Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing

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, this study retrospectively collected 254 samples (4.47%) from 200 hospitalized patients tested positive for SARS-CoV-2 for mNGS analysis from March to September 2023. Over time, XBB.1.16 dominated from May to June and HK.3 began to emerge in August and increased steadily, while FU.1 was consistently detected during this period. Further phylogenetic analysis indicated minimal variation in the evolutionary branches of Omicron variants from April to September. The concurrent detection of bacteria and fungi alongside SARS-CoV-2 using mNGS facilitated the diagnosis and management of these complex infection cases. The demographic and clinical characteristics of these patients were statistically analysed. The severity of pneumonia was associated with old age and underlying diseases. COVID-19 patients with comorbidities such as diabetes mellitus were more likely to have severe pneumonia, of which odds ratio was 2.033 (1.029~4.015, 95%CI, p =0.041). Elderly patients and those with underlying health conditions require heightened attention, particularly in cases of severe pneumonia.