Prevalence of bacteria, fungi, and virus coinfections with SARS-CoV-2 Omicron variant among patients with severe COVID-19 in Guangzhou, China, winter 2022

• Published in: Biosafety and health Vol. 6; no. 2; pp. 92 - 97
• Main Authors: Fan, Qinghong, Jiang, Mengling, Zhang, Jun, Tang, Guofang, Gao, Ming, Wen, Yingfen, Deng, Xizi, Dai, Jun, Lai, Honghao, Qian, Peng, Lin, Yaqing, He, Ruiying, Li, Liya, Li, Yueping, Li, Zhengtu, Liu, Xuesong, Li, Yimin, Yu, Na, Lan, Yun, Hu, Fengyu, Li, Feng
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-04-2024; Elsevier
• Subjects: Coinfection; Omicron BA.5.2; Omicron BF.7; SARS-CoV-2; Severe infection; SARS-CoV-2; Omicron BA.5.2; Severe infection; Coinfection; Omicron BF.7
• ISSN: 2590-0536; 2590-0536
• DOI: 10.1016/j.bsheal.2024.02.003

•The most comprehensive coinfection spectrum of bacterial, fungal, and viral coinfections in Omicron-caused severe coronavirus disease 2019 (COVID-19) during the winter of 2022 was analyzed.•Conditional pathogenic virus coinfections are quite common in the Omicron-caused severe COVID-19.•Synergistic coinfection of multiple conditional pathogens might deteriorate the Omicron infection outcomes.
The status of coinfection during the national outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.5.2 or BF.7 in China in the winter of 2022, which is suspected to contribute substantially to the overloaded severe cases, needs to be investigated. We analyzed the coinfection status of 385 severe patients infected with the Omicron variant in Guangzhou using metagenomic sequencing. We found that 317 (82.3 %) patients were coinfected with at least one additional pathogen(s), including bacteria (58.7 %), fungi (27.1 %) and viruses (73.5 %). Pseudomonas aeruginosa (P. aeruginosa) (24.2 %), Staphylococcus aureus (S. aureus) (14.0 %), and Klebsiella pneumoniae (K. pneumonia) (13.4 %) ranked as the top three coinfected bacteria. Aspergillus fumigatus (A. fumigatus) (39.5 %), Pneumocystis jirovecii (P. jirovecii) (24.4 %) and Canidia albicans (C. albicans) (22.1 %) were the top three coinfected fungi. Epstein-Barr virus (EBV) (63.1 %), Human herpesvirus 7 (HHV-7) (34.8 %), and Herpes simplex virus 1 (HSV-1) (32.6 %) were the top three coinfected viruses. Of note, the detection of multiple coinfections of potential pathogenic bacteria, fungi, and viruses, despite lacking consistent patterns, highlighted a complicated synergistic contribution to disease severity. Our study presents the most comprehensive spectrum of bacterial, fungal, and viral coinfections in Omicron-associated severe coronavirus disease 2019 (COVID-19), implying that the coinfection of conditional pathogens might synergistically deteriorate the Omicron infection outcomes.