Laboratory confirmation and identification of pathogen
Once an outbreak has been confirmed, identification of disease agent and confirmation of cases must be undertaken. When dealing with a new agent, access to advanced laboratory facilities will be required. In the case of COVID-19, it required genetic analysis to determine that the agent SARS-CoV-2 was different from SARS-CoV.
Case detection requires virus detection- either through RT-PCR, or virus antigen detection in addition to clinical manifestations of the disease. This is problematic in resource-limited settings, as the capacity and resources to conduct large-scale viral testing do not exist. Case detection would depend upon the disease- smallpox eradication was possible because of the typical presentation of smallpox. Photographs of various stages of smallpox were used to identify cases and initiate ring vaccination. Unfortunately, many viral diseases have similar clinical manifestations, and cannot be distinguished without laboratory tests.