Log File Full -- Database is in AlwaysOn
Will manual log backup affect the AlwaysOn ?
No Manual Log backups wont affect,this is same like you are doing through scheduled jobs..In Summary

Log backups can happen on any node and the log still gets truncated.  The transaction log is basically replicated amongst all replicas.

like log shipping, will AlwaysOn have log backup jobs

AlwaysOn is similar to Mirroring in areas where log will be transferred over wire..

From Bob Dorr article

Always On is a bit different than database mirroring (DBM) with respect to sending the log blocks to the secondary replica(s).   DBM flushes the log block to disk and once completed locally, sends the block to the secondary.
Always On changed this to flush the block(s) in parallel.  In fact, a secondary could have hardened log block(s) before the primary I/O completes.    This design increases performance and narrows the NOT IN SYNC window(s).

Shrinking fails because of pending log backup
if you are saying can i shrink log to reduce space.Don't do that,shrinking is a bad practice.Log space will be reused .Taking into Account factors that can prevent log space reuse,you also need to account for fact that replicas have hardened the log blocks to Disk
References:
https://blogs.msdn.microsoft.com/sqlgardner/2012/07/18/sql-2012-alwayson-and-backups-part-1-offloading-the-work-to-a-replica/