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A Cilevirus detected in Hibiscus rosa-sinensis and Citrus sinensis is a strain of Citrus leprosis virus C2 causing citrus leprosis disease in Colombia


<div><em>Citrus leprosis virus</em> C2 (CiLV-C2), a quarantine citrus pathogen in the United States, is present in Colombia. A strain of CiLV-C2 infecting <em>Hibiscus rosa-sinensis </em>(CiLV-C2H) was found in Hawaii and Florida. Recently, a mixed infection of CiLV-C2 and CiLV-C2H in sweet orange with leprosis symptoms has been recorded in Colombia. It is not clear if CiLV-C2H alone can produce symptoms in <em>Citrus</em> spp. or if there are synergistic effects between CiLV-C2 and CiLV-C2H. Next Generation Sequencing using the Illumina platform was performed to determine the genomic sequences of CiLV-C2 and CiLV-C2H in Hibiscus and Citrus. The structure of the CiLV-C2 and CiLV-C2H genomes are identical and shared 92% amino acid identity. RNA1 of CiLV-C2 and -CiLV-C2H contains 2 ORFs whereas RNA2 contains 5 ORFs. The putative coat protein gene sequence of CiLV-C2H-Florida RNA1 shared 91% nucleotide and 92-93% amino acid identity with CiLV-C2H-Hawaii and C2H-Colombia. In addition, movement protein sequences encoded by RNA2 of CiLV-C2H-Florida and CiLV-C2H-Colombia are similar and share 91% nucleotide and 94 % amino acid identity with CiLV-C2H-Hawaii. The ORFs of CiLV-C2H-Florida are more closely related to the CiLV-C2H-Colombia than to the CiLV-C2H-Hawaii. CiLV-C2 and CiLV-C2H genome specific primers were developed to detect both viruses either in single or dual infection. A real-time RT-PCR assay is needed to detect and quantify both the viruses in mixed infection.</div>