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Whole-genome-scale analysis of circulating SARS-CoV-2 during the first COVID-19 wave in an international tourist destination, Bali, Indonesia

  • Sri Masyeni ,
  • Duwi Sumohadi ,
  • Krisna Duta ,
  • Ida Ayu Mahayani ,
  • Komang Parwata ,
  • Agus Eka Darwinata ,
  • Harapan ,

Abstract

Background: The emergence of severe acute respiratory syndromes coronavirus 2 (SARS-CoV-2) variants such as B.1.17 (alpha), B.1351 (beta), and B.1.617.2 (delta) have caused a significant rise in coronavirus disease 2019 (COVID-19) cases worldwide. In response, the Indonesian government imposed restrictions on international and domestic travel, especially in areas with a high number of COVID-19 cases including Java Island and Bali. The aim of this study was to investigate the mutation patterns of indigenous SARS-CoV-2 strains in Bali.

Methods: We conducted whole-genome sequencing on isolates collected from COVID-19-confirmed patients at the end of the first wave (January – March 2021). The sequencing was carried out at the 1st BASE Pte Ltd Laboratory (Singapore) using Oxford Nanopore Platform (GridION) using IDT ARTIC nCoV-2019 V3 Panel. The phylogenetic tree was constructed on MEGA 7.0 with hCoV-19/Wuhan/WIV04/2019 as the genomic reference.

Results: Our data revealed that none of the isolates were variants of concern. Among the five lineages tracked, the viral isolates were most likely from B.1.466.2 (n=4). All viruses had D614G mutation in the spike protein with clade GH being most predominant (n=10) and followed by GR (n=1) and O (n=1). Additionally, mutations at NS3, NSP3, NSP12, and NSP6 were found.

Conclusion: At the end of the first COVID-19 wave in Bali, variants of concern were not detected which could be attributed to the heavy mobility restrictions.

References

  1. Fahriani M, Anwar S, Yufika A, Bakhtiar B, Wardani E, Winardi W, et al. Disruption of childhood vaccination during the COVID-19 pandemic in Indonesia. Narra J. 2021;1(1). Available from: http://dx.doi.org/10.52225/narraj.v1i1.7
  2. Winardi W, Wahyuni H, Hidayat M, Wirawan A, Uddin MN, Yusup M. Challenges on tuberculosis care in health care facilities during COVID-19 pandemic: Indonesian perspective. Narra J. 2022;2(2). Available from: http://dx.doi.org/10.52225/narra.v2i2.80
  3. Berlin DA, Gulick RM, Martinez FJ. Severe Covid-19. N Engl J Med. 2020;383(25):2451–60. Available from: http://dx.doi.org/10.1056/nejmcp2009575
  4. Masyeni S, Santoso MS, Widyaningsih PD, Asmara DW, Nainu F, Harapan H, et al. Serological cross-reaction and coinfection of dengue and COVID-19 in Asia: Experience from Indonesia. Int J Infect Dis. 2020/10/25. 2021;102:152–4. Available from: https://pubmed.ncbi.nlm.nih.gov/33115680
  5. Ghayda RA, Lee KH, Han YJ, Ryu S, Hong SH, Yoon S, et al. Estimation of global case fatality rate of coronavirus disease 2019 (COVID-19) using meta-analyses: Comparison between calendar date and days since the outbreak of the first confirmed case [Internet]. Cold Spring Harbor Laboratory; 2020. Available from: http://dx.doi.org/10.1101/2020.06.11.20128959
  6. Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, et al. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. Narra J. 2022;2(3):e92. Available from: http://dx.doi.org/10.52225/narra.v2i3.92
  7. Masyeni S, Iqhrammullah M, Frediansyah A, Nainu F, Tallei T, Emran T Bin, et al. Molnupiravir: A lethal mutagenic drug against rapidly mutating severe acute respiratory syndrome coronavirus 2-A narrative review. J Med Virol. 2022/04/02. 2022;94(7):3006–16. Available from: https://pubmed.ncbi.nlm.nih.gov/35315098
  8. Mudatsir M, Keam S, Winardi W, Yufika A, Rabaan AA, Rodriguez-Morales AJ, et al. Early transmission dynamics of SARS-CoV-2 in Indonesia. Trends Infect Glob Heal. 2021;1(1):1–6. Available from: http://dx.doi.org/10.24815/tigh.v1i1.20134
  9. Lai S, Bogoch I, Ruktanonchai N, Watts A, Lu X, Yang W, et al. Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study. medRxiv Prepr Serv Heal Sci. 2020;2020.02.04.20020479. Available from: https://pubmed.ncbi.nlm.nih.gov/32511631
  10. Katsnelson A. Coronavirus entry points could explain its spread. C&EN Glob Enterp. 2020;98(17):4. Available from: http://dx.doi.org/10.1021/cen-09817-scicon9
  11. .Wilson D. “Pre‑Omicron”, COVID‑19 cases peaked mid‑2021 in India, Indonesia and Japan… [Internet]. Organisation for Economic Co-Operation and Development (OECD); 2022. Available from: http://dx.doi.org/10.1787/7d18b6be-en
  12. Heguy A. Review 2: “A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa” [Internet]. MIT Press - Journals; 2021. Available from: http://dx.doi.org/10.1162/2e3983f5.3d1fbfc5
  13. Nidom R V, Indrasari S, Normalina I, Nidom AN, Afifah B, Dewi L, et al. An Updated Investigation Prior To COVID-19 Vaccination Program In Indonesia: Full-Length Genome Mutation Analysis Of SARS-CoV-2 [Internet]. Cold Spring Harbor Laboratory; 2021. Available from: http://dx.doi.org/10.1101/2021.01.26.426655
  14. Gunadi, Hendra W, Marcellus, Mohamad SH, Edwin WD, Ludhang PR, et al. Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Indonesia. Research Square. 2020.
  15. Massi MN, Abidin RS, Farouk A-E, Halik H, Soraya GV, Hidayah N, et al. Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia. PeerJ. 2022;10:e13522–e13522. Available from: https://pubmed.ncbi.nlm.nih.gov/35707124
  16. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22(13):30494. Available from: https://pubmed.ncbi.nlm.nih.gov/28382917
  17. Islam O, emran H Al, Hasan M, Anwar A, Jahid M, Hossain M. Emergence of European and North American mutant variants of SARS-CoV-2 in Southeast Asia [Internet]. Authorea, Inc.; 2020. Available from: http://dx.doi.org/10.22541/au.159112172.23549094
  18. Freed N, Silander O. nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) v3 [Internet]. ZappyLab, Inc.; 2020. Available from: http://dx.doi.org/10.17504/protocols.io.bgggjttw
  19. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013/01/16. 2013;30(4):772–80. Available from: https://pubmed.ncbi.nlm.nih.gov/23329690
  20. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012/04/27. 2012;28(12):1647–9. Available from: https://pubmed.ncbi.nlm.nih.gov/22543367
  21. Stamatakis A, Hoover P, Rougemont J. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol. 2008;57(5):758–71. Available from: http://dx.doi.org/10.1080/10635150802429642
  22. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22(21):2688–90. Available from: http://dx.doi.org/10.1093/bioinformatics/btl446
  23. Hamed SM, Elkhatib WF, Khairalla AS, Noreddin AM. Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Sci Rep. 2021;11(1):8435. Available from: https://pubmed.ncbi.nlm.nih.gov/33875719
  24. Zainulabid UA, Mat Yassim AS, Hussain M, Aslam A, Soffian SN, Mohd Ibrahim MS, et al. Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. PLoS One. 2022;17(2):e0263678–e0263678. Available from: https://pubmed.ncbi.nlm.nih.gov/35213571
  25. Yingtaweesittikul H, Ko K, Abdul Rahman N, Tan SYL, Nagarajan N, Suphavilai C. CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking. Front Med. 2021;8:790662. Available from: https://pubmed.ncbi.nlm.nih.gov/34970567
  26. Zhu M, Zeng Q, Saputro BIL, Chew SP, Chew I, Frendy H, et al. Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data. Virol J. 2022;19(1):103. Available from: https://pubmed.ncbi.nlm.nih.gov/35710544
  27. Hoan NX, Pallerla SR, Huy PX, Krämer H, My TN, Tung TT, et al. SARS-CoV-2 viral dynamics of the first 1000 sequences from Vietnam and neighbouring ASEAN countries. IJID Reg. 2022/01/20. 2022;2:175–9. Available from: https://pubmed.ncbi.nlm.nih.gov/35721434
  28. Nagy Á, Pongor S, Győrffy B. Different mutations in SARS-CoV-2 associate with severe and mild outcome. Int J Antimicrob Agents. 2020/12/23. 2021;57(2):106272. Available from: https://pubmed.ncbi.nlm.nih.gov/33347989
  29. Alam ASMRU, Islam OK, Hasan MS, Islam MR, Mahmud S, Al-Emran HM, et al. Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. J Med Virol. 2021/11/01. 2022;94(3):1035–49. Available from: https://pubmed.ncbi.nlm.nih.gov/34676891
  30. Wise J. Covid-19: Delta variant doubles risk of hospital admission compared with alpha variant, study shows. BMJ. 2021;n2152. Available from: http://dx.doi.org/10.1136/bmj.n2152
  31. Alkayyali T, Ochuba O, Srivastava K, Sandhu JK, Joseph C, Ruo SW, et al. An Exploration of the Effects of Radiofrequency Radiation Emitted by Mobile Phones and Extremely Low Frequency Radiation on Thyroid Hormones and Thyroid Gland Histopathology. Cureus. 2021;13(8):e17329–e17329. Available from: https://pubmed.ncbi.nlm.nih.gov/34567874

How to Cite

Masyeni, S., Sumohadi, D. ., Duta, K. ., Mahayani, I. A. ., Parwata, K. ., Darwinata, A. E. ., & Harapan. (2023). Whole-genome-scale analysis of circulating SARS-CoV-2 during the first COVID-19 wave in an international tourist destination, Bali, Indonesia. Bali Medical Journal, 12(2), 1484–1489. https://doi.org/10.15562/bmj.v12i2.4211

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