Perhaps they did. In the Chesapeake colonies of the 17th century most settlers would go through "seasoning" in their first year, and would often die. It's been called a complex of diseases but given the habitat and place, mosquito-borne pathogens like malaria or Dengue fever seem likely. But I am not sure whether this would make it an Old World problem, with diseases imported from the Old World via African slaves, or was at least partly a New World disease with New World strains of malaria.