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

PeerJ

article

Anggia Prasetyoputri¹  Anik B. Dharmayanthi²  Syam B. Iryanto³  Ade Andriani¹  Isa Nuryana¹  Andri Wardiana¹  Asep M. Ridwanuloh¹  Sri Swasthikawati¹  Hariyatun Hariyatun¹  Herjuno A. Nugroho²  Idris Idris²  Indriawati Indriawati¹  Zahra Noviana²  Listiana Oktavia⁴  Yuliawati Yuliawati¹  Masrukhin Masrukhin²  Erwin F. Hasrianda²  Linda Sukmarini¹  Fahrurrozi Fahrurrozi¹  Nova Dilla Yanthi¹  Alfi T. Fathurahman¹  Ari S. Wulandari¹  Ruby Setiawan²  Syaiful Rizal²  Ahmad Fathoni¹  Wien Kusharyoto¹  Puspita Lisdiyanti¹  Ratih A. Ningrum¹  Sugiyono Saputra² 

[1] Research Center for Biotechnology, National Research and Innovation Agency;Research Center for Biology, National Research and Innovation Agency;Research Center for Informatics, National Research and Innovation Agency;Research Center for Chemistry, National Research and Innovation Agency

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

DOI  :  10.7717/peerj.13132

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundIndonesia 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.ObjectivesWe 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.MethodsNasopharyngeal 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).ResultsWe successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 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 (n = 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 (n = 44) and B.1.470 (n = 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.ConclusionsWe 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.

【 授权许可】

CC BY