If you receive multiple Forms 1099-INT Interest Income or a statement with multiple accounts, and these accounts have different CUSIP numbers, you will need to enter a separate Form 1099-INT for each account. This is not an e-filing requirement.
Although in the past you were able to consolidate Form 1099-INT entries on one form, the IRS now requires you to enter each form separately if they contain different CUSIP numbers.
Per IRS Instructions for Forms 1099-INT and 1099-OID, on page 4:
Box 14. Tax-Exempt and Tax Credit Bond CUSIP No.
For single bonds or accounts containing a single bond, enter the CUSIP number of the tax-exempt bond for which tax-exempt interest is reported in box 8 or tax credit bond (including build America bond and specified tax credit bond) for which a tax credit or taxable interest, as applicable, is reported in box 1. Enter the CUSIP number of the bond for which interest was paid or tax credit was allowed. If the tax-exempt interest or the tax credit is reported in the aggregate for multiple bonds or accounts, enter “various.”
Note that any link in the information above is updated each year automatically and will take you to the most recent version of the document at the time it is accessed.