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Coinfection of SARS-CoV-2 and influenza A (H3N2) detected in bronchoalveolar lavage fluid of a patient with long COVID using metagenomic next−generation sequencing: a case report

SARS-CoV-2 and influenza A viruses are similar in transmission and respiratory symptoms but differ in virulence, treatment and vaccine availability. Metagenomic nextgeneration sequencing (mNGS) does not depend on culture and can be directly applied to nucleic acids in various sample types for unbiased sequencing.

In this study, we use GeneMind GenoLab M mNGS solution to detect coinfection with SARS-CoV-2 and influenza A virus in a patient with long COVID. The patient was admitted with fever, expectoration, fatigue, and shortness of breath. The PCR test was negative due to possible clearance of SARS-Cov-2 in the upper respiratory tract of patients with long COVID. The result showing that mNGS can improve pathogen detection in patients with negative routine test results, mixed infections, or atypical symptoms.

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