A second strain of the deadly AIDS virus, extremely rare in the United States but widespread in western Africa, has been identified in New York City, health officials said. The strain, called HIV-2, was detected in four blood samples taken recently by the New York City Department of Health, said Dr. Rand Stoneburner, director of AIDS research at the department. Stoneburner said the health department is investigating the cases. HIV-2 infections have been reported in Europe, most notably Portugal, and in Brazil. The more common HIV-1 strain of the AIDS virus is prevalent in the United States. The first documented case of HIV-2 infection in the United States was in a West African woman in Newark, N.J., in 1987.