ArticlePeerJ2022
The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia.
Article in PeerJ, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- SARS-CoV-2 lineages and naso-oropharyngeal bacterial communities in COVID-19 reinfection: A study in West Java, Indonesia.Narra J · 2025Article
- Insights into Omicron: Genomic Characterization and Inpatient Risk Assessment at Single Tertiary Hospital in Indonesia.Journal of multidisciplinary healthcare · 2025Article
- Genomic analysis of three SARS-CoV-2 waves in west Sumatra: Evolutionary dynamics and variant clustering.Heliyon · 2024Article
- Article
- SARS-CoV-2 genetic variation and bacterial communities of naso-oropharyngeal samples in middle-aged and elderly COVID-19 patients in West Java, Indonesia.Journal of Taibah University Medical Sciences · 2024Article
- From Archipelago to Pandemic Battleground: Unveiling Indonesia's COVID-19 Crisis.Journal of epidemiology and global health · 2023Review
- Molecular epidemiology of SARS-CoV-2 in Mongolia, first experience with nanopore sequencing in lower- and middle-income countries setting.Immunity, inflammation and disease · 2023Article
- SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia.IJID regions · 2023Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Article
- The impact of government pandemic policies on the vulnerability of healthcare workers to SARS-CoV-2 infection and mortality in Jakarta Province, Indonesia.Annals of medicine · 2023Article
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Authors and funding
29 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives: We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods: Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results: We successfully identified 16 lineages and six clades out of 202 samples (male Conclusions: We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.
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