The Portuguese royal family did not die out in the 1861 epidemic. The male line of Maria II descendants died out when Manoel II chocked in 1932, leaving no heirs from his wife, Augusta Victoria of Hohenzollern.
The epidemic that affected the royal palace in 1861 killed three of the sons of Maria II (Pedro V, Joao and Ferdinando), but two remained, Luiz and Augusto. Had Augusto married and left an heir there could have been a second line, but he died unmarried in his early forties.
Luiz himself had two sons, Carlos and Afonso. Had Afonso married equally and left heirs, there would have been again a junior branch, but unfortunately he did not.
The 1908 assassination of King Carlos and Crown Prince Luiz Filipe left Manoel as the only viable candidate for reproduction, and his having no children finally did the family in.
Arturo Beeche