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To add additional indexes to the WSUS 3.0 Database, connect SQL Management Studio via:
\.\pipe\MSSQL$MICROSOFT##SSEE\sql\query
and execute the following script:

CREATE NONCLUSTERED INDEX [IX_tbRevisionSupersedesUpdate] ON [dbo].tbRevisionSupersedesUpdate;
CREATE NONCLUSTERED INDEX [IX_tbLocalizedPropertyForRevision] ON [dbo].tbLocalizedPropertyForRevision;

These indexes will help to speed up the database maintenance while removing absolete items.