Yes, as Weather Vane says, 'novel virus' forces such a specifying definition on 'novel' that it is perhaps better regarded here as part of a fixed expression.
Indeed, CALD does list this usage but adds caveats:
novel [medical ... specialized]
used to refer to a new strain (= type) of a virus that has not been
seen before:
- The COVID-19 pathogen is a novel coronavirus.
- A novel virus in swine is closely related to the human hepatitis E virus. [6 Oct 2020; Proc NAS]
However, 'novel' in this sense has been around since at least the 1970s, when the terms 'novel proteins' and 'novel compounds' were often met in scientific papers. Perhaps 'new to science' is a good synonym.
In general usage, the difference between these two fairly close synonyms is brought out by this statement from Vocabulary.com:
novel If something is so new and original that it's never been seen, used or even thought of before, call it novel.
There is an emphasis on originality, freshness, a new idea being involved. A 'novelty item' is (aimed at being) a surprising, inventive, almost ingenious knickknack.
Lexico at the moment (08 Nov 2020) carries only the generally upbeat sense (doubtless the default sense prior to the 'novel virus' usage):
novel [adjective] ...
New or unusual in an interesting way.
- He hit on a novel idea to solve his financial problems.
Though 'novel virus' and 'novelty item' are terms evoking very different scenarios.