Li Xinxin, Tang Chenyue, Zhou Min, Mi Jianqing, Liu Jialin, Han Lizhong, Yu Xiaoqi, Zhang Xinxin
Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No.197 Ruijin 2nd Road, Shanghai, 200025, China.
Department of Pulmonary and Critical Care Medcine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Sci Rep. 2025 May 29;15(1):18923. doi: 10.1038/s41598-025-04111-3.
Metagenomic next-generation sequencing (mNGS) is widely used to diagnose complex infections in hospitalized patients, particularly those associated with COVID-19 which has garnered significant concern over the past five years. To investigate the molecular epidemic of the viral variant and the potential co-infection pathogens, we conducted retrospective mNGS analysis of 254 SARS-CoV-2-positive specimens collected from 200 hospitalized patients between March and September 2023. Phylogenetic analysis of the identified Omicron subvariants showed minimal evolutionary divergence, with no association between sub-lineages and pneumonia severity. Notably, mNGS demonstrated enhanced detection of polymicrobial coinfections, identifying bacterial, fungal, and viral co-pathogens in 92.5% (185/200) of cases. Pneumonia severity was associated with advanced age (proportion of elderly patients: 61.1 vs 78.3%; p = 0.032) and comorbid conditions, particularly diabetes mellitus (OR 2.03, 95% CI 1.03-4.02, p = 0.041), but showed no correlation with SARS-CoV-2 sub-lineages or coinfecting pathogens. While mNGS enhances coinfection diagnosis, COVID-19 outcomes are predominantly driven by host factors rather than Omicron subvariant evolution. Prioritized monitoring of elderly and comorbid individuals remained critical for severe pneumonia management.
宏基因组下一代测序（mNGS）被广泛用于诊断住院患者的复杂感染，尤其是与新冠病毒相关的感染，在过去五年中，新冠病毒引起了极大关注。为了调查病毒变体的分子流行情况以及潜在的合并感染病原体，我们对2023年3月至9月期间从200名住院患者中收集的254份严重急性呼吸综合征冠状病毒2（SARS-CoV-2）阳性标本进行了回顾性mNGS分析。对鉴定出的奥密克戎亚变体进行系统发育分析，结果显示进化差异极小，亚谱系与肺炎严重程度之间无关联。值得注意的是，mNGS显示出对多重微生物合并感染的检测能力增强，在92.5%（185/200）的病例中识别出细菌、真菌和病毒共病原体。肺炎严重程度与高龄（老年患者比例：61.1%对78.3%；p = 0.032）和合并症相关，尤其是糖尿病（优势比2.03，95%置信区间1.03 - 4.02，p = 0.041），但与SARS-CoV-2亚谱系或合并感染病原体无关。虽然mNGS增强了合并感染的诊断，但新冠病毒感染的结果主要由宿主因素驱动，而非奥密克戎亚变体的进化。对老年人和合并症患者进行优先监测对于重症肺炎的管理仍然至关重要。
