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

Frontiers in Medicine

Merci Monica br Pasaribu¹  Nuri Dyah Indrasari¹  Dewi Wulandari¹  Madeline Ramdhani Jasin²  Teny Tjitra Sari²  Nina Dwi Putri²  Tartila Tartila²  Fitri Prima Cakti²  Khin Saw Aye Myint³  Safarina G. Malik³  Edison Johar³  Frilasita Aisyah Yudhaputri³  Yora Permata Dewi³ 

[1] Department of Clinical Pathology, Dr. Cipto Mangunkusumo National Central Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia;Department of Paediatrics, Dr. Cipto Mangunkusumo National Central Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia;Eijkman Institute for Molecular Biology, Jakarta, Indonesia;

关键词: COVID-19;    SARS-CoV-2;    quasispecies;    whole-genome sequencing;    hospital-acquired infection;    children;   

DOI  :  10.3389/fmed.2022.835998

来源: DOAJ

【 摘 要 】

BackgroundThus 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.MethodReal-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.ResultUsing 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.

【 授权许可】

Unknown