Abstract
Indonesia's economy and global health is endangered due to the SARS-CoV-2 outbreak. Our present study aims to examine the phylogenetic analysis of SARS-CoV-2 isolates in Indonesia and compare these isolates to other Southeast Asian countries. In the present study, we retrieved 105 isolates from GISAID EpiCoV and other isolates from GenBank, NCBI. Then, we extracted the full genome and focused on the spike (S) protein gene (3882 bp). We employed Molecular Evolutionary Genetics Analysis (MEGA X) software to construct a phylogenetic analysis using the maximum likelihood approach. Here, we demonstrated and revealed the relationship between Indonesian and other Southeast Asian SARS-CoV-2 isolates. In summary, our work presents the phylogenetic analysis of 105 isolates in Indonesia. Our study assists in monitoring the deployment of the disease spreading. Furthermore, we suggest that the genomics and epidemiological surveillance investigations on COVID-19 should be enhanced, especially in Indonesia.
There is no Figure or data content available for this article
References
1. Kharisma V. D., A. N. M. Ansori (2020). Construction of Epitope-based Peptide Vaccine against SARS-CoV-2: Immunoinformatics Study. Journal of Pure and Applied Microbiology, 14, 999-1005.
2. Huang C., Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu, Z. Cheng, T. Yu, J. Xia, Y. Wei, W. Wu, X. Xie, W. Yin, H. Li, M. Liu, Y. Xiao, H. Gao, L. Guo, J. Xie, G. Wang, R. Jiang, Z. Gao, Q. Jin, J. Wang, B. Cao (2020). Clinical Features of Patients Infected with 2019 Novel Coronavirus in Wuhan, China. Lancet, 395(10223), 497-506.
3. Li X., E. G. Elena, M. H. Marichannegowda, B. Foley, C. Xiao, X. P. Kong, Y. Chen, S. Gnanakaran, B. Korber, F. Gao (2020). Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection. Science Advances, 6(27), eabb9153.
4. Dong E, H. Du, L. Gardner (2020). An Interactive Web-based Dashboard to Track COVID-19 in Real Time. Lancet Infectious Diseases, S1473-3099(20), 30120-30121.
5. Guo YR, Q. D. Cao, Z. S. Hong, Y. Y. Tan, S. D. Chen, H. J. Jin, K. S. Tan, D. Y. Wang, Y. Yan. (2020). The Origin, Transmission and Clinical Therapies on Coronavirus Disease 2019 (COVID-19) Outbreak - An Update on the Status. Military Medical Research, 7(1), 11.
6. LaTourrette K, Holste NM, Rodriguez-Peña R, Leme RA, Garcia-Ruiz H. Genome-Wide Variation in Betacoronaviruses. J Virol. 2021 Jul 12;95(15):e0049621. doi: 10.1128/JVI.00496-21. Epub 2021 Jul 12. PMID: 34037417; PMCID: PMC8274613.
7. Castillo A. E., B. Parra, P. Tapia, A. Acevedo, J. Lagos, W. Andrade, L. Arata, G. Leal, G. Barra, C. Tambley, J. Tognarelli, P. Bustos, S. Ulloa, R. Fasce, J. Fernández (2020). Phylogenetic Analysis of the First Four SARS-CoV-2 Cases in Chile. Journal of Medical Virology, 92(9), 1562-1566.
8. Ou X., Y. Liu, X. Lei, P. Li, D. Mi, L. Ren, L. Guo, R. Guo, T. Chen, J. Hu, Z. Xiang, Z. Mu, X. Chen, J. Chen, K. Hu, Q. Jin, J. Wang, Z. Qian (2020). Characterization of Spike Glycoprotein of SARS-CoV-2 on Virus Entry and Its Immune Cross-Reactivity with SARS-CoV. Nature Communications, 11, 1620.
9. Shereen M. A., S. Khan, A. Kazmi, N. Bashir, R. Siddique (2020). COVID-19 Infection: Origin, Transmission, and Characteristics of Human Coronaviruses. Journal of Advanced Research, 24, 91-98.
10. Phan T. (2020). Genetic Diversity and Evolution of SARS-CoV-2. Infection, Genetics and Evolution, 81, 104260.
11. Ansori A. N. M., V. D. Kharishma, S. S. Muttaqin, Y. Antonius, A. A. Parikesit (2020). Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene, Journal of Pure and Applied Microbiology, 14, 971-978.
12. Ansori A. N. M., V. D. Kharisma, Y. Antonius, M. R. Tacharina, F. Rantam (2020). Immunobioinformatics Analysis and Phylogenetic Tree Construction of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Spike Glycoprotein Gene. Jurnal Teknologi Laboratorium, 9(1), 13-20.
13. Turista D. D. R., A. Islamy, V. D. Kharisma, A. N. M. Ansori (2020). Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia. Journal of Pure and Applied Microbiology, 14, 1035-1042.
14. Hasöksüz M, Kiliç S, Saraç F. Coronaviruses and SARS-COV-2. Turk J Med Sci. 2020; 50(SI-1): 549-556.
15. Malik YA. Properties of Coronavirus and SARS-CoV-2. Malays J Pathol. 2020; 42(1): 3-11.
16. Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. Adv Exp Med Biol. 2021; 1318: 839-857.
17. Bchetnia M, Girard C, Duchaine C, Laprise C. The outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A review of the current global status. J Infect Public Health. 2020 Nov;13(11):1601-1610. doi: 10.1016/j.jiph.2020.07.011. Epub 2020 Aug 4. PMID: 32778421; PMCID: PMC7402212.
18. Chen B, Tian EK, He B, Tian L, Han R, Wang S, Xiang Q, Zhang S, El Arnaout T, Cheng W. Overview of lethal human coronaviruses. Signal Transduct Target Ther. 2020 Jun 10;5(1):89. doi: 10.1038/s41392-020-0190-2. PMID: 32533062; PMCID: PMC7289715.
19. Du L, Y. He, Y. Zhou, S. Liu, B. J. Zheng, S. Jiang (2009). The Spike Protein of SARS-CoV–A Target for Vaccine and Therapeutic Development. Nature Reviews Microbiology. 2009; 7: 226e36.
20. Yin C. (2020). Genotyping Coronavirus SARS-CoV-2: Methods and Implications. Genomics, S0888-7543(20), 30318-30319.
21. Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020 Apr 22;18(1):179. doi: 10.1186/s12967-020-02344-6. PMID: 32321524; PMCID: PMC7174922.
22. Khan M. I., Z. A. Khan, M. H. Baig, I. Ahmad, A. E. Farouk, Y. G. Song, J. J. Dong (2020). Comparative Genome Analysis of Novel Coronavirus (SARS-CoV-2) from Different Geographical Locations and the Effect of Mutations on Major Target Proteins: An In Silico Insight, PLoS One, 15(9), e0238344.
23. Wang C., Z. Liu, Z. Chen, X. Huang, M. Xu, T. He, Z. Zhang (2020). The Establishment of Reference Sequence for SARS-CoV-2 and Variation Analysis. Journal of Medical Virology, 92(6), 667-674.
24. Cui J., F. Li, Z. L. Shi (2019). Origin and Evolution of Pathogenic Coronaviruses. Nature Reviews Microbiology, 17(3), 181-192.
25. Lu R., X. Zhao, J. Li, P. Niu, B. Yang, H. Wu, W. Wang, H. Song, B. Huang, N. Zhu, Y. Bi, X. Ma, F. Zhan, L. Wang, T. Hu, H. Zhou, Z. Hu, W. Zhou, L. Zhao, J. Chen, Y. Meng, J. Wang, Y. Lin, J. Yuan, Z. Xie, J. Ma, W. J. Liu, D. Wang, W. Xu, E. C. Holmes, G. F. Gao, G. Wu, W. Chen, W. Shi, W. Tan (2020). Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding. Lancet, 395(10224), 565-574.
26. Kumar SU, Priya NM, Nithya SR, Kannan P, Jain N, Kumar DT, Magesh R, Younes S, Zayed H, Doss CGP. A review of novel coronavirus disease (COVID-19): based on genomic structure, phylogeny, current shreds of evidence, candidate vaccines, and drug repurposing. 3 Biotech. 2021; 11(4): 198.
27. Tang X., C. Wu, X. Li, Y. Song, X. Yao, X. Wu, Y. Duan, H. Zhang, Y. Wang, Z. Qian, J. Cui, J. Lu (2020). On the Origin and Continuing Evolution of SARS-CoV-2. National Science Review, nwaa036.
28. Wu F., S. Zhao, B. Yu, Y. M. Chen, W. Wang, Z. G. Song, Y. Hu, Z. W. Tao, J. H. Tian, Y. Y. Pei, M. L. Yuan, Y. L. Zhang, F. H. Dai, Y. Liu, Q. M. Wang, J. J. Zheng, L. Xu, E. C. Holmes, Y. Z. Zhang (2020). A New Coronavirus Associated with Human Respiratory Disease in China. Nature, 579(7798), 265-269.
29. Greenhalgh T, Jimenez JL, Prather KA, Tufekci Z, Fisman D, Schooley R. Ten scientific reasons in support of airborne transmission of SARS-CoV-2. Lancet. 2021 May 1;397(10285):1603-1605.
30. Giwa A., A. Desai (2020). Novel coronavirus COVID-19: An Overview for Emergency Clinicians. Emergency Medicine Practice, 22, 1-21.
31. Liu D. X., J. Q. Liang, T. S. Fung (2020). Human coronavirus-229E, -OC43, -NL63, and -HKU1, In: Reference Module in Life Sciences. Elsevier.
32. Anthony S. J., C. K. Johnson, D. J. Greig, S. Kramer, X. Che, H. Wells, A. L. Hicks, D. O. Joly, N. D. Wolfe, P. Daszak, W. Karesh, W. I. Lipkin, S. S. Morse, PREDICT Consortium, J. Mazet, T. Goldstein (2017). Global Patterns in Coronavirus Diversity. Virus Evolution, 3(1), vex012.
33. Payne S (2017). Family Coronaviridae. Viruses, 2017, 149â€158.
34. Su S., G. Wong, W. Shi, J. Liu, A. C. K. Lai, J. Zhou, W. Liu, Y. Bi, G. F. Gao (2016). Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends in Microbiology, 24(6), 490-502.
35. Forni D, R. Cagliani, M. Clerici, M. Sironi (2017). Molecular Evolution of Human Coronavirus Genomes. Trends in Microbiology, 25, 35-48.
36. Müller M. A., V. M. Corman, J. Jores, B. Meyer, M. Younan, A. Liljander, B. J. Bosch, E. Lattwein, M. Hilali, B. E. Musa, S. Bornstein, C. Drosten (2014). MERS Coronavirus Neutralizing Antibodies in Camels, Eastern Africa, 1983–1997. Emerging Infectious Diseases, 20, 2093-2095.
37. Munir K., S. Ashraf, I. Munir, H. Khalid, M. A. Muneer, N. Mukhtar, S. Amin, S. Ashraf, M. A. Imran, U. Chaudhry, M. U. Zaheer, M. Arshad, R. Munir, A. Ahmad, X. Zhao (2020). Zoonotic and Reverse Zoonotic Events of SARS-CoV-2 and Their Impact on Global Health. Emerging Microbes & Infections, 9(1), 2222-2235.
38. Ye Z. W., S. Yuan, K. S. Yuen, S. Y. Fung, C. P. Chan, D. Y. Jin (2020). Zoonotic Origins of Human Coronaviruses. International Journal of Biological Sciences, 16(10), 1686-1697.
39. Zhang T., Q. Wu, Z. Zhang (2020) Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Current Biology, 30(7), 1346-1351.e2.
40. Lam T. T., N. Jia, Y. W. Zhang, M. H. Shum, J. F. Jiang, H. C. Zhu, Y. G. Tong, Y. X. Shi, X. B. Ni, Y. S. Liao, W. J. Li, B. G. Jiang, W. Wei, T. T. Yuan, K. Zheng, X. M. Cui, J. Li, G. Q. Pei, X. Qiang, W. Y. Cheung, L. F. Li, F. F. Sun, S. Qin, J. C. Huang, G. M. Leung, E. C. Holmes, Y. L. Hu, Y. Guan, W. C. Cao (2020). Identifying SARS-CoV-2-Related Coronaviruses in Malayan Pangolins. Nature, 583(7815), 282-285.
41. Zhou P., X. L. Yang, X. G. Wang, B. Hu, L. Zhang, W. Zhang, H. R. Si, Y. Zhu, B. Li, C. L. Huang, H. D. Chen, J. Chen, Y. Luo, H. Guo, R. D. Jiang, M. Q. Liu, Y. Chen, X. R. Shen, X. Wang, X. S. Zheng, K. Zhao, Q. J. Chen, F. Deng, L. L. Liu, B. Yan, F. X. Zhan, Y. Y. Wang, G. F. Xiao, Z. L. Shi. Addendum: A Pneumonia Outbreak Associated with A New Coronavirus of Probable Bat Origin. Nature, 588(7836), E6.
42. Ji W., W. Wan, X. Zhao, J. Zai, X. Li (2020). Cross-Species Transmission of the Newly Identified Coronavirus 2019-nCoV. Journal of Medical Virology, 92(4), 433-440.
43. Cheng Z. J., J. Shan (2019). Novel Coronavirus: Where We Are and What We Know. Infection, 48(2), 155-163.
44. Wu D., T. Wu, Q. Liu, Z. Yang (2020). The SARS-CoV-2 Outbreak: What We Know. International Journal of Infectious Diseases, 94, 44-48.
45. Bitanihirwe B. K. Y., D. Ssewanyana (2021) The health and economic burden of the coronavirus in sub-Saharan Africa. Global Health Promotion, 28(1): 70-74.
46. Synhorst DC, Bettenhausen JL, Hall M, Thurm C, Shah SS, Auger KA, Williams DJ, Morse R, Berry JG. Healthcare Encounter and Financial Impact of COVID-19 on Children's Hospitals. J Hosp Med. 2021; 16(4): 223-226.
47. Pines JM, Zocchi MS, Black BS, Kornas R, Celedon P, Moghtaderi A, Venkat A; US Acute Care Solutions Research Group. The Effect of the COVID-19 Pandemic on the Economics of United States Emergency Care. Ann Emerg Med. 2021; S0196-0644(21)00333-4.
48. Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nat Commun. 2021 May 11;12(1):2642. doi: 10.1038/s41467-021-22905-7. PMID: 33976134; PMCID: PMC8113528.
49. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A; COVID-19 Genomics UK (COG-UK) Consortium, Peacock SJ, Robertson DL. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021; 19(7): 409-424.
50. Dyer O. Covid-19: Indonesia becomes Asia's new pandemic epicentre as delta variant spreads. BMJ. 2021; 374: n1815.
51. Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, Planchais C, Porrot F, Robillard N, Puech J, Prot M, Gallais F, Gantner P, Velay A, Le Guen J, Kassis-Chikhani N, Edriss D, Belec L, Seve A, Courtellemont L, Péré H, Hocqueloux L, Fafi-Kremer S, Prazuck T, Mouquet H, Bruel T, Simon-Lorière E, Rey FA, Schwartz O. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021; 596(7871): 276-280.
52. Rambaut A, Holmes EC, O'Toole Ã, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020; 5(11): 1403-1407.
53. Laiton-Donato K, Franco-Muñoz C, Ãlvarez-DÃaz DA, Ruiz-Moreno HA, Usme-Ciro JA, Prada DA, Reales-González J, Corchuelo S, Herrera-Sepúlveda MT, Naizaque J, SantamarÃa G, Rivera J, Rojas P, Ortiz JH, Cardona A, Malo D, Prieto-Alvarado F, Gómez FR, Wiesner M, MartÃnez MLO, Mercado-Reyes M. Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect Genet Evol. 2021; 95: 105038.
2. Huang C., Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu, Z. Cheng, T. Yu, J. Xia, Y. Wei, W. Wu, X. Xie, W. Yin, H. Li, M. Liu, Y. Xiao, H. Gao, L. Guo, J. Xie, G. Wang, R. Jiang, Z. Gao, Q. Jin, J. Wang, B. Cao (2020). Clinical Features of Patients Infected with 2019 Novel Coronavirus in Wuhan, China. Lancet, 395(10223), 497-506.
3. Li X., E. G. Elena, M. H. Marichannegowda, B. Foley, C. Xiao, X. P. Kong, Y. Chen, S. Gnanakaran, B. Korber, F. Gao (2020). Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection. Science Advances, 6(27), eabb9153.
4. Dong E, H. Du, L. Gardner (2020). An Interactive Web-based Dashboard to Track COVID-19 in Real Time. Lancet Infectious Diseases, S1473-3099(20), 30120-30121.
5. Guo YR, Q. D. Cao, Z. S. Hong, Y. Y. Tan, S. D. Chen, H. J. Jin, K. S. Tan, D. Y. Wang, Y. Yan. (2020). The Origin, Transmission and Clinical Therapies on Coronavirus Disease 2019 (COVID-19) Outbreak - An Update on the Status. Military Medical Research, 7(1), 11.
6. LaTourrette K, Holste NM, Rodriguez-Peña R, Leme RA, Garcia-Ruiz H. Genome-Wide Variation in Betacoronaviruses. J Virol. 2021 Jul 12;95(15):e0049621. doi: 10.1128/JVI.00496-21. Epub 2021 Jul 12. PMID: 34037417; PMCID: PMC8274613.
7. Castillo A. E., B. Parra, P. Tapia, A. Acevedo, J. Lagos, W. Andrade, L. Arata, G. Leal, G. Barra, C. Tambley, J. Tognarelli, P. Bustos, S. Ulloa, R. Fasce, J. Fernández (2020). Phylogenetic Analysis of the First Four SARS-CoV-2 Cases in Chile. Journal of Medical Virology, 92(9), 1562-1566.
8. Ou X., Y. Liu, X. Lei, P. Li, D. Mi, L. Ren, L. Guo, R. Guo, T. Chen, J. Hu, Z. Xiang, Z. Mu, X. Chen, J. Chen, K. Hu, Q. Jin, J. Wang, Z. Qian (2020). Characterization of Spike Glycoprotein of SARS-CoV-2 on Virus Entry and Its Immune Cross-Reactivity with SARS-CoV. Nature Communications, 11, 1620.
9. Shereen M. A., S. Khan, A. Kazmi, N. Bashir, R. Siddique (2020). COVID-19 Infection: Origin, Transmission, and Characteristics of Human Coronaviruses. Journal of Advanced Research, 24, 91-98.
10. Phan T. (2020). Genetic Diversity and Evolution of SARS-CoV-2. Infection, Genetics and Evolution, 81, 104260.
11. Ansori A. N. M., V. D. Kharishma, S. S. Muttaqin, Y. Antonius, A. A. Parikesit (2020). Genetic Variant of SARS-CoV-2 Isolates in Indonesia: Spike Glycoprotein Gene, Journal of Pure and Applied Microbiology, 14, 971-978.
12. Ansori A. N. M., V. D. Kharisma, Y. Antonius, M. R. Tacharina, F. Rantam (2020). Immunobioinformatics Analysis and Phylogenetic Tree Construction of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Spike Glycoprotein Gene. Jurnal Teknologi Laboratorium, 9(1), 13-20.
13. Turista D. D. R., A. Islamy, V. D. Kharisma, A. N. M. Ansori (2020). Distribution of COVID-19 and Phylogenetic Tree Construction of SARS-CoV-2 in Indonesia. Journal of Pure and Applied Microbiology, 14, 1035-1042.
14. Hasöksüz M, Kiliç S, Saraç F. Coronaviruses and SARS-COV-2. Turk J Med Sci. 2020; 50(SI-1): 549-556.
15. Malik YA. Properties of Coronavirus and SARS-CoV-2. Malays J Pathol. 2020; 42(1): 3-11.
16. Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. Adv Exp Med Biol. 2021; 1318: 839-857.
17. Bchetnia M, Girard C, Duchaine C, Laprise C. The outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): A review of the current global status. J Infect Public Health. 2020 Nov;13(11):1601-1610. doi: 10.1016/j.jiph.2020.07.011. Epub 2020 Aug 4. PMID: 32778421; PMCID: PMC7402212.
18. Chen B, Tian EK, He B, Tian L, Han R, Wang S, Xiang Q, Zhang S, El Arnaout T, Cheng W. Overview of lethal human coronaviruses. Signal Transduct Target Ther. 2020 Jun 10;5(1):89. doi: 10.1038/s41392-020-0190-2. PMID: 32533062; PMCID: PMC7289715.
19. Du L, Y. He, Y. Zhou, S. Liu, B. J. Zheng, S. Jiang (2009). The Spike Protein of SARS-CoV–A Target for Vaccine and Therapeutic Development. Nature Reviews Microbiology. 2009; 7: 226e36.
20. Yin C. (2020). Genotyping Coronavirus SARS-CoV-2: Methods and Implications. Genomics, S0888-7543(20), 30318-30319.
21. Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, Masciovecchio C, Angeletti S, Ciccozzi M, Gallo RC, Zella D, Ippodrino R. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020 Apr 22;18(1):179. doi: 10.1186/s12967-020-02344-6. PMID: 32321524; PMCID: PMC7174922.
22. Khan M. I., Z. A. Khan, M. H. Baig, I. Ahmad, A. E. Farouk, Y. G. Song, J. J. Dong (2020). Comparative Genome Analysis of Novel Coronavirus (SARS-CoV-2) from Different Geographical Locations and the Effect of Mutations on Major Target Proteins: An In Silico Insight, PLoS One, 15(9), e0238344.
23. Wang C., Z. Liu, Z. Chen, X. Huang, M. Xu, T. He, Z. Zhang (2020). The Establishment of Reference Sequence for SARS-CoV-2 and Variation Analysis. Journal of Medical Virology, 92(6), 667-674.
24. Cui J., F. Li, Z. L. Shi (2019). Origin and Evolution of Pathogenic Coronaviruses. Nature Reviews Microbiology, 17(3), 181-192.
25. Lu R., X. Zhao, J. Li, P. Niu, B. Yang, H. Wu, W. Wang, H. Song, B. Huang, N. Zhu, Y. Bi, X. Ma, F. Zhan, L. Wang, T. Hu, H. Zhou, Z. Hu, W. Zhou, L. Zhao, J. Chen, Y. Meng, J. Wang, Y. Lin, J. Yuan, Z. Xie, J. Ma, W. J. Liu, D. Wang, W. Xu, E. C. Holmes, G. F. Gao, G. Wu, W. Chen, W. Shi, W. Tan (2020). Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding. Lancet, 395(10224), 565-574.
26. Kumar SU, Priya NM, Nithya SR, Kannan P, Jain N, Kumar DT, Magesh R, Younes S, Zayed H, Doss CGP. A review of novel coronavirus disease (COVID-19): based on genomic structure, phylogeny, current shreds of evidence, candidate vaccines, and drug repurposing. 3 Biotech. 2021; 11(4): 198.
27. Tang X., C. Wu, X. Li, Y. Song, X. Yao, X. Wu, Y. Duan, H. Zhang, Y. Wang, Z. Qian, J. Cui, J. Lu (2020). On the Origin and Continuing Evolution of SARS-CoV-2. National Science Review, nwaa036.
28. Wu F., S. Zhao, B. Yu, Y. M. Chen, W. Wang, Z. G. Song, Y. Hu, Z. W. Tao, J. H. Tian, Y. Y. Pei, M. L. Yuan, Y. L. Zhang, F. H. Dai, Y. Liu, Q. M. Wang, J. J. Zheng, L. Xu, E. C. Holmes, Y. Z. Zhang (2020). A New Coronavirus Associated with Human Respiratory Disease in China. Nature, 579(7798), 265-269.
29. Greenhalgh T, Jimenez JL, Prather KA, Tufekci Z, Fisman D, Schooley R. Ten scientific reasons in support of airborne transmission of SARS-CoV-2. Lancet. 2021 May 1;397(10285):1603-1605.
30. Giwa A., A. Desai (2020). Novel coronavirus COVID-19: An Overview for Emergency Clinicians. Emergency Medicine Practice, 22, 1-21.
31. Liu D. X., J. Q. Liang, T. S. Fung (2020). Human coronavirus-229E, -OC43, -NL63, and -HKU1, In: Reference Module in Life Sciences. Elsevier.
32. Anthony S. J., C. K. Johnson, D. J. Greig, S. Kramer, X. Che, H. Wells, A. L. Hicks, D. O. Joly, N. D. Wolfe, P. Daszak, W. Karesh, W. I. Lipkin, S. S. Morse, PREDICT Consortium, J. Mazet, T. Goldstein (2017). Global Patterns in Coronavirus Diversity. Virus Evolution, 3(1), vex012.
33. Payne S (2017). Family Coronaviridae. Viruses, 2017, 149â€158.
34. Su S., G. Wong, W. Shi, J. Liu, A. C. K. Lai, J. Zhou, W. Liu, Y. Bi, G. F. Gao (2016). Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends in Microbiology, 24(6), 490-502.
35. Forni D, R. Cagliani, M. Clerici, M. Sironi (2017). Molecular Evolution of Human Coronavirus Genomes. Trends in Microbiology, 25, 35-48.
36. Müller M. A., V. M. Corman, J. Jores, B. Meyer, M. Younan, A. Liljander, B. J. Bosch, E. Lattwein, M. Hilali, B. E. Musa, S. Bornstein, C. Drosten (2014). MERS Coronavirus Neutralizing Antibodies in Camels, Eastern Africa, 1983–1997. Emerging Infectious Diseases, 20, 2093-2095.
37. Munir K., S. Ashraf, I. Munir, H. Khalid, M. A. Muneer, N. Mukhtar, S. Amin, S. Ashraf, M. A. Imran, U. Chaudhry, M. U. Zaheer, M. Arshad, R. Munir, A. Ahmad, X. Zhao (2020). Zoonotic and Reverse Zoonotic Events of SARS-CoV-2 and Their Impact on Global Health. Emerging Microbes & Infections, 9(1), 2222-2235.
38. Ye Z. W., S. Yuan, K. S. Yuen, S. Y. Fung, C. P. Chan, D. Y. Jin (2020). Zoonotic Origins of Human Coronaviruses. International Journal of Biological Sciences, 16(10), 1686-1697.
39. Zhang T., Q. Wu, Z. Zhang (2020) Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Current Biology, 30(7), 1346-1351.e2.
40. Lam T. T., N. Jia, Y. W. Zhang, M. H. Shum, J. F. Jiang, H. C. Zhu, Y. G. Tong, Y. X. Shi, X. B. Ni, Y. S. Liao, W. J. Li, B. G. Jiang, W. Wei, T. T. Yuan, K. Zheng, X. M. Cui, J. Li, G. Q. Pei, X. Qiang, W. Y. Cheung, L. F. Li, F. F. Sun, S. Qin, J. C. Huang, G. M. Leung, E. C. Holmes, Y. L. Hu, Y. Guan, W. C. Cao (2020). Identifying SARS-CoV-2-Related Coronaviruses in Malayan Pangolins. Nature, 583(7815), 282-285.
41. Zhou P., X. L. Yang, X. G. Wang, B. Hu, L. Zhang, W. Zhang, H. R. Si, Y. Zhu, B. Li, C. L. Huang, H. D. Chen, J. Chen, Y. Luo, H. Guo, R. D. Jiang, M. Q. Liu, Y. Chen, X. R. Shen, X. Wang, X. S. Zheng, K. Zhao, Q. J. Chen, F. Deng, L. L. Liu, B. Yan, F. X. Zhan, Y. Y. Wang, G. F. Xiao, Z. L. Shi. Addendum: A Pneumonia Outbreak Associated with A New Coronavirus of Probable Bat Origin. Nature, 588(7836), E6.
42. Ji W., W. Wan, X. Zhao, J. Zai, X. Li (2020). Cross-Species Transmission of the Newly Identified Coronavirus 2019-nCoV. Journal of Medical Virology, 92(4), 433-440.
43. Cheng Z. J., J. Shan (2019). Novel Coronavirus: Where We Are and What We Know. Infection, 48(2), 155-163.
44. Wu D., T. Wu, Q. Liu, Z. Yang (2020). The SARS-CoV-2 Outbreak: What We Know. International Journal of Infectious Diseases, 94, 44-48.
45. Bitanihirwe B. K. Y., D. Ssewanyana (2021) The health and economic burden of the coronavirus in sub-Saharan Africa. Global Health Promotion, 28(1): 70-74.
46. Synhorst DC, Bettenhausen JL, Hall M, Thurm C, Shah SS, Auger KA, Williams DJ, Morse R, Berry JG. Healthcare Encounter and Financial Impact of COVID-19 on Children's Hospitals. J Hosp Med. 2021; 16(4): 223-226.
47. Pines JM, Zocchi MS, Black BS, Kornas R, Celedon P, Moghtaderi A, Venkat A; US Acute Care Solutions Research Group. The Effect of the COVID-19 Pandemic on the Economics of United States Emergency Care. Ann Emerg Med. 2021; S0196-0644(21)00333-4.
48. Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nat Commun. 2021 May 11;12(1):2642. doi: 10.1038/s41467-021-22905-7. PMID: 33976134; PMCID: PMC8113528.
49. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A; COVID-19 Genomics UK (COG-UK) Consortium, Peacock SJ, Robertson DL. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021; 19(7): 409-424.
50. Dyer O. Covid-19: Indonesia becomes Asia's new pandemic epicentre as delta variant spreads. BMJ. 2021; 374: n1815.
51. Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, Planchais C, Porrot F, Robillard N, Puech J, Prot M, Gallais F, Gantner P, Velay A, Le Guen J, Kassis-Chikhani N, Edriss D, Belec L, Seve A, Courtellemont L, Péré H, Hocqueloux L, Fafi-Kremer S, Prazuck T, Mouquet H, Bruel T, Simon-Lorière E, Rey FA, Schwartz O. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021; 596(7871): 276-280.
52. Rambaut A, Holmes EC, O'Toole Ã, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020; 5(11): 1403-1407.
53. Laiton-Donato K, Franco-Muñoz C, Ãlvarez-DÃaz DA, Ruiz-Moreno HA, Usme-Ciro JA, Prada DA, Reales-González J, Corchuelo S, Herrera-Sepúlveda MT, Naizaque J, SantamarÃa G, Rivera J, Rojas P, Ortiz JH, Cardona A, Malo D, Prieto-Alvarado F, Gómez FR, Wiesner M, MartÃnez MLO, Mercado-Reyes M. Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Infect Genet Evol. 2021; 95: 105038.
There is no Supplemental content for this article.
How to Cite This
Ansori, A. N. M., & Antonius, Y. (2022). A phylogenetic analysis of Indonesian SARS-CoV-2 isolates from March to December 2020: Compared with Delta and Mu variant. Jurnal Teknologi Laboratorium, 11(1), 1–10. https://doi.org/10.29238/teknolabjournal.v11i1.297
Article Metrics
Download Statistics
Downloads
Download data is not yet available.
Metrics
Metrics Loading ...
Other Statistics
Copyright and Permissions
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Publishing your paper with Jurnal Teknologi Laboratorium (JTL) means that the author or authors retain the copyright in the paper. JTL granted an exclusive reuse license by the author(s), but the author(s) are able to put the paper onto a website, distribute it to colleagues, give it to students, use it in your thesis etc, even commercially. The author(s) can reuse the figures and tables and other information contained in their paper published by JTL in future papers or work without having to ask anyone for permission, provided that the figures, tables or other information that is included in the new paper or work properly references the published paper as the source of the figures, tables or other information, and the new paper or work is not direct at private monetary gain or commercial advantage.
JTL journal provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge. This journal is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. This license lets others remix, transform, and build upon the material for any purpose, even commercially.
JTL journal Open Access articles are distributed under this Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA). Articles can be read and shared for All purposes under the following conditions:
- BY: You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- SA: If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
