A year after the World Health Organisation declared COVID-19 as a pandemic, much has been learned with respect to SARS-CoV-2 epidemiology, vaccine production and disease treatment. Whole-genome sequencing (WGS) has played a significant role in contributing to our understanding of the epidemiology and biology of this virus. In this paper, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asia and the impact of technological development, access to resources, and demography of individual countries on its uptake. Facilitated by the Nottingham-Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative, we showcased a bilateral collaboration between the University of Nottingham and the Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia) to establish WGS of SARS-CoV-2 using Oxford Nanopore Technology® in Indonesia. Analyses of SARS-CoV-2 genomes deposited on GISAID from Southeast and East Asian countries reveals the importance of collecting clinical and demographic metadata and the importance of open access and data sharing. Lineage and phylogenetic analyses per 1 June 2021 found that: 1) B.1.466.2 variants were the most predominant in Indonesia, with mutations in the spike protein including D614G at 100%, N439K at 99.1%, and P681R at 69.7% frequency, 2) The variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta) were first detected in Indonesia in January 2021, 2) B.1.470 was first detected in Indonesia and spread to the neighbouring regions, and 3) The highest rate of virus transmissions between Indonesia and the rest of the world appears to be through interactions with Singapore and Japan, two neighbouring countries with high degree of access and travels to and from Indonesia. Overall, we conclude that WGS of SARS-CoV-2 using Oxford Nanopore Technology® platforms fits well with the Indonesian context and can catalyse the increase of sequencing rates in the country.

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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Tuberculosis (TB) is an airborne illness generated by Mycobacterium tuberculosis (Mtb), also one of the prominent infectious killers of adults worldwide. There is a pressing need to expand novel anti-mycobacterial drugs because of the increasing resistance of pathogenic mycobacteria to existing antibiotics. Native compounds acquired from microbial resources and medicinal cultivars have played an essential part as the origin of TB medications. The microplate resazurin reduction assay (MRRA) is generally utilized to assess natural and synthetic compounds for anti-mycobacterial activity. In our work, the MRRA method was employed to evaluate the antimycobacterial activity of extracts from curative plants using Mycobacterium smegmatis and Mycobacterium bovis BCG and to compare them to rifampicin as an anti-mycobacterial drug. The optimized MRRA utilized 2% aqueous DMSO and 62.5μg/mL resazurin as an indicator compound in 5% aqueous Tween 80. The optimal incubation time for M. smegmatis was 24h, and for M. bovis BCG was 48h. The methanolic plant extracts were acquired from various Indonesian medicinal plants known to have anti-mycobacterial activity. The various plant extracts exhibited anti-mycrobial activities confirmed by the MRRA assay. The MRRA method using M. smegmatis or M. bovis BCG as antimycobacterial targets offers a distinct advantage such as low-cost, rapid, and safe screening for anti-mycobacterial activity in a middle to high-through-putformat.