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

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

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


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.

Original languageEnglish
Article number835998
JournalFrontiers in Medicine
Publication statusPublished - 4 Mar 2022


  • children
  • COVID-19
  • hospital-acquired infection
  • immunocompromised
  • Indonesia
  • quasispecies
  • SARS-CoV-2
  • whole-genome sequencing


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