no problam to nepali travelling nepal from usa through quatar air. it has no effect on transit until now.
the big problem is when anyone wants to return usa through quatar or any airlines. quatar has stopped its service to nepal so noone can come usa through quatar air.

second thing, usa has started entry denial not only for Nepalese but also for many asian for those who are in visa or green card. they will refuse entry to usa if they feel any suspect.
they have clearly mentioned they can only quarantine for us citizens other have to return back until further notice