Table_2_Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia.xlsx

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.

研究背景：截至目前，印度尼西亚已累计报告超400万例新型冠状病毒肺炎（Coronavirus Disease 2019, COVID-19）确诊病例，以及14.4万例死亡病例；其中12.8%的感染者为18岁以下儿童。现有研究证实，严重急性呼吸综合征冠状病毒2（Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2）的全基因组病毒测序（Whole-genome viral sequencing, WGS）可用于区分医院获得性感染与社区获得性COVID-19感染。本研究聚焦雅加达地区儿科肿瘤患者的感染溯源分析，旨在基于准种、病毒载量与入院日期，评估雅加达都会区某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感染的临床与实验室特征，并验证WGS用于确认该类感染的有效性。
研究方法：采用鼻咽拭子（nasopharyngeal swab, NP swab）的实时逆转录聚合酶链反应（real-time reverse-transcription polymerase chain reaction, RT-PCR）对患者、病房陪护人员及医护人员（healthcare workers, HCWs）进行新冠感染诊断，随后对RT-PCR检测呈阳性的样本实施全基因组测序，以明确其系统发育关系。
研究结果：通过全基因组测序分析，本研究证实，该合并恶性肿瘤的儿童群体中SARS-CoV-2的传播呈现全病毒基因组高度相似的特征，提示为医院内传播。