How come armies all over the world were caught so badly flat-footed?

According to the timeline of Black Tide Rising, the US government was aware of the plague almost instantly – not about the origin, infection sources and so on, obviously, but that something’s going around and it’s bad.

Uncle Tom was aware of it as an employee of BOTA, which obviously would get any info from the government – and the book says as much, actually (about the source(s)).

But USAMRIID would definitely be on top of this one, as they actually are there mainly for that reason – that is: to actively search for possible bio/chem attacks on US (widely understood).

I do get that NB San Diego, NS Norfolk, NAS Jacksonville would be doomed from the start, but JB PH-Hickam and almost all of CVBGs deployed overseas would be much easier to quarantine (would say as much even about the Hawaii Archipelago itself). Carriers especially – they are big islands, with personnel always accounted for. Admittedly, the whole carrier group size would mean that anything between 30 and a 100 people daily would go to and from the group back to the mainland, but it still would be quite easy and fast to effect a quarantine. Especially since flight is not yet instantaneous, so plenty of patients zero for carriers would be in transit when the announcement was made, much less the problem noticed.

Russia and China have much less distributed military, but some of their bases would be much more isolated – and easy to lock down – than others’ armies…

And since the plague itself is a work of individual or small group, the seeding of US West and East Coasts would take even longer than the incubation of the bug, so first cases would be reported even before they finished, giving rest of the world much more warning that it’s implied in the book.

So, bearing in mind that the nature of the book is so that in- and out-of-universe explanation would be about the same, the question is: how come armed forces – US especially, but by no means exclusively – bungled it up so badly? No matter how crazy the "topic" is, I’m sure that the Pentagon has a plan in case of "biological, viral, latent, wide release, previously undetected, currently no vaccine, hostile activities" type of emergency…

But one needs to clearly separate lack of political willingness to acknowledge the pandemic exists from an implementation of detailed and planned ahead of time policy that doesn’t have to be even reported as it’s internal military procedural matter… From the timeline, I gather that at the time the plague was identified by government agencies it was still spreading and that was done using civilian transport hubs. That suggests that a lot of personnel transfers were still underway, and the passengers could be isolated or the transports turned around altogether.