Method for pathogen identification

A method for detecting a coronavirus, the method comprising:

• collecting a specimen, wherein the specimen comprises a cell;
• lysing the cell to form a cell lysate, wherein the cell lysate comprises an internal control enzyme naturally occurring in the cell lysate;
• contacting the cell lysate with a first substrate, wherein the first substrate comprises an Interferon Stimulated Gene-15 (ISG-15) or a fragment thereof, a ubiquitin or a fragment thereof, or a coronavirus protein fragment and a first signaling moiety conjugated to the carboxy terminus of the first substrate, wherein the first substrate is cleaved by a coronavirus enzyme, if present;
• contacting the cell lysate 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 the 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 cell;
• 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 from the cell lysate.