Trojan.Agent refers to a generic Trojan malware detection. It is used for detections that are either associated with no specific malware families or not enough information is available to pinpoint the malware family.
Trojan.Kovter is a detection for a family of malware that has many faces and targets Windows systems.
The main variants of Trojan.Kovter are aimed at performing ad-fraud and are very hard to detect and remove as they use fileless infection methods.
Kovter usually arrives in mail attachments as a Macro in a Word document file. When activated, the Macro downloads a file that creates a PowerShell command stored in the registry to gain persistence. Then the randomly named file deletes itself.
Malwarebytes protects users from Trojan.Kovter by using real-time protection.
Most of the time, Malwarebytes can detect and remove Trojan.Kovter without further user interaction.
In some cases, Malwarebytes Anti-Rootkit BETA is needed to find and delete the malicious registry key.