Citation: Vidal, A.H.; Lacorte, C.; Sanches, M.M.; Alves-Freitas, D.M.T.; Abreu, E.F.M.; Pinheiro-Lima, B.; Rosa, R.C.C.; Jesus, O.N.; Campos, M.A.; Felix, G.P.; et al. Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates. Viruses 2023, 15, 410. https://doi.org/10.3390/v15020410 Academic Editors: Kai-Shu Ling and Elizabeth Jeannette Cieniewicz Received: 2 December 2022 Revised: 25 January 2023 Accepted: 28 January 2023 Published: 1 February 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). viruses Article Characterization of Cucurbit Aphid-Borne Yellows Virus (CABYV) from Passion Fruit in Brazil: Evidence of a Complex of Species within CABYV Isolates Andreza H. Vidal 1,2 , Cristiano Lacorte 1 , Marcio M. Sanches 1,3 , Dione M. T. Alves-Freitas 1 , Emanuel F. M. Abreu 1 , Bruna Pinheiro-Lima 1,2 , Raul C. Carriello Rosa 4 , Onildo N. Jesus 5 , Magnólia A. Campos 6 , Gustavo P. Felix 1,7 , Ana Clara R. Abreu 1,7 , Yam S. Santos 1,8 , Ana Luiza M. Lacerda 1 , Arvind Varsani 9 , Fernando L. Melo 2 and Simone G. Ribeiro 1,2, * 1 Embrapa Recursos Genéticos e Biotecnologia, Brasília 70770-917, DF, Brazil 2 Instituto de Ciências Biológicas—IB, PPG BIOMOL, Universidade de Brasília, Brasília 70910-900, DF, Brazil 3 Embrapa Gado de Corte, Campo Grande 79106-550, MS, Brazil 4 Embrapa Agrobiologia, Seropédica 23891-000, RJ, Brazil 5 Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, BA, Brazil 6 Centro de Educação e Saúde, Universidade Federal de Campina Grande, Cuité 58175-000, PB, Brazil 7 Instituto de Ciências Biológicas—IB, Universidade de Brasília, Brasília 70910-900, DF, Brazil 8 Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil 9 The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA * Correspondence: simone.ribeiro@embrapa.br Abstract: High-throughput sequencing (HTS) has been an important tool for the discovery of plant viruses and their surveillance. In 2015, several virus-like symptoms were observed in passion fruit (PF) plants in Bahia state, Brazil. Using HTS technology, bioinformatics tools, RT-PCR, and Sanger sequencing, we identified the cucurbit aphid-borne yellows virus (CABYV, Polerovirus, Solemoviridae) in co-infection with cowpea aphid-borne mosaic virus (CABMV, Potyvirus, Potyviridae) in PF, in green manure, and spontaneous plants in several localities in Bahia. Complete genomes of CABYV-PF isolates were determined and analyzed with other CABYV isolates available in GenBank that have been identified in various countries. Phylogenetic analysis and pairwise identity comparison with CABYV isolates showed that CABYV-PFs are more closely related to French and Spanish isolates. Overall, analyses of all the CABYV genomes revealed that these could represent ten distinct species, and we thus proposed reclassifying these CABYV as isolates into ten species, tentatively named “Polerovirus curcubitaeprimum” to “Polerovirus curcubitaenonum”, and “Polerovirus melo”. CABYV-PF is a member of “Polerovirus curcubitaeprimum”. Keywords: polerovirus; CABYV; CABMV; mixed infection; Passiflora 1. Introduction Passion fruit is a tropical plant (genus Passiflora, family Passifloraceae) cultivated in several regions of the world, Brazil being the largest producer of yellow passion fruit (Passiflora edulis Sims). Virus diseases are a common problem in passion fruit crops and are responsible for significant reductions in the yield and quality of the fruits. Several viruses have been identified in passion fruit plants in Brazil. Outbreaks of various begomoviruses (genus Begomovirus, family Geminiviridae) have been reported in passion fruit fields in different regions of the country [1–4]. Other viruses, such as grapevine virus A (GVA, genus Vitivirus, family Betaflexiviridae)[5], passion fruit yellow mosaic virus (PFYMV, genus Tymovirus, family Tymoviridae)[6], cucumber mosaic virus (CMV, genus Cucumovirus, family Bromoviridae)[7], passion fruit green spot virus (PfGSV, genus Cilevirus, Viruses 2023, 15, 410. https://doi.org/10.3390/v15020410 https://www.mdpi.com/journal/viruses