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

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 poten...

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Published in:	PeerJ (San Francisco, CA) Vol. 10; p. e13132
Main Authors:	Prasetyoputri, Anggia, Dharmayanthi, Anik B, Iryanto, Syam B, Andriani, Ade, Nuryana, Isa, Wardiana, Andri, Ridwanuloh, Asep M, Swasthikawati, Sri, Hariyatun, Hariyatun, Nugroho, Herjuno A, Idris, Idris, Indriawati, Indriawati, Noviana, Zahra, Oktavia, Listiana, Yuliawati, Yuliawati, Masrukhin, Masrukhin, Hasrianda, Erwin F, Sukmarini, Linda, Fahrurrozi, Fahrurrozi, Yanthi, Nova Dilla, Fathurahman, Alfi T, Wulandari, Ari S, Setiawan, Ruby, Rizal, Syaiful, Fathoni, Ahmad, Kusharyoto, Wien, Lisdiyanti, Puspita, Ningrum, Ratih A, Saputra, Sugiyono
Format:	Journal Article
Language:	English
Published:	United States PeerJ. Ltd 22-03-2022 PeerJ, Inc PeerJ Inc
Subjects:	Analysis Bar codes Bioinformatics Bogor Coronaviruses COVID-19 COVID-19 - epidemiology COVID-19 vaccines Decision making DNA sequencing Epidemics Epidemiology Female Genomes Genomics Health aspects Humans Indonesia - epidemiology Indonesian lineages Infectious Diseases Laboratories Male Medical research Medicine, Experimental Molecular Biology Mortality Nanopore Nucleotide sequencing Pandemics Phylogenetics Polymerase chain reaction Public health RNA polymerase SARS-CoV-2 SARS-CoV-2 - genetics Severe acute respiratory syndrome coronavirus 2 Spike protein Vaccines Values Variant shifting Virology Whole genome sequencing Indonesia Jakarta Indonesia COVID-19 Delta variants Genomic surveillance SARS-CoV-2 Variant shifting Bogor Nanopore Indonesian lineages
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Summary:	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. 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. 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). 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. 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	2167-8359 2167-8359
DOI:	10.7717/peerj.13132