Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021

Abstract Background Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and econom...

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Autores principales:	Reviany V. Nidom, Setyarina Indrasari, Irine Normalina, Astria N. Nidom, Balqis Afifah, Lestari Dewi, Andra K. Putra, Arif N. M. Ansori, Muhammad K. J. Kusala, Mohammad Y. Alamudi, Chairul A. Nidom
Formato:	article
Lenguaje:	EN
Publicado:	SpringerOpen 2021
Materias:	COVID-19 Genome analysis Indonesia SARS-CoV-2 Spike protein Science Q
Acceso en línea:	https://doaj.org/article/71183ae072a64d4f9cc10ed7d08bc641
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spelling	oai:doaj.org-article:71183ae072a64d4f9cc10ed7d08bc6412021-11-28T12:36:13ZPhylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 202110.1186/s42269-021-00657-02522-8307https://doaj.org/article/71183ae072a64d4f9cc10ed7d08bc6412021-11-01T00:00:00Zhttps://doi.org/10.1186/s42269-021-00657-0https://doaj.org/toc/2522-8307Abstract Background Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as of 12 January 2021. Results All data of the isolates were extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver platform was employed to investigate the full-length genome mutation analysis of all isolates. This study also focused on the phylogeny analysis in unlocking the mutation of S protein in Indonesian SARS-CoV-2 isolates. WIV04 isolate that was originated from Wuhan, China was used as the virus reference according to the CoVsurver default. The result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully generated. Every single mutation in S protein was described and then visualized by utilizing BioRender platform. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. Conclusions To sum up, this study helped to observe the spread of COVID-19 transmission. However, it also proposed that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia.Reviany V. NidomSetyarina IndrasariIrine NormalinaAstria N. NidomBalqis AfifahLestari DewiAndra K. PutraArif N. M. AnsoriMuhammad K. J. KusalaMohammad Y. AlamudiChairul A. NidomSpringerOpenarticleCOVID-19Genome analysisIndonesiaSARS-CoV-2Spike proteinScienceQENBulletin of the National Research Centre, Vol 45, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	COVID-19 Genome analysis Indonesia SARS-CoV-2 Spike protein Science Q
spellingShingle	COVID-19 Genome analysis Indonesia SARS-CoV-2 Spike protein Science Q Reviany V. Nidom Setyarina Indrasari Irine Normalina Astria N. Nidom Balqis Afifah Lestari Dewi Andra K. Putra Arif N. M. Ansori Muhammad K. J. Kusala Mohammad Y. Alamudi Chairul A. Nidom Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
description	Abstract Background Indonesia has started the big project of COVID-19 vaccination program since 13 January 2021 by employing the first shot of vaccine to the President of Indonesia as the outbreak and rapid transmission of COVID-19 have endangered not only Indonesian but the global health and economy. This study aimed to investigate the full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates as of 12 January 2021. Results All data of the isolates were extracted from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCoV database. CoVsurver platform was employed to investigate the full-length genome mutation analysis of all isolates. This study also focused on the phylogeny analysis in unlocking the mutation of S protein in Indonesian SARS-CoV-2 isolates. WIV04 isolate that was originated from Wuhan, China was used as the virus reference according to the CoVsurver default. The result showed that a full-length genome mutation analysis of 166 Indonesian SARS-CoV-2 isolates was successfully generated. Every single mutation in S protein was described and then visualized by utilizing BioRender platform. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. Conclusions To sum up, this study helped to observe the spread of COVID-19 transmission. However, it also proposed that the epidemiological surveillance and genomics studies might be improved on COVID-19 pandemic in Indonesia.
format	article
author	Reviany V. Nidom Setyarina Indrasari Irine Normalina Astria N. Nidom Balqis Afifah Lestari Dewi Andra K. Putra Arif N. M. Ansori Muhammad K. J. Kusala Mohammad Y. Alamudi Chairul A. Nidom
author_facet	Reviany V. Nidom Setyarina Indrasari Irine Normalina Astria N. Nidom Balqis Afifah Lestari Dewi Andra K. Putra Arif N. M. Ansori Muhammad K. J. Kusala Mohammad Y. Alamudi Chairul A. Nidom
author_sort	Reviany V. Nidom
title	Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
title_short	Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
title_full	Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
title_fullStr	Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
title_full_unstemmed	Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
title_sort	phylogenetic and full-length genome mutation analysis of sars-cov-2 in indonesia prior to covid-19 vaccination program in 2021
publisher	SpringerOpen
publishDate	2021
url	https://doaj.org/article/71183ae072a64d4f9cc10ed7d08bc641
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Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021

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