Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Research paper Phylogenetic analysis of Alphapapillomavirus based on L1, E6 and E7 regions suggests that carcinogenicity and tissue tropism have appeared multiple times during viral evolution Alexis Rojas-Cruz, Alejandro Reyes-Bermúdez ⁎ Departamento de Biología, Facultad de Ciencias Básicas, Universidad de la Amazonia, Florencia 180002, Colombia ARTICLEINFO Keywords: Alphapapillomavirus evolution Mutations Tissue tropism Cervical cancer ABSTRACT Members of the Alphapapillomavirus genus are causative agents for cervix cancer and benign lesions in humans. These viruses are classifed according to sequence similarities in their L1 region. Yet, viral carcinogenicity has been associated with variations in the proteins encoded by the E6 and E7 genes. In order to relate evolutionary history with origin of carcinogenicity, we performed phylogenetic reconstructions using both nucleotide and predicted amino acid sequences of the L1, E6 and E7 genes. Whilst phylogenetic analysis of L1 reconstructed genus evolutionary history, phylogenies based on E6 and E7 proteins support the idea that mutations at amino acids S/Tx [V/L] (E6) and LxCxE (E7) might be responsible for carcinogenic potential. These fndings indicate that virulence within Alphapapillomavirus have appeared multiple times during evolution. Our results reveal that oncogenic potential is not a monophyletic clade-specifc adaptation but might be the result of positive selection on random mutations occurring on proteins involved in host infection during viral diversifcation. 1. Introduction Alphapapillomavirus is a genus of medically important viruses of the Papillomaviridae family (Chen et al., 2018). According to “The Papillomavirus Episteme (PaVE), (2018)” database, the genus contains 64 types identifed to date. Members infect epithelial cells and are the most common sexually transmitted infectious agent worldwide (Forman et al., 2012). These viruses can cause human cancers of the anus-genital, head and neck regions (de Villiers et al., 2004). Based on oncogenic potential, they are typically classifed as low-risk (LR) or high-risk (HR) types (Chiesa et al., 2016). Infection with high-risk genotypes are responsible for approximately 99.7% of cervical cancer, hence becoming a topic of increasing importance in health programs (Walboomers et al., 1999). Worldwide, Alpha-PVs-induced carcinoma is the fourth most common cancer in women with an incidence of 528,000 new cases in recent years, and a mortality rate of about 50% especially in developing countries, where 85% of infected women die (Ferlay et al., 2013). Human papillomaviruses possess a circular double-strand DNA genome of 8 kb in length that encodes eight open reading frames (ORFs). These, are organized into three general regions: 1) an upstream regulatory region (URR) containing elements that control transcription and replication, 2) an early gene region that encodes the E1, E2, E4, E5, E6 and E7 proteins and 3) a late region encodes the L1 and L2 structural proteins (Danos et al., 1982). To promote viral replication, E6 and E7 proteins, target diverse cellular pathways involved in proliferation and inactivation of cell-cycle checkpoints (Doorbar, 2006; Doorbar, 2005). Among all diferent viral proteins, E6 and E7 gene products are well- conserved in types that causes persistent infections and high-grade le- sions (Giuliano et al., 2002; McBride, 2017). E6 protein (P03126) contains two zinc-binding regions CxxC(x) 29 CxxC able to recognized helical motifs LxxLL in target proteins (Huibregtse et al., 1991; Schefner et al., 1990; Vande Pol and Klingelhutz, 2013). Likewise, in high-risk viruses, E6's carboxyl-terminal have a highly conserved motif that interact with PSD95/DLG1/ZO1 (PDZ) proteins (Delury et al., 2013). E7 proteins (P03129) contain three domains known as CD1, CD2 and CD3 (McLaughlin-Drubin and Münger, 2009). CD1/CD2 regions have homology to a partial part of the conserved Adenovirus E1A's CR1 and CR2 domains and CD3 is a zinc-binding site CxxC(x) 29 CxxC (Chellappan et al., 1992; Münger et al., 2001a; Songock et al., 2017). Both oncoproteins induce changes in the activity of cell cycle regulators and consequently, are shared by high-risk viral types (Howie et al., 2009; McLaughlin-Drubin and Münger, 2009). Unlike the E6 and E7 proteins, the L1 gene codes for a major capsid protein with the ability to self-assemble spontaneously into virus-like particles (VLPs) (Doorbar et al., 2016). Due to its fundamental role in https://doi.org/10.1016/j.meegid.2018.11.008 Received 22 May 2018; Received in revised form 7 November 2018; Accepted 8 November 2018 ⁎ Corresponding author. E-mail address: an.reyes@udla.edu.co (A. Reyes-Bermúdez). Infection, Genetics and Evolution 67 (2019) 210–221 Available online 17 November 2018 1567-1348/ © 2018 Elsevier B.V. All rights reserved. T