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2022;10 e13132.

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.

Anggia Prasetyoputri, Anik B Dharmayanthi, Syam B Iryanto, Ade Andriani, Isa Nuryana, Andri Wardiana, Asep M Ridwanuloh, Sri Swasthikawati, Hariyatun Hariyatun, Herjuno A Nugroho, Idris Idris, Indriawati Indriawati, Zahra Noviana, Listiana Oktavia, Yuliawati Yuliawati, Masrukhin Masrukhin, Erwin F Hasrianda, Linda Sukmarini, Fahrurrozi Fahrurrozi, Nova Dilla Yanthi, Alfi T Fathurahman, Ari S Wulandari, Ruby Setiawan, Syaiful Rizal, Ahmad Fathoni, Wien Kusharyoto, Puspita Lisdiyanti, Ratih A Ningrum, Sugiyono Saputra
Author Information
  1. Anggia Prasetyoputri: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  2. Anik B Dharmayanthi: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  3. Syam B Iryanto: Research Center for Informatics, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  4. Ade Andriani: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  5. Isa Nuryana: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  6. Andri Wardiana: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  7. Asep M Ridwanuloh: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  8. Sri Swasthikawati: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  9. Hariyatun Hariyatun: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  10. Herjuno A Nugroho: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  11. Idris Idris: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  12. Indriawati Indriawati: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  13. Zahra Noviana: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  14. Listiana Oktavia: Research Center for Chemistry, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  15. Yuliawati Yuliawati: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  16. Masrukhin Masrukhin: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  17. Erwin F Hasrianda: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  18. Linda Sukmarini: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  19. Fahrurrozi Fahrurrozi: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  20. Nova Dilla Yanthi: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  21. Alfi T Fathurahman: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  22. Ari S Wulandari: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  23. Ruby Setiawan: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  24. Syaiful Rizal: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  25. Ahmad Fathoni: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  26. Wien Kusharyoto: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  27. Puspita Lisdiyanti: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  28. Ratih A Ningrum: Research Center for Biotechnology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
  29. Sugiyono Saputra: Research Center for Biology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia.
PMID: 35341058 DOI: 10.7717/peerj.13132

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  = 116, female  = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave ( = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave ( = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 ( = 44) and B.1.470 ( = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general.
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.

Keywords

Bogor COVID-19 Delta variants Genomic surveillance Indonesian lineages Nanopore SARS-CoV-2 Variant shifting

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MeSH Term

Humans
Female
Male
SARS-CoV-2
COVID-19
Indonesia
Pandemics
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 5

Word Cloud

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