tetano
Editor, Senior Moderator
Bull Natl Res Cent
. 2021;45(1):200.
doi: 10.1186/s42269-021-00657-0. Epub 2021 Nov 21.
Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
Reviany V Nidom[SUP] 1 2 [/SUP], Setyarina Indrasari[SUP] 1 2 [/SUP], Irine Normalina[SUP] 1 2 [/SUP], Astria N Nidom[SUP] 1 [/SUP], Balqis Afifah[SUP] 1 [/SUP], Lestari Dewi[SUP] 3 [/SUP], Andra K Putra[SUP] 4 [/SUP], Arif N M Ansori[SUP] 1 5 [/SUP], Muhammad K J Kusala[SUP] 1 5 [/SUP], Mohammad Y Alamudi[SUP] 1 [/SUP], Chairul A Nidom[SUP] 1 2 6 [/SUP]
Affiliations
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.
Supplementary information: The online version contains supplementary material available at 10.1186/s42269-021-00657-0.
Keywords: COVID-19; Genome analysis; Indonesia; SARS-CoV-2; Spike protein.
. 2021;45(1):200.
doi: 10.1186/s42269-021-00657-0. Epub 2021 Nov 21.
Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021
Reviany V Nidom[SUP] 1 2 [/SUP], Setyarina Indrasari[SUP] 1 2 [/SUP], Irine Normalina[SUP] 1 2 [/SUP], Astria N Nidom[SUP] 1 [/SUP], Balqis Afifah[SUP] 1 [/SUP], Lestari Dewi[SUP] 3 [/SUP], Andra K Putra[SUP] 4 [/SUP], Arif N M Ansori[SUP] 1 5 [/SUP], Muhammad K J Kusala[SUP] 1 5 [/SUP], Mohammad Y Alamudi[SUP] 1 [/SUP], Chairul A Nidom[SUP] 1 2 6 [/SUP]
Affiliations
- PMID: 34840498
- PMCID: PMC8606223
- DOI: 10.1186/s42269-021-00657-0
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.
Supplementary information: The online version contains supplementary material available at 10.1186/s42269-021-00657-0.
Keywords: COVID-19; Genome analysis; Indonesia; SARS-CoV-2; Spike protein.