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So I remember from reading the HH novels that many of the loyalist marines that didn't get under ground died during the virus portion of the Exterminatus and I've also read stories of SM fighting in the vacuum of space....I would understand that some of the marines may have had breathing slits or their helmet off and that the firestorm portion of the Exterminatus would cook others alive, but how do these germs get through the armor yet they can fight in space?
Am I missing something here?

Most of the Deathguard that were kill all had battle damage. and all the joints have a softer Kevlar like material. a simple slit and boom marines infected/dead.

Ps: Space marines can survive the vacuum of space, its a organ that lets them I believe.

Later marks of power armour are vaccuum-capable, so I would assume they would also be virus-proof.

I don't recall if anything was ever said about the earlier marks being fully sealed, though. Certainly MkI armour wasn't, and it wouldn't surprise me if MkII and MkIII were also not a perfect seal.

Battle damage makes sense, I should've known that SM had an organ that let them survive in the vacuum.
Thanks!

If I recall correctly the organ referred to basically makes the Space Marine sweat out a plastic coat over their body. I don't think that the SM can do it themselves, it has to be externally stimulated (by some injection maybe? I'm not sure exactly). It's stimulated manually before battle if it looks like vacuum fighting is a thing that might happen. If the organ wasn't stimulated beforehand then Space Marines can't handle vacuum any better than we could (well, they could probably survive without breathing for an absurdly long period, and put themselves into hibernation if that wasn't long enough, but you get the point...)

Depends on the model of power armor. Sororitas and Astartes power armor are both environmentally sealed, which means a complete hermetic seal which a virus would not be able to get through.

Some other kinds of power armor, such as those obtained by nobles or rich mercenaries, would probably not be so high-quality.

Rites of Initiation wrote:Phase 16 - Mucranoid. This small organ is implanted in the lower intestine where its hormonal secretions are absorbed by the colon. These secretions initiate a modification of the sweat glands. This modification normally makes no difference to the Marine until activated by appropriate chemotherapy. As a result of this treatment, the Marine sweats an oily, naturally cleansing substance which coats the skin. This protects the Marine against extremes of temperature and even offers a slight degree of protection in vacuum. Mucranoid chemotherapy is standard procedure on long space voyages and when fighting in vacuum or near vacuum.

Note: "slight degree" that likely means a marine has more time to remedy the situation in event of his armour being breached than a regular human would, not that he can survive indefinitely in a situation that would kill a regular human.

Mk2 onwards were fully sealed and suitable for use in deep space.

Modern marks of PA are able to operate in space, and so would be Virus proof.

However if there is any sort of damage in the seal the person inside the guy is screwed. Even if the leak would be fine in a vacuum, by the suit having the ability to keep an air supply to the marine even if the suit leaks and his natural ability to tolerate it even without his suit, the virus will still get him.

It's seemingly acidic:
Betrayal page 47:
"The armour wasn't always enough, I knew that not even Maximus battle plate, not always - even locked shut and on internal air - in sufficient concentration is can eat through suit seals, visor-ports even"

Why does that remind me of the Andromeda strain

 Flanker wrote:
, but how do these germs get through the armor yet they can fight in space?
Am I missing something here?

From Galaxy in Flames.

Warriors fell to their knees as the virus penetrated their armoured bodies, deadly corrosive agents laced into the virus structure of the weapons dissolving exposed pipes and armour joints, or finding their way inside through battle damage......

....Even many of those who reached the safety of the sealed bunkers died in agony as they shut the doors only to find they had brought the lethal virus inside with them.