medicine, Universitas Hasanuddin, Makassar, South Sulawesi, Indonesia (No. 845/UN4.6.5.31/PP36/2020).

Microarray Data Deposition

The following information was supplied regarding the deposition of microarray data:

https://www.epicov.org/epi3/frontend#252fd0

Data Availability

The following information was supplied regarding data availability:

The SARS-CoV-2 genome sequences used in this study are available via GISAID

(https://www.epicov.org/epi3/frontend#252fd0):

EPI_ISL_1247019; EPI_ISL_1247873; EPI_ISL_1248934; EPI_ISL_1249610; EPI_ISL_1250222; EPI_ISL_1258423; EPI_ISL_1258424; EPI_ISL_1258463; EPI_ISL_1258464; EPI_ISL_1258465; EPI_ISL_1263319; EPI_ISL_1263320; EPI_ISL_1263321; EPI_ISL_1263322; EPI_ISL_1263323; EPI_ISL_1630277; EPI_ISL_1630278; EPI_ISL_1630279; EPI_ISL_1630280; EPI_ISL_1630281; EPI_ISL_2691912; EPI_ISL_2692137; EPI_ISL_2692142; EPI_ISL_2692143; EPI_ISL_2692144; EPI_ISL_2692169; EPI_ISL_2692170; EPI_ISL_2692171; EPI_ISL_2692179; EPI_ISL_2692205; EPI_ISL_2692206; EPI_ISL_2692531; EPI_ISL_2692533; EPI_ISL_2692706; EPI_ISL_2692880; EPI_ISL_2692882; EPI_ISL_2692883; EPI_ISL_2692884; EPI_ISL_2692886; EPI_ISL_2692887; EPI_ISL_2692889; EPI_ISL_2692891; EPI_ISL_2692892; EPI_ISL_2692896; EPI_ISL_2692897; EPI_ISL_2692899; EPI_ISL_2692900; EPI_ISL_2692902; EPI_ISL_2692903; EPI_ISL_2692905.

Funding

This work is supported by the Ministry of Research and Technology/National Research and Innovation Agency of Republic Indonesia (Ristek-BRIN) in collaboration with Indonesia Endowment Fund for Education (Lembaga Pengelola Dana Pendidikan/LPDP) (Grant no. 13/FI/P-KCOVID-19.2B3/X/2020). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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