Total Infectome Characterization of Respiratory Infections during the 2022–23 COVID-19 Outbreak in China Revealed Extensive Coinfections with Links to SARS-CoV-2 Status, Age, and Disease Severity
Zhongzhou Yang,
Kanru Cai,
Yuqi Liao,
Wei-Chen Wu,
Li Xing,
Minxuan Hu,
Jiali Ren,
Jieyun Zhang,
Xiuyun Zhu,
Ke Yuan,
Shunyao Wang,
Hui Huang,
Chunhui Yang,
Mingxia Zhang,
Mang Shi,
Hongzhou Lu
Affiliations
Zhongzhou Yang
Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
Kanru Cai
Institute for Hepatology, National Clinical Research Center for Infectious Disease, The Third People’s Hospital of Shenzhen, Shenzhen 518112, China
Yuqi Liao
Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
Wei-Chen Wu
Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
Li Xing
BGI Genomics, BGI-Shenzhen, Shenzhen 518000, China
Minxuan Hu
Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
Jiali Ren
BGI Genomics, BGI-Shenzhen, Shenzhen 518000, China
Jieyun Zhang
Institute for Hepatology, National Clinical Research Center for Infectious Disease, The Third People’s Hospital of Shenzhen, Shenzhen 518112, China
Xiuyun Zhu
Institute for Hepatology, National Clinical Research Center for Infectious Disease, The Third People’s Hospital of Shenzhen, Shenzhen 518112, China
Ke Yuan
BGI Genomics, BGI-Shenzhen, Shenzhen 518000, China
Shunyao Wang
BGI Genomics, BGI-Shenzhen, Shenzhen 518000, China
Hui Huang
BGI Genomics, BGI-Shenzhen, Shenzhen 518000, China
Chunhui Yang
Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
Mingxia Zhang
Institute for Hepatology, National Clinical Research Center for Infectious Disease, The Third People’s Hospital of Shenzhen, Shenzhen 518112, China
Mang Shi
Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
Hongzhou Lu
Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The Third People’s Hospital of Shenzhen, Shenzhen 518112, China
Between 7 December 2022 and 28 February 2023, China experienced a new wave of COVID-19 that swept across the entire country and resulted in an increasing amount of respiratory infections and hospitalizations. The purpose of this study is to reveal the intensity and composition of coinfecting microbial agents. In total, 196 inpatients were recruited from The Third People’s Hospital of Shenzhen, and 169 respiratory and 73 blood samples were collected for metagenomic next-generation sequencing. The total “Infectome” was characterized and compared across different groups defined by the SARS-CoV-2 detection status, age groups, and severity of disease. Our results revealed a total of 22 species of pathogenic microbes (4 viruses, 13 bacteria, and 5 fungi), and more were discovered in the respiratory tract than in blood. The diversity of the total infectome was highly distinguished between respiratory and blood samples, and it was generally higher in patients that were SARS-CoV-2-positive, older in age, and with more severe disease. At the individual pathogen level, HSV-1 seemed to be the major contributor to these differences observed in the overall comparisons. Collectively, this study reveals the highly complex respiratory infectome and high-intensity coinfection in patients admitted to the hospital during the period of the 2023 COVID-19 pandemic in China.
