I was not expecting to provoke this much discussion!

Here's the article on Hinamizawa Syndrome from the When They Cry wiki. Read only if you don't care about spoilers.

http://whentheycry.wikia.com/wiki/Hinamizawa_Syndrome

...although not in this particular context. Specifically, my concern when the idea first came to me was how agents might be protected from zombie plagues ('cause they don't all spread through bites, you know). It then expanded to more conventional diseases as well as chemical weapons and exposure to radiation.

While I never actually wrote anything up (apart from a mention of Laura going through a decontamination process after suffering an open wound in the Fallout universe), I have a few theories/suggestions. First, the aforementioned decon process. Agents that have been exposed to something nasty would be immediately shunted to Medical when they portal back to HQ. They go through a chain of showers, genetic scanners, and medical tests before being certified as clean.

Secondly, perhaps their disguises offer some measure of protection against biological unpleasantness. How? In the same way that Bleeprin erases bad memories. Don't think about it, or else it'll stop working. Not very interesting, but it gets those concerns out of the way.

Finally, as other people have mentioned, there are always artificial/non-human agents that can be sent in. Perhaps the Flowers have specific teams for ultra-hazardous continuums.

Like I said, theories and suggestions.

If all else fails, you could send in a purely synthetic agent, right? I'm not really familiar with this continuum, but as far as I know, diseases don't generally infect other species, and an agent with a completely different biochemistry would be nearly impossible to infect with a virus from earth. Though it sounds supernatural, this is just my two-cents on the matter. Again, feel free to correct me if I'm wrong, as I said I only have a passing familiarity with Higurashi.

What is the disease's transmission vector? Is it airborne? Waterborne? Transmitted via contact with contaminated body fluids? Or is it completely supernatural (people just suddenly become infected)?

In any case, a regular NBC suit and a full decontamination process when re-entering HQ is in order. The real question is: "is there actually any badfic in that particular continuum"? If not, then we stay the heck away from that scary disease.