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The molecularly cloned virus known as SIVmac239/YEnef causes extensive lymphocyte activation in unstimulated peripheral mononuclear cell cultures and induces an acute disease syndrome in macaque monkeys. Here we describe the histopathological and immunophenotypic changes and viral localization in peripheral lymph nodes, spleen, and gastrointestinal tract (including the gut-associated lymphoid tissue (GALT) in rhesus monkeys inoculated with SIVmac239/YEnet beginning at day 3 postinoculation (pi). The findings are compared with those of rhesus monkeys inoculated with the same dose of parental SIVmac239. Histopathological examination of peripheral lymphoid tissue and GALT demonstrated marked hyperplasia of T-cell-dependent regions and involution of germinal centers as early as day 7 pi. The most striking lesions were multifocal areas of lymphohistiocytic gastroenteritis and colitis. Cellular infiltrates peaked between day 7 and 14 pi and were composed primarily of CD3+ T lymphocytes and HAM-56+ monocyte/macrophages. Many of these inflammatory cells were also strongly immunoreactive for teh nuclear proliferation antigen Ki-67. Despite the presence of severe gastrointestinal pathology by day 7 pi, no significant difference in the numbers of virus-positive cells in the gastrointestinal tract was observed between these animals and SIVmac239-infected animals examined at the same time point. However, the distribution of virus in the gastrointestinal tract was markedly different, with virus localized to lymphoid nodules of GALT in SIVmac239-infected animals and restricted to areas of lymphohistiocytic gastroenteritis and colitis in animals infected with SIVmac239/YEnef. Our data indicate that the acute disease syndrome induced by SIVmac239/YEnef is not simply related to increased viral replication in the gastrointestinal tract but is likely due to inappropriate virus-induced T lymphocyte activation and proliferation in GALT and subsequent mucosal destruction.