Genetic Variation of Structural and Functional Genes of SARS-CoV-2 Isolates Circulating in Banyumas (Indonesia)


Anwar Rovik(1*), Clearensia Ade Bina Noviani(2)

(1) Center for Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada. Jl. Teknika Utara, Barek, DI Yogyakarta, Indonesia, 55281 Faculty of Biology, Universitas Jenderal Soedirman. Jl. Dr Soeparno No 56, Purwokerto, Central Java, Indonesia, 53122, Indonesia
(2) Faculty of Biology, Universitas Gadjah Mada. Jl. Teknika Selatan, Sleman DI Yogyakarta, Indonesia, 55281, Indonesia
(*) Corresponding Author

Abstract


Scientists are performing various measurements to overcome the COVID-19 pandemic. The genomic mutations of SARS-CoV-2 can change their pathogenicity, infectivity, transmission, and antigenicity. This present study aimed to know a) the genetic variation of structural and functional genes of SARS-CoV-2 circulating in Banyumas and b) the potential of the Cilacap’s Harbour as a human mobility portal on the genetic variations of SARS-CoV-2 circulating in Banyumas, Central Java (Indonesia). Genomic sequence of SARS-CoV-2 isolates were taken from the Global Initiative on Sharing All Influenza Data (GISAID) and the National Center for Biotechnology Information (NCBI) online platforms. A gene cut was carried out from Wuhan reference isolate, fifteen isolates from Banyumas, and two isolates from Cilacap (Central Java) using Unipro UGENE v. 33.0 software, considering the annotation of the Wuhan-1 isolate. Genetic variations were detected among SARS-CoV-2 isolates circulating in Banyumas. The structural protein (envelope, membrane, nucleocapsid) encoding gene and the RdRp gene were highly conserved to Wuhan reference genome (Wuhan-Hu-1). Meanwhile, the ORF and the spike-encoding genes were less identical to the Wuhan reference genome. This study also proposed that human mobility from outside Central Java through Cilacap’s Harbour did not affect the genetic variation of SARS-CoV-2 isolates circulating in Banyumas (Central Java).


Keywords


Banyumas, genetic variation, mutations, public mobilization, SARS-CoV-2

Full Text:

PDF

References


Anggraini, N. B. & Listyorini, D. (2021). S-D614G Mutation Reveals the Euro-America and East-Asia Origin SARS-CoV-2 Virus Spread in Indonesia. Jurnal Riset Biologi dan Aplikasinya, 3(2), 45-53. DOI: 10.26740/jrba.v3n2.p45-53.

Decaro, N. & Lorusso, A. (2020). Novel human Coronavirus (SARS-CoV-2): A Lesson from Animal Coronaviruses. Veterinary Microbiology, 244: 108693. DOI: 10.1016/j.vetmic.2020.108693.

Djalante, R., Lassa, J., Setiamarga, D., Sudjatma, A., Indrawan, M., Haryanto, B., Mahfud, C., Sinapoy, M. S., Djalante, S., Rafliana, I., Gunawan, L. A., Surtiari, G. A. K. & Wasilah, H. (2020). Review and Analysis of Current Responses to COVID-19 in Indonesia: Period of January to March 2020. Progress in Disaster Science, 6: 100091. DOI: 10.1016/j.pdisas.2020.100091

Gralinski, L. E. & Menachery, V. D. (2020). Return of the Coronavirus: 2019-nCoV. Viruses, 12(2), 135. DOI: 10.3390/v12020135.

Gunadi, Wibawa, T., Marcellus, Hakim, M. S., Daniwijaya, E. W., Rizki, L. P., Supriyati, E., Nugrahaningsih, D. A. A., Afiahayati, Siswanto, Iskandar, K., Anggorowati, N, Kalim, A. S., Puspitarani, D. A., Athollah, K., Arguni, E., Nuryastuti, T. & Wibawa, T. (2020). Full-length Genome Characterization and Phylogenetic Analysis of SARS-CoV-2 Virus Strains from Yogyakarta and Central Java, Indonesia. PeerJ, 8, e10575. DOI: 10.7717/peerj.10575.

Hakim, M. S., Annisa, L., Supriyati, E., Daniwijaya, E. W., Wibowo, R. A., Arguni, E. & Nuryastuti, T. (2020). Understanding of the Origin, Molecular Biology And Continuing Evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Berkala Ilmu Kedokteran, 42(3): 17-29. DOI: 10.19106/JMedSciSI005202202003.

Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R. & Rambaut, A. (2021). SARS-CoV-2 Variants, Spike Mutations and Immune Escape. Nature Reviews Microbiology, 19(7): 409-424. DOI: 10.1038/s41579-021-00573-0.

Jamison, D. A., Narayanan, A. S., Trovao, N. S., Guarnieri, J. W., Topper, J. M., Moraes-Viera, P. M., Zaksas, V., Singh, K. K., Wurtele, E. S. & Behesthti, A. (2022). A Comprehensive SARS-CoV-2 and COVID-19 review, Part 1: Intracellular Overdrive for SARS-CoV-2 Infection. European Journal of Human Genetics, 30: 889-898. DOI: 10.1038/s41431-022-01108-8.

Lesbon, J. C. C., Poleti, M. D., de Mattos Oliveira, E. C., Patané, J. S. L., Clemente, L. G., Viala, V. L., Ribeiro, G., Giovanetti, M., de Alcantara, L. C. J., Teixeira, O., Nonato, M. C., de Lima, L. P. O., Martins, A. J., Dos Santos Barros, C. R., Marqueze, E. C., de Souza Todão Bernardino, J., Moretti, D. B., Brassaloti, R. A., de Lello Rocha Campos Cassano, R, Mariani, P. D. S. C, Slavov, S. N , Dos Santos, R. B., Rodrigues, E. S., Santos, E. V., Borges, J. S., de La Roque, D. G. L., Kitajima, J. P., Santos, B., Assato, P. A., da Silva da Costa, F. A., Banho, C. A., Sacchetto, L., Moraes, M. M., Palmieri, M., da Silva, F. E. V., Grotto, R. M. T., Souza-Neto, J. A., Nogueira, M. L., Coutinho, L. L., Calado, R. T., Neto, R. M., Covas, D. T., Kashima, S., Elias, M. C., Sampaio, S. C. & Fukumasu, H. (2021). Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results. Viruses, 13(12): 2474. DOI: 10.3390/v13122474. Erratum in: Viruses, 14(9).

Li, T., Huang, T., Guo, C., Wang, A., Shi, X., Mo, X., Lu, Q., Sun, J., Hui, T., Tian, G., Wang, L. & Yang, J. (2021). Genomic Variation, Origin Tracing, and Vaccine Development of SARS-CoV-2: A Systematic Review. Innovation (Cambrige (Mass)), 2(2): 100116. DOI: 10.1016/j.xinn.2021.100116.

Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Chen, J., Meng, Y., Wang, J., Lin, Y., Yuan, J., Xie, Z., Ma, J., Liu, W. J., Wang, D., Xu, W., Holmes, E. C., Gao, G. F., Wu, G., Chen, W., Shi, W. & Tan, W. (2020). Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding. Lancet, 395(10224): 565-574. DOI: 10.1016/S0140-6736(20)30251-8.

Marcov, P.V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I. & Katzourakis, A. (2023). The Evolution of SARS-CoV-2. Nature Reviews Microbiology. DOI: 10.1038/s41579-023-00878-2.

Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., Thakur, N., Collier, D. A., Mlcochova, P., COVID-19 Genomics UK (COG-UK) Consortium, Duncan, L. M., Carabelli, A. M., Kenyon, J. C., Lever, A. M., De Marco, A., Saliba, C., Culap, K., Cameroni, E., Matheson, N. J., Piccoli, L., Corti, D., James, L. C., Robertson, D. L., Bailey, D. & Gupta, R. K. (2021). Recurrent Emergence of SARS-CoV-2 Spike Deletion H69/V70 and its Role in the Alpha Variant B.1.1.7. Cell Reports, 35(13): 109292. DOI: 10.1016/j.celrep.2021.109292.

Nidom, R. V., Indrasari, S., Normalina, I., Nidom, A. N., Afifah, B., Dewi, L., Putra, A. K., Ansori, A. N. M., Kusala, M. K. J., Alamudi, M. Y. & Nidom, C. A. (2021). Phylogenetic and Full-Length Genome Mutation Analysis of SARS-CoV-2 in Indonesia Prior to The COVID-19 Vaccination Program in 2021. Bulletin of the National Research Centre, 45: 200. DOI: 10.1186/s42269-021-00657-0.

Rovik, A., Pratama, A. & Rahayu, A. (2021). Tropical Climate Less Affects Covid-19 Transmission Than Population Density: a Perspective of Indonesia. Jurnal Kesehatan Indonesia, 14(1): 11-20. DOI: 10.20473/jkl.v14i1.2022.11-20.

Tegally, H., Wilkinson, E., Lessells, R. J., Giandhari, J., Pillay, S., Msomi, N., Mlisana, K., Bhiman, J. N., von Gottberg, A., Walaza, S., Fonseca, V., Allam, M., Ismail, A., Glass, A. J., Engelbrecht, S., Van Zyl, G., Preiser, W., Williamson, C., Petruccione, F., Sigal, A., Gazy, I., Hardie, D., Hsiao, N. Y., Martin, D., York, D., Goedhals, D., San, E. J., Giovanetti, M., Lourenço, J., Alcantara, L. C. J. & de Oliveira, T. (2021). Sixteen Novel Lineages of SARS-CoV-2 in South Africa. Letters Nature Medicine, 27: 440-446. DOI: 10.1038/s41591-021-01255-3.

Toptan, T., Hoehl, S., Westhaus, S., Bojkova, D., Berger, A., Rotter, B., Hoffmeier, K., Ciesek, S. & Widera, M. (2020). Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs. International Journal of Molecular Sciences, 21(12): 4396. DOI: 10.3390/ijms21124396.

Turnip, O. N., Fadhillah, C., Rovik, A. & Rahayu, A. (2023). Epidemiological Features and Phylogeny of SARS-CoV-2 Circulating in Southeast Asia in Early Pandemic. Journal of Microbiology and Infectious Disease, 12(1): 139-147. DOI: 10.5799/jmid.1218631.

Vinjamuri, S., Li, L. & Bouvier, M. 2022. SARS-CoV-2 ORF8: One Protein, Seemingly One Structure, and Many Functions. Frontiers in Immunology, 13. 1035559. DOI: 10.3389/fimmu.2022.1035559.

Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H. H., Michailidis, E., Gaebler, C., Agudelo, M., Cho, A., Wang, Z., Gazumyan, A., Cipolla, M., Luchsinger, L., Hillyer, C. D., Caskey, M., Robbiani, D. F., Rice, C. M., Nussenzweig, M. C., Hatziioannou, T. & Bieniasz, P. D. (2020). Escape from Neutralizing Antibodies by SARS-CoV-2 Spike Protein Variants. Elife, 9: e61312. DOI: 10.7554/eLife.61312.

Wijayanti, N., Gazali, F. M., Supriyati, E., Hakim, M. S., Arguni, E., Daniwijaya, M. E. W., Nuryastuti, T., Nuhamunada, M., Nabilla, R., Haryana, S. M. & Wibawa, T. (2022). Evolutionary Dynamics of SARS-CoV-2 Circulating in Yogyakarta and Central Java, Indonesia: Sequence Analysis Covering Furin Cleavage Site (FCS) Region of the Spike Protein. International Microbiology, 25: 531-540. DOI: 10.1007/s10123-011-00239-8.

Wu, W., Cheng, Y., Zhou, H., Sun, C. & Zhang, S. (2023). The SARS-CoV-2 Nucleocapsid Protein: Its Role in the Viral Life Cycle, Structure and Functions, and Use as A Potential Target In The Development of Vaccines and Diagnostics. Virology Journal, 20(6). DOI: 10.1186/s12985-023-01968-6.

Yang, W. & Shaman, J. (2022). COVID-19 Pandemic Dynamics in India, the SARS-CoV-2 Delta Variant and Implications for vaccination. Journal of the Royal Society Interface, 19, 20210900. DOI: 10.1098/rsif.2021.0900.

https://worldometer.com

https://gisaid.org/




DOI: https://doi.org/10.15575/biodjati.v8i1.25132

Refbacks

  • There are currently no refbacks.


Copyright (c) 2023 Jurnal Biodjati

License URL: https://creativecommons.org/licenses/by-nc-nd/4.0/

Indexing By :

      

      

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

 

View My Stats