Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements

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.

Sequence analysis of SARS-CoV-2 Delta variant isolated from Makassar, South Sulawesi, Indonesia

“…During June–October 2021, 6643 Delta sequences were submitted to GISAID [ 7 ]. In this period, the proportion of the original Delta variants decreased to approximately 2% of all submitted genomes due to the competition from its sublineages AY.23 (64.5%) and AY.24 (21.3%) [ 24 ]. Of the 62 samples of the Delta variant in Makassar, 57 (91.9%) and 5 (8.1%) samples of AY.23 and AY.24 were detected, respectively.…”

“…Based on the analysis of the mutations in our study, all Delta sequences had P323L and G671S mutations in the nsp12/RdRp as well as D614G in the Spike. Previous research has also found that the co‐occurrence of D614G/spike and P323L/RdRp mutations is common in sequences obtained from Indonesia [ 24 ]. D614G and P323L mutations in SARS-CoV-2 was linked with severe COVID-19 cases by a recent study that analyzed the mutation patterns with respect to the severity of illness [ 44 ].…”

A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains

“…It is also well considered as the major circulating mutation in Indonesia [ 9 ]. Furthermore, D614G is also responsible for amino acid mutations in other regions as well, such as in P323L in RNA-dependent polymerase or NSP12, where it was associated with D614G as contributing factor in the viral infectivity [ 17 , 20 ]. On the other hand, Q57H mutation in NS3-ORF3A assists viruses in evading induction immune responses including interferon-stimulated gene, cytokine, and chemokine, as it causes truncation of ORF3B [ 21 , 22 ].…”

COVID-19 Vaccination and Clinical Outcomes at a Secondary Referral Hospital During the Delta Variant-dominant Period in West Sumatra, Indonesia

“…This single-center retrospective cohort study involved patients with COVID-19 during the second wave of COVID-19 cases in Indonesia, during which the Delta variant predominated [ 4 , 20 ]. The participants were patients who presented to the COVID-19 emergency room at Andalas University Teaching Hospital between June 1, 2021 and August 31, 2021.…”