S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia
DOI:
https://doi.org/10.26740/jrba.v3n2.p45-53Keywords:
Keywords, COVID-19, SARS-CoV-2 virus, S-D614G mutation, spike gene and RdRp gene, phylogenetics.Abstract
COVID-19 is a pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The first case was found in the city of Wuhan, Hubei province, China. The first case in Indonesia was reported in March 2020 and currently there are 0.5 million cases with a death rate of 3.1%. This rapid increase in cases is thought to due to presence of the mutant strain S-D614G, which causes a faster rate of infection and spread. The purpose of this study was to determine the presence of S-D614G mutations in Indonesian samples in order to find the origin of COVID-19 which was spread in Indonesia based on the Spike gene sequences and the RdRp genes from 25 countries, and one control sequence China/Wuhan-Hu-1 obtained from the NCBI and GISAID databases. Mutation analysis was carried out through multiple alignments using BioEdit software. Phylogenetic tree reconstruction using MEGA6 software with the Neighbor Joining method. This study found mutation of S-D614G in one Indonesian sample, namely the Indonesian/SBY9 sample along with 23 samples from Europe, America, and Africa. The phylogenetic tree reconstruction confirmed these findings; the mutated samples were closely related to samples from these continents, while the non-mutated Indonesian samples were closely related to sample from East Asia. These findings indicate that the origin of the SARS-CoV-2 virus in Indonesia possibly came from the East Asia cluster and the European-American cluster.
References
Baud, D., X. Qi, X., Nielsen-Saines, K., Musso, D., Pomar, L., Favre, G. (2020). Real estimates of mortality following COVID-19 infection. The Lancet Infectious Diseases. 773. https://doi: 10.1016/S1473-3099(20)30195-X.
Bhattacharyya, C., Das, C., Ghosh, A., Singh A,K., Mukherjee, S., Majumder, P, P., Basu, A., Biswas, N,K. (2020). Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes. bioRxiv. https://www.biorxiv.org/content/10.1101/2020.05.04.075911v1.full
Biswas, N.K., Majumder, P.P. (2020). Analysis of RNA Sequences of 3636 SARS-COV-2 Collected From 55 Countries Reveals Selective Sweep of One Virus Type. Indian J Med Res. 151(5), 450-458. https:// doi: 10.4103/ijmr.IJMR_1125_20.
Bloomfield, S. F. Pharm, B., Boyle, C., Larson, E.L. (2007). The effectiveness of hand hygiene procedures in reducing the risks of infections in home and community settings including handwashing and alcohol-based hand sanitizers. American Journal of Infection Control - Amer J Infect Control.35. https://doi: 10.1016/j.ajic.2007.07.001.
CSIS Indonesia. (2020). Indeks intensitas Covid-19. https://covid19.csis.or.id (Accesed 6th of September 2020).
Decaro, N., Lorusso, A. (2020). Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Veterinary Microbiology. 244.https://doi.org/10.1016/j.vetmic.2020.108693
Gralinski, L.E., Menachery, V.D. (2020). Return of the coronavirus: 2019-nCoV. Viruses MDPI. 12(2), 135. https://doi.org/10.3390/v12020135
Gudbjartsson, D.F., Helgason, A., Jonsson, H., Magnusson, O.T. (2020). Spread of SARS-CoV-2 in the Icelandic Population. The New England Journal of Medicine. 382, (2302-2315). http://doi: 10.1056/NEJMoa2006100
Hu, J. He, C.L., Gao, Q.Z., Cao, X., Long, Q., Deng, H., Huang, L., Chen, J., Wang, K., Tang, N., Huang, A. (2020). The D614G mutation of SARS-CoV-2 Spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera. bioRxiv. https://doi.org/10.1101/2020.06.20.161323.
Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 395(10223). https://doi.org/10.1016/S0140-6736(20)30183-5
Indonesian Ministry of Health. 2020. Pedoman Pencegahan Dan Pengendalian Coronavirus Disesase (Covid-19). Revisi Ke-5. pp. 21.
Jin, X., Lian, J.S., Hu, J.H., Gao, J., Zheng, L., Zhang, Y.M., Hao, S.R., Jia, H.Y., Cai, H., Zhang, X.L., Yu, G.D., Xu, K,J., Wang, X.Y., Gu, J.Q., Zhang, S.Y., Ye, C.Y., Jin, C.L., Lu, Y.F., Yu, X., Yu, X.P., Huang, J.R., Xu, K.L., Ni, Q., Yu, C.B., Zhu, B., Li, Y.T., Liu, J., Zhao, H., Zhang, X., Yu, L., Guo, Y.Z., Su, J.W., Tao, J.J., Lang, G.J., Wu, X.X., Wu, W.R., Qv, T.T., Xiang, D.R., Yi, P., Shi, D., Chen, Y., Ren, Y., Qiu, Y.Q., Li, L.J., Sheng, J., Yang, Y. (2020). Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms. Gut. 69, 1002-1009. http://dx.doi.org/10.1136/gutjnl-2020-320926
Khot, W.Y., Nadkar, M.Y. (2020). The Novel Coronavirus Outbreak-A Global Threat. Journal of Association of Physicians of India. 68(3), 67-71.
Korber, B. Fischer, W.M., Gnanakaran, S., Yoon, H., Abfalterer, J.T.W., Giorgi, B.F.EE., Bhattacharya, T., Parker, M.D., Partridge, D.G., Evans, C.M., Freeman, T.M., de Silva, T.I., LaBranche, C.C., Monteifiori, D.C. (2020). Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. bioRxiv. https://doi.org/10.1101/2020.04.29.069054
Laha, S. Chakraborty, J., Das, S., Manna, S.K., Biswas, S., Chatterjee, R. (2020). Characterizations of SARS-CoV-2 mutational profile, Spike protein stability and viral transmission. bioRxiv. . https://doi.org/10.1101/2020.05.03.066266
Mahase, E. (2020). Coronavirus covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate. BMJ. 368. https://doi: 10.1136/bmj.m641.
Parikesit, A.A., Nurdiansyah, R. (2020). The predicted structure for the anti-sense SiRNA of the RNA polymerase enzyme (RdRp) Gene of the SARS-CoV-2. Jurnal Ilmu-ilmu Hayati.19 (1), 97-108.
Rothan, H.A., Byrareddy, S.N. (2020). The Epidemology and Phatogenesis of Coronavirus Diseases (COVID-19) Outbreak. Journal of Autoimunity. 109, 1-4. https://doi: 10.1016/j.jaut.2020.102433.
Safrizal, Z.A., Putra, D.I., Sofyan, S., Bimo. (2020). Pedoman Umum Menghadapi Pandemi COVID-19 Bagi Pemerintah Daerah. Kementrian Dalam Negeri: Jakarta.
Satgas Penanganan COVID-19. (2020). Peta Sebaran Kasus Per Provinsi. https://covid19.go.id/peta-sebaran. (Accesed 6th of September 2020).
Susilo, A., Rumende, C.M., Pitoyo, C.W., Santoso, W.D., Yulianti, M., Herikurniawan., Sinto, R., Singh, G., Nainggolan, L., Nelwan, E.J., Chen, L.K., Widhani, A., Wijaya, E., Wicaksana, B., Maksum, M., Annisa, F., Jasirwan, C.O., Yunihastuti, E. (2020). Coronavirus Disease 2019: Tinjauan Literatur Terkini. Jurnal Penyakit dalam Indonesia. 7(1), 45-69. http://dx.doi.org/10.7454/jpdi.v7i1.415.
Worldometers. (2020) WorldoMeter: Real Time World Statistics. Current World Population. Worldo Meter. https://www.worldometers.info/coronavirus/. (Accessed 6th of September 2020).
Wren-Lewis, S. (2020) The economic effects of a pandemic, Economics in the Time of COVID-19. https://www.socialeurope.eu/the-economic-effects-of-a-pandemic
Zhang, L, Jackson, C.B, Mou H., Ojha, A., Peng, H., Quinlan, B.D., Rangarajan, E.S., Pan A., Vanderheiden, A., Suthar, M.S., Li, W., Izard, T., Rader, C., Farzan, M., Choe, H. (2020) SARS-CoV-2 Spike-protein D614G mutation increases virion Spike density and infectivity. Nature Communication. 11:6013 https://doi.org/10.1038/s41467-020-19808-4.
Zhu, W., Chen, C.Z., Gorshkov, K., Xu, M., Lo, D.C., Zheng, W. (2020). RNA-Dependent RNA Polymerase as a Target for COVID-19 Drug Discovery. SAGE Journals. 25(10), 1141-1151. https://doi: 10.1177/2472555220942123.
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