animals Article Isolation, Identification and Characterization of a Novel Megalocytivirus from Cultured Tilapia (Oreochromis spp.) from Southern California, USA Khalid Shahin 1,2 , Kuttichantran Subramaniam 3 , Alvin C. Camus 4 , Zeinab Yazdi 1 , Susan Yun 1 , Samantha A. Koda 3 , Thomas B. Waltzek 3 , Felipe Pierezan 5 , Ruixue Hu 1 and Esteban Soto 1, *   Citation: Shahin, K.; Subramaniam, K.; Camus, A.C.; Yazdi, Z.; Yun, S.; Koda, S.A.; Waltzek, T.B.; Pierezan, F.; Hu, R.; Soto, E. Isolation, Identification and Characterization of a Novel Megalocytivirus from Cultured Tilapia (Oreochromis spp.) from Southern California, USA. Animals 2021, 11, 3524. https:// doi.org/10.3390/ani11123524 Academic Editors: Mohamed Faisal and Jun Li Received: 5 November 2021 Accepted: 29 November 2021 Published: 10 December 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 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/). 1 Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA; kshahin@ucdavis.edu or kh.shahin87@gmail.com (K.S.); yazdi@ucdavis.edu (Z.Y.); scyun@ucdavis.edu (S.Y.); huruixue@webmail.hzau.edu.cn (R.H.) 2 Aquatic Animal Diseases Laboratory, Aquaculture Department, National Institute of Oceanography and Fisheries, Suez P.O. Box 43511, Egypt 3 Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA; kuttichantran@ufl.edu (K.S.); samanthakoda@ufl.edu (S.A.K.); tbwaltzek@ufl.edu (T.B.W.) 4 Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; camus@uga.edu 5 School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-010, Brazil; fpierezan@gmail.com * Correspondence: sotomartinez@ucdavis.edu; Tel.: +1-530-7522440 Simple Summary: Aquaculture is the world’s fastest-growing food production sector, with tilapia (Oreochromis spp.) among the most important cultured species. First reported in red seabream, Pagrus major, in 1990, an increasing number of megalocytiviruses are responsible for losses that threaten the production and economic sustainability of important cultured fish species, including tilapia. In the current study, we describe an epizootic in tilapia fingerlings from Southern California, USA and report the discovery of a novel megalocytivirus associated with the mortalities. Abstract: In spring 2019, diseased four-month-old tilapia (Oreochromis spp.) from an aquaculture farm in Southern California, USA were received for diagnostic evaluation with signs of lethargy, anorexia, abnormal swimming, and low-level mortalities. At necropsy, non-specific external lesions were noted including fin erosion, cutaneous melanosis, gill pallor, and coelomic distension. Internal changes included ascites, hepatomegaly, renomegaly, splenomegaly, and multifocal yellow-white nodules in the spleen and kidney. Cultures of spleen and kidney produced bacterial colonies identified as Francisella orientalis. Homogenized samples of gill, brain, liver, spleen, and kidney inoculated onto Mozambique tilapia brain cells (OmB) developed cytopathic effects, characterized by rounding of cells and detaching from the monolayer 6–10 days post-inoculation at 25 ◦ C. Transmission electron microscopy revealed 115.4 ± 5.8 nm icosahedral virions with dense central cores in the cytoplasm of OmB cells. A consensus PCR, targeting the DNA polymerase gene of large double- stranded DNA viruses, performed on cell culture supernatant yielded a sequence consistent with an iridovirus. Phylogenetic analyses based on the concatenated full length major capsid protein and DNA polymerase gene sequences supported the tilapia virus as a novel species within the genus Megalocytivirus, most closely related to scale drop disease virus and European chub iridovirus. An intracoelomic injection challenge in Nile tilapia (O. niloticus) fingerlings resulted in 39% mortality after 16 days. Histopathology revealed necrosis of head kidney and splenic hematopoietic tissues. Keywords: Megalocytivirus; co-infection; Francisella; tilapia Animals 2021, 11, 3524. https://doi.org/10.3390/ani11123524 https://www.mdpi.com/journal/animals