Phylogeny of Egyptian isolates of Cucumber mosaic virus (CMV) and Tomato mosaic virus (ToMV) infecting Solanum lycopersicum Mona Rabie & Claudio Ratti & Matteo Calassanzio & Engy Abdel Aleem & Faiza Aref Fattouh Accepted: 11 January 2017 # Koninklijke Nederlandse Planteziektenkundige Vereniging 2017 Abstract Four Cucumber mosaic virus (CMV) (CMV- HM 1–4) and nine Tomato mosaic virus (ToMV) (ToMV AH 1–9) isolates detected in tomato samples collected from different governorates in Egypt during 2014, were here characterized. According to the coat protein gene sequence and to the complete nucleotide sequence of total genomic RNA1, RNA2 and RNA3 of CMV-HM3 the new Egyptian isolates are related to members of the CMV subgroup IB. The nine ToMV Egyptian isolates were characterized by sequence anal- ysis of the coat protein and the movement protein genes. All isolates were grouped within the same branch and showed high relatedness to all considered isolates (98– 99%). Complete nucleotide sequence of total genomic RNA of ToMVAH4 isolate was obtained and its com- parison showed a closer degree of relatedness to isolate 99–1 from the USA (99%). To our knowledge, this is the first report of CMV isolates from subgroup IB in Egypt and the first full length sequencing of an ToMV Egyp- tian isolate. Keywords CMV . ToMV . Phylogenetic analysis . CMV subgroup . Tomato Tomato is considered the primary vegetable crop in Egypt in terms of cash value and total tonnage produced (Anonymous 2013). CMV (genus Cucumovirus) has caused severe epidemics in many crops and it has been included in the BTop 10 plant viruses^ in a recent mo- lecular pathology review (Scholthof et al. 2011). Phylo- genetic studies reveal that the CMV isolates can be divided into three main subgroups, I, II and III and that subgroup I can be further divided into IA and IB de- pending on the sequence of the 5´ UTR of the genomic RNA3 (Roossinck et al. 1999; Liu et al. 2009; King et al. 2011; Jacquemond 2012; Tepfer et al. 2016). Analysis of at least one part of each genomic segment is necessary for confident genotyping of CMV strains (Jacquemond 2012). The genome of CMV is a single-stranded, positive- sense RNA having three RNA segments, RNA1 and RNA2 code for core elements of the replicase complex and viral movement while RNA3 codes for movement (MP) and coat (CP) proteins (Shi et al. 2003; Lin et al. 2004; Su et al. 2010). ToMV belongs to the genus Tobamovirus (Adams et al. 2009) and its genome consists of a single RNA 6300 nt long that encodes for four different proteins related to virus replication and movement (Kubota et al. 2003). This study aims to report full-length sequencing and molecular characterization by phylogenetic assessment of CMV and ToMV isolates recently detected in Egypt. During the 2014 growing season (June to October) leaves of tomato plants (90 samples) showing virus- related symptoms were collected from different local fields of selected governorates in Egypt. Eur J Plant Pathol DOI 10.1007/s10658-017-1164-2 M. Rabie (*) : E. A. Aleem : F. A. Fattouh Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt e-mail: Mona_rabie55@yahoo.com C. Ratti : M. Calassanzio DipSA – Patologia Vegetale, Università di Bologna, Viale G. Fanin, 40 -, 40127 Bologna, Italy