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These soldiers were infected with the vocal cord parasites that reacted to the language Kikongo, as these soldiers spoke Kikongo. The parasites infected them, which once they were showing symptoms, there was no hope.
When Ocelot discovered there was a disease, he told Venom Snake to put them in the Quarantine Zone. Several of them were ultimately cured via wolbachia after Code Talker identified the strain, albeit with the cost of them being rendered sterile as a result. However, some of them ultimately became a victim of a more severe outbreak the second time around, this time by modified X-rays that emitted beta radiation (deliberately caused by Huey Emmerich), with Snake being forced to kill them.