Research Article
BibTex RIS Cite
Year 2022, Volume: 12 Issue: 04, 139 - 147, 15.12.2022
https://doi.org/10.5799/jmid.1218631

Abstract

References

  • 1. Lu R, Zhao X, Li J, et al. 2020. Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020; 395: 565–574.
  • 2. Khailany RA, Safdar M, Ozaslan M. Genomic characterization of a novel SARS-CoV-2. Gene Rep 2020; 19: 100682.
  • 3. Zhou L, Ayeh SK, Chidambaram V, et al. Modes of transmission of SARS-CoV-2 and evidence for preventive behavioral interventions. BMC Infect Dis 2021; 21: 496.
  • 4. Ozaslan M, Safdar M, Halil KI, Khailany RA. Practical measures to prevent COVID-19: a mini-review. J Biol Sci 2020; 20: 100–102.
  • 5. COVID Live. Accessed by https://www.worldometers.info/coronavirus/.
  • 6. Tordoff DM, Greninger AL, Roychoudhury P, et al. Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. Lancet Reg Health Am 2021;1:100018.
  • 7. Pachetti M, Marini B, Benedetti F, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med 2020; 18(1):179.
  • 8. Global Initiative on Sharing ALL Influenza Data (GISAID). Accessed by https://www.gisaid.org/.
  • 9. Yao H, Lu X, Chen Q, et al. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell Discov 2020; 6: 76.
  • 10. Hakim MS, Annisa L, Supriyati E, et al. Current understanding of the origin, molecular biology, and continuing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Med Sci 2020; 52(3): 54-66.
  • 11. The National Center of Biotechnology Information (NCBI). Accessed by https://ncbi.nlm.nih.gov/.
  • 12. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020; 382:8.
  • 13. Abdullahi IN, Emeribe AU, Ajayi OA, Oderinde BS, Amadu DO, Osuji AI. Implications of SARS-CoV-2 genetic diversity and mutations on pathogenicity of the COVID-19 and biomedical interventions. J Taibah Univ Med Sci 2020; 15(4): 258-264.
  • 14. Dowd JB, Andriano L, Brazel DM, Mills MC. Demoghrapich science aids in understanding the spread and fatality rates of Covid19. PNAS 2020; 117: 9696-9698.
  • 15. Aisyah DN, Mayadewi CA, Diva H, Kozlakidis Z, Siswanto, Adisasmito W. A spatial-temporal description of the SARS-CoV-2 infections in Indonesia during the first six months of the outbreak. PLoS ONE 2020; 15(12): e0243703.
  • 16. Mboi N, Surbakti IM, Trihandini I, et al. On the road to universal health care in Indonesia, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet 2018; 392: 581–591. 17. World Health Organization (WHO). 2018. Noncommunicable diseases country profiles. License: CC BY-NC-SA 3.0 IGO. ISBN 978-92-4-151462-0.
  • 18. Clark A, Jit M, Gash CW, et al. Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modeling study. Lancet Glob Health 2020; 8: e1003–17.
  • 19. Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biol 2018; 16(8): e3000003.
  • 20. Tabibzadeh A, Zamani F, Laali A, et al. SARS-CoV-2 Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran. Infection, Genetics, and Evolution; 2020 ;84: 104387.
  • 21. Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 2020; 180: 281–292.
  • 22. Chan JF, Kong K, Zhu Z, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. Microbes Infect 2020; 9.
  • 23. Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits a higher case fatality rate. Int J Clin Pract 2020; 74(8): e13525.
  • 24. Zhang H, Penninger JM, Li Y, Zhong N, Slutsky AS. Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med 2020; 46(4): 586-590.

Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic

Year 2022, Volume: 12 Issue: 04, 139 - 147, 15.12.2022
https://doi.org/10.5799/jmid.1218631

Abstract

Objectives: This study aims to understand the epidemiological and level of genetic similarity in the SARS-CoV-2 from different geographical areas in The Southeast Asia Region during an early pandemic.
Methods: The data on COVID-19 cases in Southeast Asia was collected from https://worldometer.info/ and extracted independently. Complete genome SARS-CoV-2 nucleotide sequence data was obtained from GISAID and NCBI online platforms. The sequences were aligned using MEGA X software and identified RdRp and Spike genes using UGENE software. The phylogenetic was constructed using MEGA X software to know the similarity of these genes among isolates in the Southeast Asia region.
Results: The result showed that the first case in Southeast Asia was reported in January 2020. The highest number of COVID-19 cases and death were reported from populous and suffering countries. The phylogenetic results showed an identical solid (100%) among isolates, except for the Philippines-5 isolate. The Wuhan-Hu-1 (China) SARS-CoV-2 isolate (Acc. NC_045512) was transmitted to other countries in Southeast Asia regions with various mutations in the spike protein.
Conclusion: During the early pandemic, all countries in the Southeast Asia regions reported COVID-19 cases. Indonesia became the country with the highest number of COVID-19 cases and deaths. The level of similarity of the RdRp gene in the SARS-CoV-2 in Southeast Asia is higher than the Spike genes. J Microbiol Infect Dis 2022; 12(4):139-148.

References

  • 1. Lu R, Zhao X, Li J, et al. 2020. Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 2020; 395: 565–574.
  • 2. Khailany RA, Safdar M, Ozaslan M. Genomic characterization of a novel SARS-CoV-2. Gene Rep 2020; 19: 100682.
  • 3. Zhou L, Ayeh SK, Chidambaram V, et al. Modes of transmission of SARS-CoV-2 and evidence for preventive behavioral interventions. BMC Infect Dis 2021; 21: 496.
  • 4. Ozaslan M, Safdar M, Halil KI, Khailany RA. Practical measures to prevent COVID-19: a mini-review. J Biol Sci 2020; 20: 100–102.
  • 5. COVID Live. Accessed by https://www.worldometers.info/coronavirus/.
  • 6. Tordoff DM, Greninger AL, Roychoudhury P, et al. Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. Lancet Reg Health Am 2021;1:100018.
  • 7. Pachetti M, Marini B, Benedetti F, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med 2020; 18(1):179.
  • 8. Global Initiative on Sharing ALL Influenza Data (GISAID). Accessed by https://www.gisaid.org/.
  • 9. Yao H, Lu X, Chen Q, et al. Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo. Cell Discov 2020; 6: 76.
  • 10. Hakim MS, Annisa L, Supriyati E, et al. Current understanding of the origin, molecular biology, and continuing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Med Sci 2020; 52(3): 54-66.
  • 11. The National Center of Biotechnology Information (NCBI). Accessed by https://ncbi.nlm.nih.gov/.
  • 12. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020; 382:8.
  • 13. Abdullahi IN, Emeribe AU, Ajayi OA, Oderinde BS, Amadu DO, Osuji AI. Implications of SARS-CoV-2 genetic diversity and mutations on pathogenicity of the COVID-19 and biomedical interventions. J Taibah Univ Med Sci 2020; 15(4): 258-264.
  • 14. Dowd JB, Andriano L, Brazel DM, Mills MC. Demoghrapich science aids in understanding the spread and fatality rates of Covid19. PNAS 2020; 117: 9696-9698.
  • 15. Aisyah DN, Mayadewi CA, Diva H, Kozlakidis Z, Siswanto, Adisasmito W. A spatial-temporal description of the SARS-CoV-2 infections in Indonesia during the first six months of the outbreak. PLoS ONE 2020; 15(12): e0243703.
  • 16. Mboi N, Surbakti IM, Trihandini I, et al. On the road to universal health care in Indonesia, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet 2018; 392: 581–591. 17. World Health Organization (WHO). 2018. Noncommunicable diseases country profiles. License: CC BY-NC-SA 3.0 IGO. ISBN 978-92-4-151462-0.
  • 18. Clark A, Jit M, Gash CW, et al. Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modeling study. Lancet Glob Health 2020; 8: e1003–17.
  • 19. Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biol 2018; 16(8): e3000003.
  • 20. Tabibzadeh A, Zamani F, Laali A, et al. SARS-CoV-2 Molecular and Phylogenetic analysis in COVID-19 patients: A preliminary report from Iran. Infection, Genetics, and Evolution; 2020 ;84: 104387.
  • 21. Walls AC, Park Y-J, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 2020; 180: 281–292.
  • 22. Chan JF, Kong K, Zhu Z, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. Microbes Infect 2020; 9.
  • 23. Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits a higher case fatality rate. Int J Clin Pract 2020; 74(8): e13525.
  • 24. Zhang H, Penninger JM, Li Y, Zhong N, Slutsky AS. Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med 2020; 46(4): 586-590.
There are 23 citations in total.

Details

Primary Language English
Subjects Health Care Administration
Journal Section Research Article
Authors

Oktaviani Naulita Turnıp This is me

Chairunnisa Fadhillah This is me

Anwar Rovık This is me

Ayu Rahayu This is me

Publication Date December 15, 2022
Published in Issue Year 2022 Volume: 12 Issue: 04

Cite

APA Turnıp, O. N., Fadhillah, C., Rovık, A., Rahayu, A. (2022). Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic. Journal of Microbiology and Infectious Diseases, 12(04), 139-147. https://doi.org/10.5799/jmid.1218631
AMA Turnıp ON, Fadhillah C, Rovık A, Rahayu A. Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic. J Microbil Infect Dis. December 2022;12(04):139-147. doi:10.5799/jmid.1218631
Chicago Turnıp, Oktaviani Naulita, Chairunnisa Fadhillah, Anwar Rovık, and Ayu Rahayu. “Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic”. Journal of Microbiology and Infectious Diseases 12, no. 04 (December 2022): 139-47. https://doi.org/10.5799/jmid.1218631.
EndNote Turnıp ON, Fadhillah C, Rovık A, Rahayu A (December 1, 2022) Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic. Journal of Microbiology and Infectious Diseases 12 04 139–147.
IEEE O. N. Turnıp, C. Fadhillah, A. Rovık, and A. Rahayu, “Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic”, J Microbil Infect Dis, vol. 12, no. 04, pp. 139–147, 2022, doi: 10.5799/jmid.1218631.
ISNAD Turnıp, Oktaviani Naulita et al. “Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic”. Journal of Microbiology and Infectious Diseases 12/04 (December 2022), 139-147. https://doi.org/10.5799/jmid.1218631.
JAMA Turnıp ON, Fadhillah C, Rovık A, Rahayu A. Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic. J Microbil Infect Dis. 2022;12:139–147.
MLA Turnıp, Oktaviani Naulita et al. “Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic”. Journal of Microbiology and Infectious Diseases, vol. 12, no. 04, 2022, pp. 139-47, doi:10.5799/jmid.1218631.
Vancouver Turnıp ON, Fadhillah C, Rovık A, Rahayu A. Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in the Southeast Asia in Early Pandemic. J Microbil Infect Dis. 2022;12(04):139-47.