Cryptic crossword clue
Virus that is pierced by old medical instrument 6

The most common and most likely answer to this crossword clue is the 6 letter word BOUGIE

I've seen this crossword clue in The Guardian
B
O
U
G
I
E

Buddy explains!

The straight part
We know that "medical instrument" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case medical instrument = bougie.
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.

What does BOUGIE mean?

BOUGIE noun
  1. A tapered cylindrical instrument for introducing an object into a tubular anatomical structure, or to dilate such a structure, as with an esophageal bougie.
  2. A wax candle.
BOUGIE adjective
  1. (usually derogatory) Behaving like or pertaining to people of a higher social status, middle-class / bourgeois people (sometimes carrying connotations of fakeness, elitism, or snobbery).
  2. Fancy or good-looking, without the same connotations of snobbery or pretentiousness as in sense 1.

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