What we see from your debug output is that gpgv is not returning any
sensible information:

Summary:
  Good: 
  Bad: 
  Worthless: 
  SoonWorthless: 
  NoPubKey: 


You could try running apt-key verify manually on a few InRelease files (like 
apt-key verify 
/var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_xenial_InRelease) and see if 
that gives us any clue - or at least look at the files (especially in 
partial/), maybe they are garbage.

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https://bugs.launchpad.net/bugs/1642386

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