You've mentioned channels, but also referred to Amazon Prime - this isn't a channel, but a streaming app (just like Netflix, YouTube & the BBC iPlayer). Channel 999 is one of the UHD channels, so let's go from the base up here.
I suspect - but you may want to confirm by checking on https://www.virginmedia.com/help/virgin-tv-box - that you have a TiVo & a V6,
If so... the TiVo doesn't support UHD which is why you won't get channels 228 or 999 (VM UHD) or 531 (BT Sport Ultimate)
The Amazon Prime app is one of a few that is also only available on the V6 and not the TiVo.
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