You can file a Joint Return for California, but your wife also needs to file a Part-Year Resident return separately for Virginia.
Prepare this return for her first, then your California Resident return. California will ask about wages earned/taxes paid to another state, and give you credit for tax paid to Virginia, but may need a copy of Virginia W-2 or Virginia tax return as documentation.
Here's more info from the California FTB:
https://www.ftb.ca.gov/individuals/Filing-status-information.shtml
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