title: Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.
abstract: Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential.
authors.affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Stenglein
authors.affiliation: Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Elliott R
authors.initials: ER
authors.lastname: Jacobson
authors.affiliation: Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Li-Wen
authors.initials: LW
authors.lastname: Chang
authors.affiliation: Wildwood Veterinary Hospitals, Portola Valley, California, United States of America.
authors.forename: Chris
authors.initials: C
authors.lastname: Sanders
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
authors.forename: Michelle G
authors.initials: MG
authors.lastname: Hawkins
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
authors.forename: David S-M
authors.initials: DS
authors.lastname: Guzman
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America.
authors.forename: Tracy
authors.initials: T
authors.lastname: Drazenovich
authors.affiliation: California Academy of Sciences, San Francisco, California, United States of America.
authors.forename: Freeland
authors.initials: F
authors.lastname: Dunker
authors.affiliation: Kamaka Exotic Animal Veterinary Services, Mountlake Terrace, Washington, United States of America.
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Kamaka
authors.affiliation: Acacia Animal Hospital, Escondito, California, United States of America.
authors.forename: Debbie
authors.initials: D
authors.lastname: Fisher
authors.affiliation: Zoo/Exotic Pathology Services, West Sacramento, California, United States of America.
authors.forename: Drury R
authors.initials: DR
authors.lastname: Reavill
authors.affiliation: Arkansas Livestock & Poultry Commission Veterinary Diagnostic Laboratory, Little Rock, Arkansas, United States of America.
authors.forename: Linda F
authors.initials: LF
authors.lastname: Meola
authors.affiliation: Cincinnati Zoo, Cincinnati, Ohio, United States of America.
authors.forename: Gregory
authors.initials: G
authors.lastname: Levens
authors.affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America; Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: DeRisi
mesh_terms: D000818:Animals; D000836:Animals, Zoo / Q000097:blood / Q000378:metabolism / Q000821:virology; D001117:Arenaviridae Infections / Q000378:metabolism / Q000473:pathology / Q000662:veterinary* / Q000821:virology; D018050:Arenavirus / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D001483:Base Sequence; D017821:Boidae / Q000821:virology; D002478:Cells, Cultured; D018562:Disease Transmission, Infectious / Q000662:veterinary*; D015321:Gene Rearrangement; D016679:Genome, Viral; D008099:Liver / Q000378:metabolism / Q000473:pathology / Q000821:virology; D008969:Molecular Sequence Data; D057805:Pets / Q000097:blood / Q000378:metabolism / Q000821:virology; D010802:Phylogeny; D012367:RNA, Viral / Q000097:blood / Q000737:chemistry / Q000378:metabolism; D011995:Recombination, Genetic; D012911:Snakes / Q000097:blood / Q000378:metabolism / Q000821:virology*; D014481:United States; D014779:Virus Replication
chemical_list: D012367:RNA, Viral