But I don't think this makes any sense. If the disease is a vitamin deficiency, and these people have been there for a while and have been eating rice and dried fish the whole time, shouldn't this "epidemic" be a longstanding problem and not something that's just happened recently?
Well, that’s probably because the author skimmed the historical parallels between the current situation and how beriberi came to be a thing in Meiji era Japan and how it was eventually eradicated…probably expected a Japanese audience to get the reference and fill in the gaps (Takaki Kanehiro and his contributions to Japanese medicine/nutritional understanding is fairly well known).
See, back in the days rice was a staple food, but poor people had brown rice which had its bran coating intact. Polished white rice was considered a luxurious food meant for the rich back in the days, but polishing the bran off the rice also meant that it can be stored longer, so the military will pay to have the rice polished so it can be stored in the warehouses. Similarly, in major Japanese cities the warehouses of local merchants tend to be stocked with polished white rice since it’s much more shelf-stable, and they can pass the price increases onto their customers.
The ability to store polished rice for long periods of time meant that the Japanese military gave their soldiers and sailors as much white rice as they wanted, but charged for other (more perishable and expensive) foods - the idea was that it’ll limit uptake and simplify logistics - technically Japanese soldiers and sailors were granted a cash allowance to pay for the additional supplemental food items. For poorer sailors during voyages, many of them ended up eating nothing but white rice and salt so they can send money off the supplementary items allowance from their paychecks home. Army soldiers can theoretically forage for extra ingredients..but not always. It was observed that during longer campaigns or voyages, poorer soldiers and sailors who had nothing but polished white rice and salt developed beriberi, while their richer officers didn’t, despite them being in close proximity with each other. The only difference is that the officers also ate other things paid out of their larger cash allowance or out of their own pockets from the mess halls and galleys. When those poorer soldiers and sailors returned back to their families out in the countryside, their beriberi conditions improved or went away. Why was that? Their families at home can’t afford polished white rice from city merchants, so they had to have barley or locally grown rice (which is unpolished brown rice - either one will have double the cooking time of plain white rice). Where’s the B1 stored in rice? Within the bran coating that was polished off. The oil within the bran can go rancid over time and ruin the rice.
How did the Japanese Navy fought off Beriberi? They mixed barley onto their white rice (which was resisted by some sailors due to its “poor folk kibble” image…and this was further exacerbated by the fact that prisons started doing the same), but the army didn’t follow suit and suffered from it for 15 more years. Why didn’t they? Imperial navy officers were trained in the UK and were taught epidemiology while the Imperial army officers were trained in Prussia and were taught germ theory. In epidemiology all factors were considered as root to afflictions while germ theory concentrates on a malignant source of illness. The idea that you can become sick due to some kind of “imbalance” was a concept in ancient Chinese medicine (which amongst much Chinese know-how was adopted by Japan and held for centuries during the Shogunate era). This was seen as passé for Meiji Japan trying to absorb western ideas and catch up. While the core tenets of traditional Chinese medication seem like superstition, the benefit of a nutritionally balanced diet does deliver results here.
The Japanese emperor eventually ordered the army to add barley to their rice rations mostly out of pragmatism.
In the manga, the victims tend to be single men on exile who were on the fish-and-polished rice diet and little else. This is similar to the diets of Meiji day laborers in large Japanese cities like Osaka and Tokyo. For the urban lower and middle class, there was a folk remedy…which was to mix beans into the white rice, which also boosted its nutritional profile. It was however held as something shameful meant for the poor and ignorant. Even for the upper classes picky eaters can die from Beri-beri.