Sequence analysis of SARS-CoV-2 Delta variant isolated from Makassar, South Sulawesi, Indonesia

Muhammad Nasrum Massi; Rizalinda Sjahril; Handayani Halik; Gita Vita Soraya; Najdah Hidayah; Muhammad Yogi Pratama; Muhammad Faruk; Irda Handayani; Faris Muhammad Gazali; Mohamad Saifudin Hakim; Tri Wibawa

doi:10.1016/j.heliyon.2023.e13382

Sequence analysis of SARS-CoV-2 Delta variant isolated from Makassar, South Sulawesi, Indonesia

Heliyon. 2023 Feb;9(2):e13382. doi: 10.1016/j.heliyon.2023.e13382. Epub 2023 Jan 31.

Authors

Muhammad Nasrum Massi^{1

2

3}, Rizalinda Sjahril^{1

3}, Handayani Halik^{2

4}, Gita Vita Soraya⁵, Najdah Hidayah^{2

6}, Muhammad Yogi Pratama^{7

8}, Muhammad Faruk⁹, Irda Handayani¹⁰, Faris Muhammad Gazali¹¹, Mohamad Saifudin Hakim¹², Tri Wibawa¹²

Affiliations

¹ Department of Clinical Microbiology, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
² Hasanuddin University Medical Research Center (HUM-RC) Laboratory, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
³ Microbiology Laboratory, Hasanuddin University Hospital, Makassar, Indonesia.
⁴ Mega Rezky University, Makassar, Indonesia.
⁵ Department of Biochemistry, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
⁶ Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), Tangerang Selatan, Indonesia.
⁷ Department of Pathology Anatomy, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
⁸ Division of Vascular and Endovascular Surgery, Department of Surgery, New York University Langone Medical Center, New York, NY, USA.
⁹ Department of Surgery, Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia.
¹⁰ Clinical Pathology Laboratory, Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia.
¹¹ Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia.
¹² Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.

Abstract

Introduction: This study aimed to perform mutation and phylogenetic analyses of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta variants and analyze the characteristic signs and symptoms of patients infected with SARS-CoV-2 Delta variant originated from Makassar during the Delta outbreak.Methods: We collected samples from patients who were infected with coronavirus disease 2019 (COVID-19) between June and October 2021. We selected the Quantitative Reverse Transcription-Polymerase Chain Reaction (PCR)-positive samples with a cycle threshold value of <30 for whole genome sequencing. Total viral ribonucleic acid (RNA) was isolated from 34 PCR-positive nasopharyngeal swab samples, and whole genome sequencing was performed using the Oxford Nanopore GridlON sequencer. Phylogenetic and maximum clade credibility analyses were performed using the Bayesian Markov chain Monte Carlo method.

Results: It was found that 33 patients were infected with the SARS-CoV-2 Delta variant in this cohort study, among whom 63.6% (21) patients were female. According to the clinical data, 24 (72.7%), 7 (21.2%), and 2 (6.1%) patients had mild, moderate, and severe COVID-19 infections. Phylogenetic analysis based on the spike and RNA-dependent RNA polymerase (RdRp) genes showed that the collected samples were clustered in the main lineage of B.1.617.2 (Delta variant). The Delta variants had a high frequency of distinct mutations in the spike protein region, including T19R (94.12%), L452R (88.23%), T478K (91.17%), D614G (97%), P681R (97%), and D950 N (97%). Other unique mutations found in a smaller frequency in our samples were present in the N-terminal domain, including A27T (2.94%) and A222V (14.70%), and in the receptor-binding domain, including Q414K (5.88%), G446V (2.94%), and T470 N (2.94%).

Conclusion: This study revealed the unique mutations in the S protein region of Delta variants. T19R, L452R, T478K/T478R, D614G, P681R, and D950 N were the most common substitutions in Makassar's Delta variant.

Keywords: COVID-19; Delta variant; SARS-CoV-2; VOC; Whole genome sequencing.