You can file jointly or separately. The least paperwork would be to file separately by mail and write NRA in the box for the SSN of your spouse. But that might not be the best option moneywise.
If you file jointly, you do need to apply for an ITIN for your spouse. She doesn't have to be in the US for that nor does she need to have a visa. If she has no passport, you can use 2 other types of documents listed in the instructions for form W7: https://www.irs.gov/instructions/iw7/ch01.html
If you file jointly, you also need to attach a statement that you both choose to treat your wife as resident alien. That means, she will also have to report worldwide income for the entire year. She can use the foreign paid tax credit of foreign earned income exclusion to avoid double taxation.
We can not tell you, which way is better. You would have to report your return both ways and see if filing jointly gives you enough benefit to make all the paperwork worthwhile.
Have a look at publication 519: https://www.irs.gov/publications/p519/
