Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract  

作　　者：Xiangxing Jin Lili Ren Xianwen Ren Jianwei Wanag 

机构地区：[1]NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory,National Institute of Pathogen Biology,Chinese Academy of Medical Sciences&Peking Union Medical College,Beijing 102629,China [2]Changping Laboratory,Beijing 102206,China [3]Key Laboratory of Pathogen Infection Prevention and Control(Ministry of Education),State Key Laboratory of Respiratory Health and Multimorbidity,National Institute of Pathogen Biology,Chinese Academy of Medical Sciences&Peking Union Medical College,Beijing 102629,China [4]Key Laboratory of Respiratory Disease Pathogenomics,Chinese Academy of Medical Sciences&Peking Union Medical College,Bejing 100730,China [5]National Key Laboratory of Immunity and Inflammation,Chinese Academy of Medical Sciences&Peking Union Medical College,Beijing 100730,China

出　　处：《Biosafety and Health》2025年第1期5-16,共12页生物安全与健康(英文)

基　　金：Science Fund for Creative Research Groups of the National Natural Science Foundation of China(82221004);the National Natural Science Foundation(81930063);the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences(2021-12M-1-038);Changping Laboratory research fund.

摘　　要：It is crucial to understand how severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)sheds in human respiratory tract,but this question remains elusive due to technical limitations.In this study,we integrated published human metagenomic data of SARS-CoV-2 and developed a novel algorithm named RedeCoronavS to systematically dissect SARS-Cov-2 shedding modes with single-cell data as reference.Our study demonstrated that SARS-CoV-2 particles were the dominant mode of viral shedding in the very early infection phase(<24 h after hospitalization).Within the first week after hospitalization,SARS-CoV-2 replicas within host cells dominated viral shedding alongside viral particles.One week later,viral fragments became the dominant mode in patients with mild or moderate symptoms,while viral replicas still dominated in some patients with severe symptoms.In addition to epithelial cells,SARS-CoV-2 replicas in neutrophils,macrophages,and plasma cells also played significant roles and were associated with sampling time and disease severity.

关 键 词：Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) Coronavirus disease 2019(COVID-19) Viral shedding RNA-Seq Single-cell analysis 

分 类 号：R373[医药卫生—病原生物学]