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

Frontiers in Medicine

article

Nina Dwi Putri¹  Edison Johar²  Yora Permata Dewi²  Nuri Dyah Indrasari³  Dewi Wulandari³  Merci Monica br Pasaribu³  Teny Tjitra Sari¹  Fitri Prima Cakti¹  Madeline Ramdhani Jasin¹  Tartila Tartila¹  Frilasita Aisyah Yudhaputri²  Safarina G. Malik²  Khin Saw Aye Myint² 

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

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

DOI  :  10.3389/fmed.2022.835998

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

CC BY