title: A new genotype of bovine leukemia virus in South America identified by NGS-based whole genome sequencing and molecular evolutionary genetic analysis.
abstract: BACKGROUND
  Bovine leukemia virus (BLV) is a member of retroviridae family, together with human T cell leukemia virus types 1 and 2 (HTLV-1 and -2) belonging to the genes deltaretrovirus, and infects cattle worldwide. Previous studies have classified the env sequences of BLV provirus from different geographic locations into eight genetic groups. To investigate the genetic variability of BLV in South America, we performed phylogenetic analyses of whole genome and partial env gp51 sequences of BLV strains isolated from Peru, Paraguay and Bolivia, for which no the molecular characteristics of BLV have previously been published, and discovered a novel BLV genotype, genotype-9, in Bolivia.
  
  
  RESULTS
  In Peru and Paraguay, 42.3 % (139/328) and over 50 % (76/139) of samples, respectively, were BLV positive. In Bolivia, the BLV infection rate was up to 30 % (156/507) at the individual level. In Argentina, 325/420 samples were BLV positive, with a BLV prevalence of 77.4 % at the individual level and up to 90.9 % at herd level. By contrast, relatively few BLV positive samples were detected in Chile, with a maximum of 29.1 % BLV infection at the individual level. We performed phylogenetic analyses using two different approaches, maximum likelihood (ML) tree and Bayesian inference, using 35 distinct partial env gp51 sequences from BLV strains isolated from Peru, Paraguay, and Bolivia, and 74 known BLV strains, representing eight different BLV genotypes from various geographical locations worldwide. The results indicated that Peruvian and Paraguayan BLV strains were grouped into genotypes-1, -2, and -6, while those from Bolivia were clustered into genotypes-1, -2, and -6, and a new genotype, genotype-9. Interestingly, these results were confirmed using ML phylogenetic analysis of whole genome sequences obtained by next generation sequencing of 25 BLV strains, assigned to four different genotypes (genotypes-1, -2, -6, and -9) from Peru, Paraguay, and Bolivia. Comparative analyses of complete genome sequences clearly showed some specific substitutions, in both structural and non-structural BLV genes, distinguishing the novel genotype-9 from known genotypes.
  
  
  CONCLUSIONS
  Our results demonstrate widespread BLV infection in South American cattle and the existence of a new BLV genotype-9 in Bolivia. We conclude that at least seven BLV genotypes (genotypes-1, -2, -4, -5, -6, -7, and -9) are circulating in South America.
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. palati.mairepati@riken.jp.|Laboratory of Viral Infectious Diseases, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Saitama, 351-0198, Japan. palati.mairepati@riken.jp.
authors.forename: Meripet
authors.initials: M
authors.lastname: Polat
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. takesima@riken.jp.|Laboratory of Viral Infectious Diseases, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Saitama, 351-0198, Japan. takesima@riken.jp.
authors.forename: Shin-Nosuke
authors.initials: SN
authors.lastname: Takeshima
authors.affiliation: Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Takara-machi 13-1, Kanazawa, Ishikawa, 920-8640, Japan. khosomic@med.kanazawa-u.ac.jp.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Hosomichi
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. mukti8181@hotmail.com.
authors.forename: Jiyun
authors.initials: J
authors.lastname: Kim
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. takumiyasaka0712@gmail.com.
authors.forename: Taku
authors.initials: T
authors.lastname: Miyasaka
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. kyamada@ecei.tohoku.ac.jp.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Yamada
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. m.araingaramirez@unmc.edu.
authors.forename: Mariluz
authors.initials: M
authors.lastname: Arainga
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. tmurakam@umich.edu.
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Murakami
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. pipora331@gmail.com.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Matsumoto
authors.affiliation: LAVET, Carampangue 595, Valdivia, Chile. lab.lavet@gmail.com.
authors.forename: Veronica
authors.initials: V
authors.lastname: de la Barra Diaz
authors.affiliation: Department of Virology, Faculty of Veterinary Sciences, National University of La Plata, 60 and 118, CC 296, 1900, La Plata, Argentina. javierpanei@fcv.unlp.edu.ar.|IGEVET, CCT La Plata-CONICET, Facultad de Ciencias Veterinarias, National University of La Plata, 60 and 118, CC 296, 1900, La Plata, Argentina. javierpanei@fcv.unlp.edu.ar.
authors.forename: Carlos Javier
authors.initials: CJ
authors.lastname: Panei
authors.affiliation: Department of Virology, Faculty of Veterinary Sciences, National University of La Plata, 60 and 118, CC 296, 1900, La Plata, Argentina. etgonzal@fcv.unlp.edu.ar.
authors.forename: Ester Teresa
authors.initials: ET
authors.lastname: González
authors.affiliation: Institute for Animal Science, Shitara-cho, Aichi, 441-2433, Japan. misaokanemaki@yahoo.co.jp.
authors.forename: Misao
authors.initials: M
authors.lastname: Kanemaki
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. pochi-ko@deluxe.ocn.ne.jp.
authors.forename: Misao
authors.initials: M
authors.lastname: Onuma
authors.affiliation: IGEVET, CCT La Plata-CONICET, Facultad de Ciencias Veterinarias, National University of La Plata, 60 and 118, CC 296, 1900, La Plata, Argentina. ggiovam@yahoo.com.ar.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Giovambattista
authors.affiliation: Viral Infectious Diseases Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. aida@riken.jp.|Laboratory of Viral Infectious Diseases, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Wako, Saitama, 351-0198, Japan. aida@riken.jp.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Aida
mesh_terms: D000818:Animals; D001838:Bolivia / Q000453:epidemiology; D002417:Cattle; D016000:Cluster Analysis; D016583:Enzootic Bovine Leukosis / Q000453:epidemiology / Q000821:virology*; D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D001909:Leukemia Virus, Bovine / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010239:Paraguay / Q000453:epidemiology; D010568:Peru / Q000453:epidemiology; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D012367:RNA, Viral