case_images: PMC10505437_01
case_images: Lung computed tomography (CT) scan. (A) CT scan of the first admission on December 20, 2022. This image showed emphysema and multiple ground-glass image changed in both lungs. (B) CT scan of the second admission on February 22, 2023. This image showed emphysema, and multiple ground-glass opacities in both lungs were obviously absorbed.
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case_images: December 20, 2022. At that time, his body temperature was 38.7 C, he felt weak all over his body, and the nucleic acid test for SARS-CoV-2 was positive. Combined with the results of lung CT ( Figure 1A ), the patient was diagnosed with viral pneumonia. During hospitalization, his condition improved after intravenous injections of sulperazone, levofloxacin, and methylprednisolone, and he was discharged on January 3, 2023. Lung CT showed obvious absorption of the lung infection ( Figure 1B ).
case_images: Results of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) of this patient. (A) The coverage of Influenza A virus H3N2 detected by mNGS. The coverage was 96.3%. (B) The coverage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detected by mNGS. The coverage was 49.37%. (C) A total of 57590 reads were identified as microbial genome sequences. The percentage of Influenza A virus H3N2 is 15%, the percentage of SARS-CoV-2 is 3.26%.
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case_images: The mNGS results yielded 18882 sequences for influenza A virus (8637 sequences belonging to H3N2, the rest 10245 sequences of influenza A failed to identify subtypes because they could not be mapped to specific locations of subtypes) and 1875 sequences for SARS-CoV-2 ( Figure 2 ).
case_images: The timeline of the patient for disease course. It shows the process of patients from admission to discharge, mainly including pathogen identification (blue), presentation (green), and treatment (light blue). CT, computed tomography; qPCR, quantitative polymerase chain reaction; SARS-Cov-2, severe acute respiratory syndrome coronavirus 2; TB, Mycobacterium tuberculosis; MP, Mycoplasma pneumoniae; LP, Legionella pneumophila; CP, Chlamydia pneumoniae; NM, Neisseria meningococcus; PA, Pseudomonas aeruginosa; KP, Klebsiella pneumoniae; SA, Staphylococcus aureus; SP, Streptococcus pneumoniae; BALF, bronchoalveolar lavage fluid; IV, intravenous injection.
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case_images: The disease course is shown in  Figure 3 .