Px4, cube orange and dronekit impacting GPS accuracy

I am using px4 1.11.3 with cube orange and controlling the UAV through dronekit using the USB port of the cube orange board. I am using Here 2 GPS connected to the GPS1 port.
While dronekit is not running, the UAV is flying nicely and position hold is very stable. But once dronekit code is running (I am sending some mavlink messages in regular interval ~ 0.5 seconds) , number of satellites is dropping from 18 to 12-13 and VDOP and HDOP are increasing. From the log, i can see that GPS accuracy is decreasing (in the level of 5 meters compared to 0.5 - 1 meters without dronekit).
uORB message for gps from console does not show any increase in size, CPU load is around ~30-35% in both the cases.
Can anyone please suggest what might be going wrong here and how to resolve it?

Try to check spacing between GPS module and USB cable. There might be some interferences.