The most common and most likely answer to this crossword clue is the 5 plus 9 letter word AVIAN INFLUENZA
A
V
I
A
N
I
N
F
L
U
E
N
Z
A
Buddy explains!
The straight part
We know that "Viral infection contracted during flight" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case viral infection contracted during flight = avian influenza.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.