The Identification of First COVID-19 Cluster in Indonesia

Setiawaty, Vivi; Kosasih, Herman; Mardian, Yan; Ajis, Emita; Prasetyowati, Endang Burni; Siswanto, Siswanto; Karyana, Muhammad

doi:10.4269/ajtmh.20-0554

Cited by 38 publications

(41 citation statements)

References 10 publications

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“…Nonetheless, the first Indonesian cases (i.e. a cluster of two) were detected in Jakarta and officially announced on 2 March 2020 [10], [13], [14]. As these patients immediately underwent quarantine and hospitalization, it was less likely that the first sequencing sample was the result of direct transmission from this cluster, only ten days apart.…”

Section: Phylogenetic Relationship Based On Pango Lineages Exists Between Differentmentioning

confidence: 99%

“…There was a widely-held belief that the hot tropical climate and high intensity of UV rays in Indonesia would be sufficient to hinder SARS-CoV-2 survival and spread in the air, much like the first SARS epidemic where cases were low compared to its originating place in China [2], [11], [12]. Therefore, before March 2020, Indonesia only carried out early testing and screening of individuals with symptoms and travel links [13], [14].…”

Section: Introductionmentioning

confidence: 99%

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

Cahyani¹,

Putro

Ridwanuloh

et al. 2021

Preprint

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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.

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Section: Phylogenetic Relationship Based On Pango Lineages Exists Between Differentmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Cahyani¹,

Putro

Ridwanuloh

et al. 2021

Preprint

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“…Since the first confirmed case of COVID-19 in Indonesia in early March 2020, all aspects of medical services in Indonesia have been affected [8]. It is ranged from primary care service until surgery service [9], [10], [11].…”

Section: Discussionmentioning

confidence: 99%

Effect of Coronavirus Disease-19 Pandemic to the Volume of Total Hip and Knee Arthroplasty Surgical Service: Experience from a Single Tertiary Orthopedic Hospital in Indonesia

Santoso

Persada

Anwar

et al. 2020

Open Access Maced J Med Sci

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The difficult situation of the coronavirus disease (COVID)-19 pandemic may affect to hip and knee arthroplasty service. Retrospective study was performed to patients who received elective total hip/total knee arthroplasty (THA/TKA) from January to September 2020 at Prof. Dr. R. Soeharso Orthopaedic Hospital, Surakarta, Indonesia. There were a total of 64 THA and 227 TKA from January to September of 2020. There was an extreme decrease in the number of TKA surgery during April, May, and June in 2020. The effect of coronavirus disease-19 pandemic to the decrease of arthroplasty service was mainly in the first 3 months period.

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“…Globally, as of 19 October 2020, there have been 39,944,882 confirmed cases of COVID-19 including 1,111,998 deaths, reported to WHO(2). Indonesia reported their first case of infection on 2 March 2020(3), and the first 11 cases described had partial N gene sequence 100% similarity with the SARS-CoV-2 sequence from Wuhan(4). As of 21 October 2020, the numbers have risen to 373,109 confirmed, 12,857 dead and 297,509 recovered cases(5).…”

Section: Introductionmentioning

confidence: 99%

Comparison study of commercial COVID-19 RT-PCR kits propose an approach to evaluate their performances

Krismawati

Mahendra²,

Hartanto³

et al. 2021

Preprint

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With the increasing number of COVID-19 cases in Indonesia, scalable and high-throughput diagnostic testing is essential nationwide. Currently, RT-PCR has been the preferred method of viral detection and many manufacturers offer commercial kits for routine clinical diagnostics. In response to the incoming of various kits, there is a need to assess their performance and compatibility of use in clinical laboratories. Kit characteristics impact the testing workflow of these laboratories and some factors can render a kit to perform sub-optimally, leading to false results that are misleading for public safety. Here, we evaluated six commercial kits that are predominantly distributed to appointed testing facilities across Indonesia. Their performance was assessed based on their ease of use, availability, robustness and accuracy for scalable testing in a manual set-up. Our findings demonstrated that all six kits are suitable for use in routine diagnostics, but their considerations for use may vary according to different use-cases. To better guide considerations in procurement of kits, our study provided a systematic approach for laboratories to assess the performance of new incoming kits.

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The Identification of First COVID-19 Cluster in Indonesia

Cited by 38 publications

References 10 publications

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

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

Effect of Coronavirus Disease-19 Pandemic to the Volume of Total Hip and Knee Arthroplasty Surgical Service: Experience from a Single Tertiary Orthopedic Hospital in Indonesia

Comparison study of commercial COVID-19 RT-PCR kits propose an approach to evaluate their performances

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