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In the present work we describe both the prevalence and the histopathologic features of a novel papillomavirus (referred as McPV2) that naturally infects the rodent Mastomys coucha. Viral DNA could be isolated not only from anogenital wart-like lesions but also from healthy tissues (e.g. liver, kidney, spleen and intestine) without apparent signs of infection. Our finding of a second papillomavirus infecting M. coucha, phylogenetically very distant from the previously known MnPV, reinforces the growing view of warm-blooded vertebrates as being hosts for a number of different papilloma virus types that are not necessarily closely related. The histological descriptions of McPV2-associated anogenital lesions provided here, together with earlier knowledge on MnPV-associated skin carcinogenesis, define M. coucha as an excellent system where the link between infection towards malignancy can be studied in molecular, histochemical and immunological terms in immunocompetent animals. The availability of such an in vivo model also offers the unique opportunity to address defined questions about prophylactic and therapeutic strategies against different papillomavirus infections in their natural host. To date, McPV2 is the first rodent papillomavirus found in anogenital lesions.