Putri Nina Dwi, Johar Edison, Dewi Yora Permata, Indrasari Nuri Dyah, Wulandari Dewi, Br Pasaribu Merci Monica, Sari Teny Tjitra, Cakti Fitri Prima, Jasin Madeline Ramdhani, Tartila Tartila, Yudhaputri Frilasita Aisyah, Malik Safarina G, Myint Khin Saw Aye
Department of Paediatrics, Dr. Cipto Mangunkusumo National Central Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.
Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
Front Med (Lausanne). 2022 Mar 4;9:835998. doi: 10.3389/fmed.2022.835998. eCollection 2022.
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.
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.
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.
截至目前，印度尼西亚已记录了超过400万例确诊的新冠病毒病病例和14.4万例死亡病例；其中12.8%的病例为18岁以下儿童。严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的全基因组病毒测序（WGS）已被证明有助于区分医院获得性感染与社区获得性2019冠状病毒病（COVID-19）感染。我们的研究强调了使用WGS来调查雅加达儿科肿瘤患者的感染源。我们研究的目的是评估临床和实验室特征，以及基于准种、病毒载量和入院日期，使用WGS来确认雅加达大都市一家三级医院单个病房内一群免疫功能低下儿童的医院获得性COVID-19感染的有效性。
使用来自鼻咽（NP）拭子的实时逆转录聚合酶链反应（RT-PCR）对患者以及病房中的监护人及医护人员（HCW）进行诊断，随后对RT-PCR阳性病例进行WGS以建立其系统发育关系。
通过WGS，我们发现一群患有潜在恶性肿瘤的儿童中SARS-CoV-2传播的特征是全病毒基因组高度相似，这表明存在医院内传播。
