Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements
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Abstract
Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham–Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in the Research Center for Biotechnology, National Research and Innovation Agency (BRIN), to carry out a small number of SARS-CoV-2 WGS in Indonesia using Oxford Nanopore Technology (ONT). Analyses of SARS- CoV-2 genomes deposited on GISAID reveal the importance of clinical and demographic metadata collection and the importance of open access and data sharing. Lineage and phylogenetic analyses of two periods defined by the Delta variant outbreak reveal that: (1) B.1.466.2 variants were the most predominant in Indonesia before the Delta variant outbreak, having a unique spike gene mutation N439K at more than 98% frequency, (2) Delta variants AY.23 sub-lineage took over after June 2021, and (3) the highest rate of virus transmissions between Indonesia and other countries was through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia.
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SciScore for 10.1101/2021.07.06.451270: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: The metadata included collection date, location, origin of samples, passage history, and sequencing technology. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Libraries were loaded on a MinION device and flow cell. MinIONsuggested: (MinION, RRID:SCR_017985)ONT’s MinKNOW software was used to run sequencing. MinKNOWsuggested: NoneThe Rampart software was applied to monitor coverage of each barcoded sample in real-time by running fast base-calling. Rampartsuggested: (Rampart, RRID:SCR_016742)Up to 1 June 2021, there were 1830 sequences that were aligned … SciScore for 10.1101/2021.07.06.451270: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: The metadata included collection date, location, origin of samples, passage history, and sequencing technology. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Libraries were loaded on a MinION device and flow cell. MinIONsuggested: (MinION, RRID:SCR_017985)ONT’s MinKNOW software was used to run sequencing. MinKNOWsuggested: NoneThe Rampart software was applied to monitor coverage of each barcoded sample in real-time by running fast base-calling. Rampartsuggested: (Rampart, RRID:SCR_016742)Up to 1 June 2021, there were 1830 sequences that were aligned and the 5’ and 3’ ends trimmed using MAFFT v. MAFFTsuggested: (MAFFT, RRID:SCR_011811)The tree was then visualized and annotated with FigTree where the nodes were ordered and rooted [75]. FigTreesuggested: (FigTree, RRID:SCR_008515)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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