title: Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells.
abstract: The Flavivirus genus includes a large number of medically relevant pathogens that cycle between humans and arthropods. This host alternation imposes a selective pressure on the viral population. Here, we found that dengue virus, the most important viral human pathogen transmitted by insects, evolved a mechanism to differentially regulate the production of viral non-coding RNAs in mosquitos and humans, with a significant impact on viral fitness in each host. Flavivirus infections accumulate non-coding RNAs derived from the viral 3'UTRs (known as sfRNAs), relevant in viral pathogenesis and immune evasion. We found that dengue virus host adaptation leads to the accumulation of different species of sfRNAs in vertebrate and invertebrate cells. This process does not depend on differences in the host machinery; but it was found to be dependent on the selection of specific mutations in the viral 3'UTR. Dissecting the viral population and studying phenotypes of cloned variants, the molecular determinants for the switch in the sfRNA pattern during host change were mapped to a single RNA structure. Point mutations selected in mosquito cells were sufficient to change the pattern of sfRNAs, induce higher type I interferon responses and reduce viral fitness in human cells, explaining the rapid clearance of certain viral variants after host change. In addition, using epidemic and pre-epidemic Zika viruses, similar patterns of sfRNAs were observed in mosquito and human infected cells, but they were different from those observed during dengue virus infections, indicating that distinct selective pressures act on the 3'UTR of these closely related viruses. In summary, we present a novel mechanism by which dengue virus evolved an RNA structure that is under strong selective pressure in the two hosts, as regulator of non-coding RNA accumulation and viral fitness. This work provides new ideas about the impact of host adaptation on the variability and evolution of flavivirus 3'UTRs with possible implications in virulence and viral transmission.
authors.affiliation: Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina.
authors.forename: Claudia V
authors.initials: CV
authors.lastname: Filomatori
authors.affiliation: Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina.
authors.forename: Juan M
authors.initials: JM
authors.lastname: Carballeda
authors.affiliation: Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina.
authors.forename: Sergio M
authors.identifier: 0000-0003-4434-7930
authors.initials: SM
authors.lastname: Villordo
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Aguirre
authors.affiliation: Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina.
authors.forename: Horacio M
authors.initials: HM
authors.lastname: Pallarés
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Ana M
authors.identifier: 0000-0002-2494-0879
authors.initials: AM
authors.lastname: Maestre
authors.affiliation: Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Irma
authors.identifier: 0000-0002-1724-7005
authors.initials: I
authors.lastname: Sánchez-Vargas
authors.affiliation: Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Carol D
authors.initials: CD
authors.lastname: Blair
authors.affiliation: Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", ANLIS, Pergamino, Argentina.
authors.forename: Cintia
authors.initials: C
authors.lastname: Fabri
authors.affiliation: Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", ANLIS, Pergamino, Argentina.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Morales
authors.affiliation: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Ana
authors.initials: A
authors.lastname: Fernandez-Sesma
authors.affiliation: Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina.
authors.forename: Andrea V
authors.initials: AV
authors.lastname: Gamarnik
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D015152:Blotting, Northern; D009033:Culicidae / Q000821:virology*; D003715:Dengue / Q000235:genetics; D003716:Dengue Virus / Q000235:genetics*; D056084:Genetic Fitness / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D007303:Insect Vectors / Q000821:virology; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000235:genetics*; D014162:Transfection
chemical_list: D020413:3' Untranslated Regions; D012367:RNA, Viral