Hello - can SEP be set-up to alert me if certain virus thresholds are identified/reached? 

Sort of.

Go to Monitors page and select the Notifications tab and Notification conditions

Select Add and Single Risk Event or New Rsik Found

You can setup conditions for severity and type

Yes you can set, here is the document

Creating notifications in the Symantec Endpoint Protection Manager

http://www.symantec.com/business/support/index?page=content&id=TECH91622

Hi,

Thank you for posting in Symantec community.

Q.Hello - can SEP be set-up to alert me if certain virus thresholds are identified/reached? 

--> Yes, it can be set-up within provided options.

You can construct custom filters by using the Basic Settings and Advanced Settings to change the information that you want to see. You can save your filter settings to the database so that you can generate the same view again in the future. When you save your settings, they are saved in the database. The name you give to the filter appears in the Use a saved filter list box for that type of logs and reports.

Saving and deleting filters

http://www.symantec.com/docs/HOWTO27267

In SEP 12.1 there are weekly scheduled reports & pre-defined notifications configured by Symantec.

Schedule Reports location: SEPM --> Reports --> Scheduled Reports

Predefined Notifications location:

SEPM--> Monitors--> Notifications --> View Notifications --> Notifications Conditions

Related articles:

About the preconfigured notifications

http://www.symantec.com/docs/HOWTO55128

About the different types of Symantec Endpoint Protection Manager Reports

http://www.symantec.com/docs/TECH95538