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. 2022 Mar 4:9:835998.
doi: 10.3389/fmed.2022.835998. eCollection 2022.

Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia

Nina Dwi Putri  1 , Edison Johar  2 , Yora Permata Dewi  2 , Nuri Dyah Indrasari  3 , Dewi Wulandari  3 , Merci Monica Br Pasaribu  3 , Teny Tjitra Sari  1 , Fitri Prima Cakti  1 , Madeline Ramdhani Jasin  1 , Tartila Tartila  1 , Frilasita Aisyah Yudhaputri  2 , Safarina G Malik  2 , Khin Saw Aye Myint  2
Affiliations

Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia

Nina Dwi Putri et al. Front Med (Lausanne). .

Abstract

Background: Thus far, Indonesia has recorded over 4,000,000 confirmed COVID-19 cases and 144,000 fatalities; 12.8% of cases have been in children under 18 years. Whole-genome viral sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been demonstrated to help differentiate hospital-acquired infection from community-acquired coronavirus disease 2019 (COVID-19) infection. Our study highlighted the use of WGS to investigate the origin of infection among pediatric oncology patients in Jakarta. The aim of our study was to evaluate clinical and laboratory characteristics and also the efficacy of using WGS to confirm hospital-acquired COVID-19 infection in a cluster of immunocompromised children within a single ward of a tertiary hospital in metropolitan Jakarta based on quasispecies, viral load, and admission dates.

Method: Real-time reverse-transcription polymerase chain reaction (RT-PCR) from nasopharyngeal (NP) swabs was used to diagnose the patients and also guardians and healthcare workers (HCWs) in the ward, followed by WGS of RT-PCR positive cases to establish their phylogenetic relationships.

Result: Using WGS, we showed that SARS-CoV-2 transmission in a cluster of children with underlying malignancy was characterized by high similarity of whole virus genome, which suggests nosocomial transmission.

Keywords: COVID-19; Indonesia; SARS-CoV-2; children; hospital-acquired infection; immunocompromised; quasispecies; whole-genome sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree comparing whole genome of SARS-CoV-2 from the five pediatric cases with SARS-CoV-2 lineage B.1.470 from around the world and reference genome (Wuhan Hu1). Label indicates collection site/collection date/GISAID accession number. The scale bar represents the number of nucleotide substitution per site.
See this image and copyright information in PMC

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