AbstractBackgroundAs pathogens such as influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can easily cause pandemics, rapid diagnostic tests are crucial for implementing efficient quarantine measures, providing effective treatments to patients, and preventing or containing a pandemic infection. Here, we developed the immunochromatography-NanoSuit® method, an improved immunochromatography method combined with a conventional scanning electron microscope (SEM), which enables observation of immunocomplexes labeled with a colloidal metal.Methods and FindingsThe detection ability of our method is comparable to that of real-time reverse transcription-polymerase chain reaction and the detection time is approximately 15 min. Our new immunochromatography-NanoSuit® method suppresses cellulose deformity and makes it possible to easily focus and acquire high-resolution images of gold/platinum labeled immunocomplexes of viruses such as influenza A, without the need for conductive treatment as with conventional SEM. Electron microscopy (EM)-based diagnosis of influenza A exhibited 94% clinical sensitivity (29/31) (95% confidence interval [95%CI]: 78.58–99.21%) and 100% clinical specificity (95%CI: 97.80–100%). EM-based diagnosis was significantly more sensitive (71.2%) than macroscopic diagnosis (14.3%), especially in the lower influenza A-RNA copy number group. The detection ability of our method is comparable to that of real-time reverse transcription-polymerase chain reaction.ConclusionsThis simple and highly sensitive quantitative analysis method involving immunochromatography can be utilized to diagnose various infections in humans and livestock, including highly infectious diseases such as COVID-19.