Abstract The large double-stranded DNA genome of murine cytomegalovirus (MCMV) is stable both in vitro and in vivo in the absence of immune pressure. However, one month after inoculation of plaque-purified MCMV into T cell-deficient mice, viral clones emerge with mutations in the viral MHC class I-like molecule, m157, due to selection by natural killer (NK) cells. While the emergence of escape mutants is dependent on the cognate interaction of m157 with the Ly49H NK cell activation receptor, the mechanism for mutant virus selection has not been fully dissected. Surprisingly, we show here that diverse mutations were already present in the salivary glands of C57BL/6 mice 14 days post-infection, much earlier than previously reported. Upon re-inoculation, MCMV was then subjected to purifying selection with one dominant clone emerging. To address the role of NK cells and the specific organs involved, we designed a single nucleotide polymorphism genotyping assay to quantify selection for a mutant virus with a single point mutation in m157 during a mixed infection. Remarkably, our results suggest that the escape mutant was initially selected in the spleen, but not the liver, as early as 2 days post-infection. Together, these findings suggest that the selective pressure exerted by NK cells on MCMV occurs primarily in the spleen during the initial rounds of viral replication, indicating that the host innate immune system exerts pressure on the virus almost immediately upon infection.
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