Method for pathogen identification

A method for detecting a coronavirus, the method comprising:

• providing a specimen, wherein the specimen comprises a plurality of cells;
• contacting the specimen with a first substrate, wherein the first substrate comprises a first signaling moiety conjugated to a carboxy terminus of the first substrate, the first substrate further comprising an Interferon Stimulated Gene-15 (ISG-15) or a fragment thereof, a ubiquitin or a fragment thereof, or a coronavirus protein fragment, and wherein the first substrate is cleaved by a coronavirus enzyme;
• contacting the specimen with a second substrate, wherein the second substrate comprises a control peptide and a second signaling moiety conjugated to the control peptide, wherein the second substrate is cleaved by an internal control enzyme;
• determining the presence of a first fluorescent signal from an unconjugated first signaling moiety produced by the coronavirus enzyme cleaving the first substrate wherein the presence of the first fluorescent signal indicates a presence of the coronavirus in the specimen;
• determining the presence of a second fluorescent signal from an unconjugated second signaling moiety produced by the internal control enzyme cleaving the control peptide wherein the presence of the second fluorescent signal indicates a presence of the internal control enzyme within the cell;
• and
• determining the first fluorescent signal from the unconjugated first signaling moiety and the second fluorescent signal from the unconjugated second signaling moiety to detect the coronavirus, the internal control enzyme or both in the specimen.