I'm Doug, and I'm very sorry to hear of your situation. My goal is to provide you with excellent service today.
While it is typical to file for divorce and in the same process seek custody issues, it is not a legal requirement to do so.
Typically a person will only file for custody when they are not sure that they want to file for a divorce, or when the statutory requirement for a divorce have not yet been met, but they want to separate and take their children with them. Under VA law, a no fault divorce may only be filed for once the parties have lived separate and apart for one year, if they have children.
This application for custody is a way for the parents---through the legal process--- to determine which of them will have primary custody of the children and for the court to issue a child support order against the parent who will not have primary residential custody of the children.
It is no unusual to also see an application for spousal support filed at the same time.
Also be aware that VA does not have any legal form of separation. Separation in VA is the state of living apart, and what she likely means is that she will be seeking a court of custody, child support and possibly spousal support, in the near future.
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I wish you and yours the best in 2015,