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You will be able to file a married filing joint return for federal purposes.  But depending upon your situation based upon the following information, it does appear you would need to file as married filing separately in West Virginia and your spouse would file married filing separately within Virginia.

West Virginia and Virginia are reciprocal states.  This means the wages earned in the state you work in are treated as if they are earned within your state of residence.  For you, since you reside in West Virginia but work in Virginia, assuming your employer has the W-220 exemption form on file, you will only be required to file a West Virginia state tax return.

As for your spouse, it sounds like she has established her domicile in Virginia by purchasing a home.  If her intent is always to return to the home in Virginia, then she would be considered to be a domiciliary resident of Virginia.  However, she would be considered an actual resident of Virginia if she was within the state for more than 183 days during the taxable year.  Please see this link for more details.

Virginia will not allow you to file a married filing joint return since you would be considered a nonresident while your spouse would potentially be considered a resident.  The only way you could file joinly in Virginia is if you both elect to be treated as Virginia residents.

West Virginia will treat you as a resident if you maintained a physical presence for more than 183 days of the taxable year.  If one spouse changes their state of residency during the year, you will not be able to file a joint return within West Virginia.  You will need to file as married filing separately for West Virginia.  Please see this link for more details.