Commercial Fixed Wing
Flight Crew Air Transport Pilot (ATP)
Confusion; Communication Breakdown; Situational Awareness; Time Pressure
ATC Issue All Types; Deviation / Discrepancy - Procedural Published Material / Policy
Air Traffic Control Issued New Clearance; Flight Crew Returned To Clearance
Human Factors; Procedure
After departing ZZZ we received an ATC clearance to proceed direct to ZZZZZ. After referencing the FMC I replied that ZZZZZ was not on our flight plan and that we where routed RZZZ after ZZZZZ1. ATC then asked to verify our routing after ZZZZZ1; this is where we discovered what we had loaded into the FMC; and our Jepp app was different than our ATC clearance. We worked out routing with ATC and proceeded to ZZZ1.Waiting for the aircraft to arrive late in ZZZ the Captain called Dispatch to discuss a northerly routing they had us planned for that appeared to take us closer to some weather than our more normal routes. The Dispatcher agreed and it was decided to change the route. The amendment came through and reflected the new routing. Once on the aircraft the route that uplinked to the FMC was the new routing as well.Relevant factors include first and foremost time compression from the late inbound aircraft exacerbated by slow deplaning and mechanics in the flight deck; a nonstandard gate that required a lengthy walk to and from ops for paperwork as well and 6 MELs one of which was added at the last minute. Additionally; it's rare to get a PDC clearance furthermore the format has changed since it was the norm; this coupled with expectation bias resulted in misreading the PDC. The departure and first few fixes of the PDC were exactly the same as our 'new' routing additionally a line under the route titled 'REVISED SEGMENT' stated NONE. All combined with COVID and the fact we are not flying as much as we used to.In this case it had been in excess of an hour and a half since the Captain had called Dispatch and discussed the route change to when we departed. Along with the time compression; multiple amendments and MELs I had forgotten about the route change until we were airborne talking to ATC. In the future whenever there is a route change initiated by the flight crew and or Dispatch; I will be sure to mention it as a threat during the departure briefing in an effort to promote a more rigorous scrutinizing of the clearance; flight plan and loaded route.
Late changes to filed oceanic route clearance led to confusion of clearance after takeoff. As these reports usually start; we were under abnormal time constraints with a late inbound aircraft. Dealing with 5 MELs to decipher; and another last minute MEL addition; coupled with amendments to both our route and our release.Having called Dispatch while waiting for the inbound aircraft; I requested slightly different routing due to some forecast turbulence plots on our original route. The Dispatcher agreed and reran our flight plan. It turned out to be a minute shorter in flight time and seemed like it would be a smoother route.Here's where it went awry. I was led down the wrong path by two factors; (traps). First our 'new' clearance; on the release; was similar to our old; and; as it turns out; only filed clearance. Secondly; the clearance printout from ATC; has two sections. The first reads **filed route** which was exactly the same for the first two positions but is an incomplete route. The second reads; ***revised segment *** which read; NONE. As I was confirming the route and there were no revisions according to the clearance; I used the master flight plan print out as my cross check. Climbing out of ZZZ; we were given direct to a point not loaded into our FMC. After some confusion we figured out that the 'old' route was the one ATC got and subsequently had given us. It seems that while we had been given an amendment to our flight plan on our paperwork; ATC had not gotten the 'new' route. While still in radar contact and talking to ZZZ departure; we re-filed in the air to the route we both; had paperwork (master flight plan) for and had loaded in the FMC. Clearance was given and we proceeded on the route without further ado.Recommendation would be to allow a FULL route; meaning the entire route; to be printed off with the actual clearance. Instead; for some reason we only get the first few points and if; as in our case; there is nothing in the ***revised*** sections; we are  to assume the rest of the route is the same as our paperwork. Obviously a trap in our case.Lessons for myself; resist expectation bias; confirm route on both documents; (clearance and master flight plan); and most importantly; after having so much time off; be extra methodical; ESPECIALLY when hurried by outside influences.
Air carrier flight crew reported during climbout they received a route change that was not on the filed route.