My wife submitted a tax return married filed single and now realizes that was an error and we should have filed jointly. I have not yet filed what should we do?

You will have to amend your wife's tax return by filling out Form 1040X, change your filing status to Married Filing Jointly, and add in your income.  If you expect a balance due, follow Karen's advice, and make a payment.  You might want to extend for yourself - your wife doesn't need to extend since she's filed.

You will need to file a federal and state extension by tomorrow and pay any balance due.

https://ttlc.intuit.com/questions/1899507-how-do-i-amend-married-filing-separately-returns-to-married-filing-jointly

Thank you - one challenge is that her tax return has not yet been accepted. What should I do if it is not accepted before the deadline?

If it rejects, you don't need to extend, or amend.  Just change the filing status and add in your income.