Hello John,
You can do this either only by monitoring specific directories or by setting up rules specific for VirusTotal checks.
An example of monitoring specific directories could be:
<syscheck>
<directories check_all="yes" whodata="yes">C:\Users\*\Documents</directories>
<directories check_all="yes" whodata="yes">C:\Users\*\Desktop</directories>
<directories check_all="yes" whodata="yes">C:\Users\*\Downloads</directories>
<ignore type="sregex">.ini$|.jpg$|.png$|.lnk$|.log$|.txt$</ignore>
</syscheck>
As you can see, you can also set it to ignore some file types since they are not usually malicious.
An example of filtering the alerts by setting up a rule group, where you can categorize these alerts and then configure the VirusTotal integration:
<group name="threat-intel,">
<rule id="444556" level="13">
<if_group>syscheck</if_group>
<field name="file">^c:\\users\\\.+.exe$|^c:\\users\\\.+.bat$|^c:\\users\\\.+.cmd$|^c:\\users\\\.+.com$|^c:\\users\\\.+.ps1$|^c:\\users\\\.+.vbs$|^c:\\users\\\.+.vb$|^c:\\users\\\.+.wsf$|^c:\\users\\\.+.ws$|^c:\\users\\\.+.scr$</field>
<description>Dangerous File copied on users folder: $(file)</description>
</rule>
</group>
<integration>
<name>virustotal</name>
<api_key>API_KEY</api_key> <!-- Replace with your VirusTotal API key -->
<group>threat-intel</group>
<alert_format>json</alert_format>
</integration>
In this way, you can filter and therefore limit the files checked against VirusTotal.
I hope this could be helpful.