Affiliation:
1. Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine Shandong University Jinan Shandong China
2. Beijing Center for Disease Prevention and Control Beijing Academy for Preventive Medicine Beijing China
3. State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China
4. Research Unit of Discovery and Tracing of Natural Focus Diseases Chinese Academy of Medical Sciences Beijing China
Abstract
AbstractThe seasonal human coronaviruses (HCoVs) have zoonotic origins, repeated infections, and global transmission. The objectives of this study are to elaborate the epidemiological and evolutionary characteristics of HCoVs from patients with acute respiratory illness. We conducted a multicenter surveillance at 36 sentinel hospitals of Beijing Metropolis, China, during 2016–2019. Patients with influenza‐like illness (ILI) and severe acute respiratory infection (SARI) were included, and submitted respiratory samples for screening HCoVs by multiplex real‐time reverse transcription‐polymerase chain reaction assays. All the positive samples were used for metatranscriptomic sequencing to get whole genomes of HCoVs for genetical and evolutionary analyses. Totally, 321 of 15 677 patients with ILI or SARI were found to be positive for HCoVs, with an infection rate of 2.0% (95% confidence interval, 1.8%–2.3%). HCoV‐229E, HCoV‐NL63, HCoV‐OC43, and HCoV‐HKU1 infections accounted for 18.7%, 38.3%, 40.5%, and 2.5%, respectively. In comparison to ILI cases, SARI cases were significantly older, more likely caused by HCoV‐229E and HCoV‐OC43, and more often co‐infected with other respiratory pathogens. A total of 179 full genome sequences of HCoVs were obtained from 321 positive patients. The phylogenetical analyses revealed that HCoV‐229E, HCoV‐NL63 and HCoV‐OC43 continuously yielded novel lineages, respectively. The nonsynonymous to synonymous ratio of all key genes in each HCoV was less than one, indicating that all four HCoVs were under negative selection pressure. Multiple substitution modes were observed in spike glycoprotein among the four HCoVs. Our findings highlight the importance of enhancing surveillance on HCoVs, and imply that more variants might occur in the future.
Subject
Infectious Diseases,Virology
Cited by
1 articles.
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