Nanopore-based diagnostic systems are a promising tool for counting viruses in a specimen one by one. However, despite intensive R&D efforts, it remains difficult to recognize virus subtypes by nanopore devices. We thus propose a novel diagnostic system that combines a specialized virus recognition procedure with a nanopore detection procedure. This recognition procedure consists of three steps: 1) capture target viruses using specific probes for recognition; 2) release captured targets; and 3) detect released targets by nanopore. Proof-of-concept tests are conducted using avidin-modified fluorescent particles (as a model for viruses) and biotin-modified alkane thiol (as a model for probes). The avidin-modified particles are confirmed to be captured on electrode by biotin-modified probes and then, the particles are electrochemically released from the electrode. Consequently, the released particles are successfully detected by nanopore devices. Furthermore, the concept is also proved by using human influenza viruses (H1N1, A/PR/8/34) and sugar chain (6'-sialyllactose)-modified probes. This suggests that our concept is applicable to various infectious diseases by changing probes (ligands).