{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T14:04:19Z","timestamp":1789999459133,"version":"4.0.1"},"reference-count":117,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2019,6,10]],"date-time":"2019-06-10T00:00:00Z","timestamp":1560124800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010661","name":"Horizon 2020","doi-asserted-by":"publisher","award":["734548"],"award-info":[{"award-number":["734548"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"name":"French Government's Investissement d'Avenir program, Laboratoire d'Excellence &quot;Integrative Biology of Emerging Infectious Diseases, IBEID","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_12014"],"award-info":[{"award-number":["MC_UU_12014"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Although the role of exogenous small interfering RNA (siRNA) and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) pathways in mosquito antiviral immunity is increasingly better understood, there is still little knowledge regarding the role of mosquito cellular microRNA (miRNA). Identifying direct interactions between the mosquito miRNAs and the RNA genome of arboviruses and choosing the relevant miRNA candidates to explore resulting antiviral mechanisms are critical. Here, we carried out genomic analyses to identify Aedes aegypti miRNAs that potentially interact with various lineages and genotypes of chikungunya, dengue, and Zika viruses. By using prediction tools with distinct algorithms, several miRNA binding sites were commonly found within different genotypes\/and or lineages of each arbovirus. We further analyzed those miRNAs that could target more than one arbovirus, required a low energy threshold to form miRNA-viralRNA (vRNA) complexes, and predicted potential RNA structures using RNAhybrid software. We predicted miRNA candidates that might participate in regulating arboviral replication in Ae. aegypti. Even without any experimental validation, which should be done as a next step, this study can shed further light on the role of miRNA in mosquito innate immunity and targets for future studies.<\/jats:p>","DOI":"10.3390\/v11060540","type":"journal-article","created":{"date-parts":[[2019,6,10]],"date-time":"2019-06-10T11:39:47Z","timestamp":1560166787000},"page":"540","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Assessing the Potential Interactions between Cellular miRNA and Arboviral Genomic RNA in the Yellow Fever Mosquito, Aedes aegypti"],"prefix":"10.3390","volume":"11","author":[{"given":"Pei-Shi","family":"Yen","sequence":"first","affiliation":[{"name":"Unit of Arboviruses and Insect Vectors, Department of Virology, Institut Pasteur, 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chun-Hong","family":"Chen","sequence":"additional","affiliation":[{"name":"National Health Research Institutes, National Institute of Infectious Diseases and Vaccinology, Miaoli 35053, Taiwan"},{"name":"National Mosquito-Borne Diseases Control Research Center, Miaoli 35053, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6673-4697","authenticated-orcid":false,"given":"Vattipally","family":"Sreenu","sequence":"additional","affiliation":[{"name":"MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Kohl","sequence":"additional","affiliation":[{"name":"MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna-Bella","family":"Failloux","sequence":"additional","affiliation":[{"name":"Unit of Arboviruses and Insect Vectors, Department of Virology, Institut Pasteur, 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,6,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Powers, A.M., and Waterman, S.H. (2017). A decade of arboviral activity-Lessons learned from the trenches. PLoS Negl. Trop. Dis., 11.","DOI":"10.1371\/journal.pntd.0005421"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.antiviral.2009.10.008","article-title":"Present and future arboviral threats","volume":"85","author":"Weaver","year":"2010","journal-title":"Antivir. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1038\/nature06536","article-title":"Global trends in emerging infectious diseases","volume":"451","author":"Jones","year":"2008","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.chom.2016.03.002","article-title":"Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host Switching","volume":"19","author":"Grubaugh","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/S0065-3527(03)60006-0","article-title":"Dynamics of flavivirus infection in mosquitoes","volume":"60","author":"Kramer","year":"2003","journal-title":"Adv. Virus Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3741","DOI":"10.3390\/v7072795","article-title":"Tissue Barriers to Arbovirus Infection in Mosquitoes","volume":"7","author":"Franz","year":"2015","journal-title":"Viruses"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-61779-037-9_1","article-title":"Defense and counterdefense in the RNAi-based antiviral immune system in insects","volume":"721","year":"2011","journal-title":"Methods Mol. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.jinsphys.2012.07.004","article-title":"Beyond RNAi: Antiviral defense strategies in Drosophila and mosquito","volume":"59","author":"Merkling","year":"2013","journal-title":"J. Insect Physiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"820","DOI":"10.3390\/v7020820","article-title":"The role of RNA interference (RNAi) in arbovirus-vector interactions","volume":"7","author":"Blair","year":"2015","journal-title":"Viruses"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.coviro.2015.10.001","article-title":"Arbovirus-mosquito interactions: RNAi pathway","volume":"15","author":"Olson","year":"2015","journal-title":"Curr. Opin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"511","DOI":"10.3390\/insects3020511","article-title":"New Insights into Control of Arbovirus Replication and Spread by Insect RNA Interference Pathways","volume":"3","author":"Donald","year":"2012","journal-title":"Insects"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Miesen, P., Joosten, J., and Van Rij, R.P. (2016). PIWIs Go Viral: Arbovirus-Derived piRNAs in Vector Mosquitoes. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1006017"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.1099\/vir.0.013201-0","article-title":"Advances in dissecting mosquito innate immune responses to arbovirus infection","volume":"90","author":"Fragkoudis","year":"2009","journal-title":"J. Gen. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"17240","DOI":"10.1073\/pnas.0406983101","article-title":"RNA interference acts as a natural antiviral response to O\u2019nyong-nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae","volume":"101","author":"Keene","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Campbell, C.L., Black, W.C., Hess, A.M., and Foy, B.D. (2008). Comparative genomics of small RNA regulatory pathway components in vector mosquitoes. BMC Genom., 9.","DOI":"10.1186\/1471-2164-9-425"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Sanchez-Vargas, I., Scott, J.C., Poole-Smith, B.K., Franz, A.W.E., Barbosa-Solomieu, V., Wilusz, J., Olson, K.E., and Blair, C.D. (2009). Dengue Virus Type 2 Infections of Aedes aegypti Are Modulated by the Mosquito\u2019s RNA Interference Pathway. PLoS Pathog., 5.","DOI":"10.1371\/journal.ppat.1000299"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"E176","DOI":"10.1073\/pnas.1412984112","article-title":"Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota","volume":"112","author":"Carissimo","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Dietrich, I., Shi, X., McFarlane, M., Watson, M., Blomstr\u00f6m, A.-L., Skelton, J.K., Kohl, A., Elliott, R.M., and Schnettler, E. (2017). The Antiviral RNAi Response in Vector and Non-vector Cells against Orthobunyaviruses. PLoS Negl. Trop. Dis., 11.","DOI":"10.1371\/journal.pntd.0005272"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Miesen, P., Ivens, A., Buck, A.H., and Van Rij, R.P. (2016). Small RNA Profiling in Dengue Virus 2-Infected Aedes Mosquito Cells Reveals Viral piRNAs and Novel Host miRNAs. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0004452"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Brackney, D.E., Scott, J.C., Sagawa, F., Woodward, J.E., Miller, N.A., Schilkey, F.D., Mudge, J., Wilusz, J., Olson, K.E., and Blair, C.D. (2010). C6\/36 Aedes albopictus Cells Have a Dysfunctional Antiviral RNA Interference Response. PLoS Negl. Trop. Dis., 4.","DOI":"10.1371\/journal.pntd.0000856"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1099\/vir.0.053850-0","article-title":"Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells","volume":"94","author":"Schnettler","year":"2013","journal-title":"J. Gen. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Morazzani, E.M., Wiley, M.R., Murreddu, M.G., Adelman, Z.N., and Myles, K.M. (2012). Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002470"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Hess, A.M., Prasad, A.N., Ptitsyn, A., Ebel, G.D., E Olson, K., Barbacioru, C., Monighetti, C., and Campbell, C.L. (2011). Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense. BMC Microbiol., 11.","DOI":"10.1186\/1471-2180-11-45"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","article-title":"Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila","volume":"128","author":"Brennecke","year":"2007","journal-title":"Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"15968","DOI":"10.1038\/srep15968","article-title":"Dengue virus infection alters post-transcriptional modification of microRNAs in the mosquito vector Aedes aegypti","volume":"5","author":"Etebari","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e00456-17","DOI":"10.1128\/mSphere.00456-17","article-title":"Global Transcriptome Analysis of Aedes aegypti Mosquitoes in Response to Zika Virus Infection","volume":"2","author":"Etebari","year":"2017","journal-title":"mSphere"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"433","DOI":"10.3389\/fimmu.2018.00433","article-title":"Viral miRNAs Alter Host Cell miRNA Profiles and Modulate Innate Immune Responses","volume":"9","author":"Naqvi","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13578-015-0009-y","article-title":"The expression profile of Aedes albopictus miRNAs is altered by dengue virus serotype-2 infection","volume":"5","author":"Liu","year":"2015","journal-title":"Cell Biosci."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Saldana, M.A., Etebari, K., Hart, C.E., Widen, S.G., Wood, T.G., Thangamani, S., Asgari, S., and Hughes, G.L. (2017). Zika virus alters the microRNA expression profile and elicits an RNAi response in Aedes aegypti mosquitoes. PLoS Negl. Trop. Dis., 11.","DOI":"10.1371\/journal.pntd.0005760"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1892","DOI":"10.1099\/jgv.0.000832","article-title":"Understanding the role of microRNAs in the interaction of Aedes aegypti mosquitoes with an insect-specific flavivirus","volume":"98","author":"Lee","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1111\/imb.12070","article-title":"MicroRNA levels are modulated in Aedes aegypti after exposure to Dengue-2","volume":"23","author":"Campbell","year":"2014","journal-title":"Insect Mol. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"265","DOI":"10.2217\/fmb.11.11","article-title":"Mosquito RNAi is the major innate immune pathway controlling arbovirus infection and transmission","volume":"6","author":"Blair","year":"2011","journal-title":"Futur. Microbiol."},{"key":"ref_33","first-page":"3011","article-title":"Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs","volume":"17","author":"Yi","year":"2003","journal-title":"Genome Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/nrm2632","article-title":"Biogenesis of small RNAs in animals","volume":"10","author":"Kim","year":"2009","journal-title":"Nat. Rev. Mol. Cell Boil."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/nrm3838","article-title":"Regulation of microRNA biogenesis","volume":"15","author":"Ha","year":"2014","journal-title":"Nat. Rev. Mol. Cell Boil."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1261\/rna.1972910","article-title":"Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway","volume":"16","author":"Ghildiyal","year":"2010","journal-title":"RNA"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.cell.2007.05.056","article-title":"Drosophila microRNAs Are Sorted into Functionally Distinct Argonaute Complexes after Production by Dicer-1","volume":"130","author":"Horwich","year":"2007","journal-title":"Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1093\/nar\/gkt1038","article-title":"Intertwined pathways for Argonaute-mediated microRNA biogenesis in Drosophila","volume":"42","author":"Yang","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1038\/nrd4359","article-title":"Therapeutic targeting of microRNAs: Current status and future challenges","volume":"13","author":"Li","year":"2014","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/cdd.2014.112","article-title":"The complexity of miRNA-mediated repression","volume":"22","author":"Wilczynska","year":"2015","journal-title":"Cell Death Differ."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.tcb.2006.12.007","article-title":"Repression of protein synthesis by miRNAs: How many mechanisms?","volume":"17","author":"Pillai","year":"2007","journal-title":"Trends Cell Boil."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1101\/gr.139758.112","article-title":"Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation","volume":"23","author":"Hausser","year":"2013","journal-title":"Genome Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1002\/bies.201300104","article-title":"MicroRNA binding sites in the coding region of mRNAs: Extending the repertoire of post-transcriptional gene regulation","volume":"36","author":"Hausser","year":"2014","journal-title":"BioEssays"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1101\/gr.089367.108","article-title":"New class of microRNA targets containing simultaneous 5\u2032-UTR and 3\u2032-UTR interaction sites","volume":"19","author":"Lee","year":"2009","journal-title":"Genome Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"8870","DOI":"10.1128\/JVI.02774-12","article-title":"Role of RNA Interference (RNAi) in Dengue Virus Replication and Identification of NS4B as an RNAi Suppressor","volume":"87","author":"Kakumani","year":"2013","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Mukherjee, S., and Hanley, K.A. (2010). RNA interference modulates replication of dengue virus in Drosophila melanogaster cells. BMC Microbiol., 10.","DOI":"10.1186\/1471-2180-10-127"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Maharaj, P.D., Widen, S.G., Huang, J., Wood, T.G., and Thangamani, S. (2015). Discovery of Mosquito Saliva MicroRNAs during CHIKV Infection. PLoS Negl. Trop. Dis., 9.","DOI":"10.1371\/journal.pntd.0003386"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Shrinet, J., Jain, S., Jain, J., Bhatnagar, R.K., and Sunil, S. (2014). Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development. PLoS Negl. Trop. Dis., 8.","DOI":"10.1371\/journal.pntd.0002616"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1186\/s13071-017-1966-2","article-title":"Identification of microRNAs expressed in the midgut of Aedes albopictus during dengue infection","volume":"10","author":"Su","year":"2017","journal-title":"Parasites Vectors"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1111\/1744-7917.12339","article-title":"Integrated analysis of miRNAs and transcriptomes in Aedes albopictus midgut reveals the differential expression profiles of immune-related genes during dengue virus serotype-2 infection","volume":"23","author":"Liu","year":"2016","journal-title":"Insect Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"10276","DOI":"10.1073\/pnas.1303603110","article-title":"Wolbachia uses a host microRNA to regulate transcripts of a methyltransferase, contributing to dengue virus inhibition in Aedes aegypti","volume":"110","author":"Zhang","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"8457","DOI":"10.1128\/JVI.00317-14","article-title":"Expression of Mosquito MicroRNA Aae-miR-2940-5p Is Downregulated in Response to West Nile Virus Infection To Restrict Viral Replication","volume":"88","author":"Slonchak","year":"2014","journal-title":"J. Virol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"17666","DOI":"10.1038\/s41598-017-18043-0","article-title":"Aedes aegypti microRNA miR-2b regulates ubiquitin-related modifier to control chikungunya virus replication","volume":"7","author":"Dubey","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.chom.2009.05.012","article-title":"Ubiquitination, Ubiquitin-like Modifiers, and Deubiquitination in Viral Infection","volume":"5","author":"Isaacson","year":"2009","journal-title":"Cell Host Microbe"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1186\/s13071-014-0488-4","article-title":"miR-281, an abundant midgut-specific miRNA of the vector mosquito Aedes albopictus enhances dengue virus replication","volume":"7","author":"Zhou","year":"2014","journal-title":"Parasites Vectors"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1002\/jmv.23815","article-title":"miR-252 of the Asian tiger mosquito Aedes albopictus regulates dengue virus replication by suppressing the expression of the dengue virus envelope protein","volume":"86","author":"Yan","year":"2014","journal-title":"J. Med. Virol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s42003-017-0011-5","article-title":"Synthetic miRNAs induce dual arboviral-resistance phenotypes in the vector mosquito Aedes aegypti","volume":"1","author":"Yen","year":"2018","journal-title":"Commun. Boil."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3656","DOI":"10.1073\/pnas.1810771116","article-title":"Engineered resistance to Zika virus in transgenic Aedes aegypti expressing a polycistronic cluster of synthetic small RNAs","volume":"116","author":"Buchman","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.3390\/v4113209","article-title":"Virus pathogen database and analysis resource (ViPR): A comprehensive bioinformatics database and analysis resource for the coronavirus research community","volume":"4","author":"Greer","year":"2012","journal-title":"Viruses"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"D593","DOI":"10.1093\/nar\/gkr859","article-title":"ViPR: An open bioinformatics database and analysis resource for virology research","volume":"40","author":"Pickett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1111\/imb.12152","article-title":"MicroRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi","volume":"24","author":"Hu","year":"2015","journal-title":"Insect Mol. Biol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in Drosophila","volume":"5","author":"Enright","year":"2003","journal-title":"Genome Boil."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Sturm, M., Hackenberg, M., Langenberger, D., and Frishman, D. (2010). TargetSpy: A supervised machine learning approach for microRNA target prediction. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-292"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"W467","DOI":"10.1093\/nar\/gkv555","article-title":"sRNAtoolbox: An integrated collection of small RNA research tools","volume":"43","author":"Rueda","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"W451","DOI":"10.1093\/nar\/gkl243","article-title":"RNAhybrid: Microrna target prediction easy, fast and flexible","volume":"34","author":"Rehmsmeier","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_67","first-page":"E1895","article-title":"Transcriptome-wide microRNA and target dynamics in the fat body during the gonadotrophic cycle of Aedes aegypti","volume":"114","author":"Zhang","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1099\/vir.0.82858-0","article-title":"Changing patterns of chikungunya virus: Re-emergence of a zoonotic arbovirus","volume":"88","author":"Powers","year":"2007","journal-title":"J. Gen. Virol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Tsetsarkin, K.A., VanLandingham, D.L., McGee, C.E., Higgs, S., and Holmes, E.C. (2007). A Single Mutation in Chikungunya Virus Affects Vector Specificity and Epidemic Potential. PLoS Pathog., 3.","DOI":"10.1371\/journal.ppat.0030201"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Vazeille, M., Moutailler, S., Coudrier, D., Rousseaux, C., Khun, H., Huerre, M., Thiria, J., Dehecq, J.-S., Fontenille, D., and Schuffenecker, I. (2007). Two Chikungunya Isolates from the Outbreak of La Reunion (Indian Ocean) Exhibit Different Patterns of Infection in the Mosquito, Aedes albopictus. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0001168"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.ijid.2017.03.006","article-title":"Global expansion of chikungunya virus: Mapping the 64-year history","volume":"58","author":"Wahid","year":"2017","journal-title":"Int. J. Infect. Dis."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2483","DOI":"10.1099\/jgv.0.000249","article-title":"Alphavirus RNA synthesis and non-structural protein functions","volume":"96","author":"Rupp","year":"2015","journal-title":"J. Gen. Virol."},{"key":"ref_73","first-page":"1","article-title":"Chapter 1 The History and Evolution of Human Dengue Emergence","volume":"72","author":"Vasilakis","year":"2008","journal-title":"Adv. Clin. Chem."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1016\/S0140-6736(14)60572-9","article-title":"Dengue","volume":"385","author":"Guzman","year":"2015","journal-title":"Lancet"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/0035-9203(52)90043-6","article-title":"Zika virus. II. Pathogenicity and physical properties","volume":"46","author":"Dick","year":"1952","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/0035-9203(53)90021-2","article-title":"Paper: Epidemiological notes on some viruses isolated in Uganda (Yellow fever, Rift Valley fever, Bwamba fever, West Nile, Mengo, Semliki forest, Bunyamwera, Ntaya, Uganda S and Zika viruses)","volume":"47","author":"Dick","year":"1953","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"9","DOI":"10.4269\/ajtmh.1954.3.9","article-title":"Immunity to Certain Arthropod-Borne Viruses among Indigenous Residents of Egypt","volume":"3","author":"Smithburn","year":"1954","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"223","DOI":"10.4049\/jimmunol.69.2.223","article-title":"Neutralizing antibodies against certain recently isolated viruses in the sera of human beings residing in East Africa","volume":"69","author":"Smithburn","year":"1952","journal-title":"J. Immunol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"248","DOI":"10.4049\/jimmunol.72.4.248","article-title":"Neutralizing antibodies against certain viruses in the sera of residents of India","volume":"72","author":"Smithburn","year":"1954","journal-title":"J. Immunol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1093\/oxfordjournals.aje.a119630","article-title":"Neutralizing antibodies against arthropod-borne viruses in the sera of long-time residents of malaya and borneo1","volume":"59","author":"Smithburn","year":"1954","journal-title":"Am. J. Epidemiol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/0035-9203(54)90006-1","article-title":"Zika virus: A report on three cases of human infection during an epidemic of jaundice in Nigeria","volume":"48","author":"MacNamara","year":"1954","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/0035-9203(63)90100-7","article-title":"Arthropod-borne virus antibodies in sera from residents of South-East Asia","volume":"57","author":"Pond","year":"1963","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"323","DOI":"10.4269\/ajtmh.1958.7.323","article-title":"Serological survey for a arthropod-borne virus infections in the Philippines","volume":"7","author":"Hammon","year":"1958","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1017\/S0022172400025997","article-title":"Zika virus infections in Nigeria: Virological and seroepidemiological investigations in Oyo State","volume":"83","author":"Fagbami","year":"1979","journal-title":"J. Hyg."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1080\/00034983.1975.11686983","article-title":"Arthropod-borne viral infections of man in Nigeria, 1964\u20131970","volume":"69","author":"Moore","year":"1975","journal-title":"Ann. Trop. Med. Parasitol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/0035-9203(81)90100-0","article-title":"Triwibowo Zika virus, a cause of fever in Central Java, Indonesia","volume":"75","author":"Olson","year":"1981","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/0035-9203(64)90201-9","article-title":"Zika Virus Infection in Man","volume":"58","author":"Simpson","year":"1964","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2536","DOI":"10.1056\/NEJMoa0805715","article-title":"Zika Virus Outbreak on Yap Island, Federated States of Micronesia","volume":"360","author":"Duffy","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"ref_89","first-page":"1085","article-title":"Zika Virus, French Polynesia, South Pacific, 2013","volume":"20","author":"Roche","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_90","doi-asserted-by":"crossref","unstructured":"Oehler, E., Watrin, L., Larre, P., Leparc-Goffart, I., Lastere, S., Valour, F., Baudouin, L., Mallet, H.P., Musso, D., and Ghawche, F. (2014). Zika virus infection complicated by Guillain-Barre syndrome\u2014Case report, French Polynesia, December 2013. Euro Surveill, 19.","DOI":"10.2807\/1560-7917.ES2014.19.9.20720"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.3201\/eid2110.150847","article-title":"Zika Virus Outbreak, Bahia, Brazil","volume":"21","author":"Campos","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1590\/0074-02760150192","article-title":"First report of autochthonous transmission of Zika virus in Brazil","volume":"110","author":"Zanluca","year":"2015","journal-title":"Mem\u00f3rias do Inst. Oswaldo Cruz"},{"key":"ref_93","unstructured":"World Health Organization (2016). Zika Virus Microcephaly and Guillain-Barr\u00e9 Syndrome, World Health Organization. Available online: http:\/\/apps.who.int\/iris\/bitstream\/10665\/204633\/1\/zikasitrep_17Mar2016_eng.pdf."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/S0140-6736(16)00273-7","article-title":"Microcephaly in Brazil: How to interpret reported numbers?","volume":"387","author":"Victora","year":"2016","journal-title":"Lancet"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"55","DOI":"10.15585\/mmwr.mm6503e1","article-title":"Zika Virus Spreads to New Areas - Region of the Americas, May 2015-January 2016","volume":"65","author":"Hennessey","year":"2016","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Faye, O., Freire, C.C.M., Iamarino, A., Faye, O., De Oliveira, J.V.C., Diallo, M., Zanotto, P.M.A., and Sall, A.A. (2014). Molecular Evolution of Zika Virus during Its Emergence in the 20th Century. PLoS Negl. Trop. Dis., 8.","DOI":"10.1371\/journal.pntd.0002636"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1056\/NEJMra1602113","article-title":"Zika Virus","volume":"374","author":"Petersen","year":"2016","journal-title":"N. Engl. J. Med."},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Haddow, A.D., Schuh, A.J., Yasuda, C.Y., Kasper, M.R., Heang, V., Huy, R., Guzman, H., Tesh, R.B., and Weaver, S.C. (2012). Genetic Characterization of Zika Virus Strains: Geographic Expansion of the Asian Lineage. PLoS Negl. Trop. Dis., 6.","DOI":"10.1371\/journal.pntd.0001477"},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Etebari, K., Asad, S., Zhang, G., and Asgari, S. (2016). Identification of Aedes aegypti Long Intergenic Non-coding RNAs and Their Association with Wolbachia and Dengue Virus Infection. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0005069"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/srep00996","article-title":"Stability of miRNA 5\u2032terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy","volume":"2","author":"Hibio","year":"2012","journal-title":"Sci. Rep."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1101\/gr.205146.116","article-title":"microRNA target prediction programs predict many false positives","volume":"27","author":"Li","year":"2017","journal-title":"Genome Res."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nmeth.1247","article-title":"mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein\u2013enriched transcripts","volume":"5","author":"Hammell","year":"2008","journal-title":"Nat. Methods"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1038\/ng2135","article-title":"The role of site accessibility in microRNA target recognition","volume":"39","author":"Kertesz","year":"2007","journal-title":"Nat. Genet."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1534\/g3.113.006742","article-title":"The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector","volume":"3","author":"Akbari","year":"2013","journal-title":"G3 (Bethesda)"},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Li, S., A Mead, E., Liang, S., and Tu, Z. (2009). Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs. BMC Genom., 10.","DOI":"10.1186\/1471-2164-10-581"},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"Mayoral, J.G., Etebari, K., Hussain, M., Khromykh, A.A., and Asgari, S. (2014). Wolbachia Infection Modifies the Profile, Shuttling and Structure of MicroRNAs in a Mosquito Cell Line. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0096107"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/j.chom.2016.02.007","article-title":"A broad RNA virus survey reveals both miRNA dependence and functional sequestration","volume":"19","author":"Scheel","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.molmed.2016.11.003","article-title":"MicroRNA Regulation of RNA Virus Replication and Pathogenesis","volume":"23","author":"Trobaugh","year":"2017","journal-title":"Trends Mol. Med."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nature12869","article-title":"RNA viruses can hijack vertebrate microRNAs to suppress innate immunity","volume":"506","author":"Trobaugh","year":"2014","journal-title":"Nature"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1038\/nm1639","article-title":"Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes","volume":"13","author":"Huang","year":"2007","journal-title":"Nat. Med."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1016\/j.molcel.2009.06.003","article-title":"Cellular MicroRNA and P Bodies Modulate Host-HIV-1 Interactions","volume":"34","author":"Nathans","year":"2009","journal-title":"Mol. Cell"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1159\/000348504","article-title":"MicroRNA-23b Inhibits Enterovirus 71 Replication through Downregulation of EV71 VPl Protein","volume":"56","author":"Wen","year":"2013","journal-title":"Intervirology"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"5645","DOI":"10.1128\/JVI.02655-12","article-title":"Human MicroRNA hsa-miR-296-5p Suppresses Enterovirus 71 Replication by Targeting the Viral Genome","volume":"87","author":"Zheng","year":"2013","journal-title":"J. Virol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"5381","DOI":"10.1074\/jbc.M114.626325","article-title":"miR-28-3p Is a Cellular Restriction Factor That Inhibits Human T Cell Leukemia Virus, Type 1 (HTLV-1) Replication and Virus Infection*","volume":"290","author":"Bai","year":"2015","journal-title":"J. Boil. Chem."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1126\/science.1108784","article-title":"A cellular microRNA mediates antiviral defense in human cells","volume":"308","author":"Lecellier","year":"2005","journal-title":"Science"},{"key":"ref_116","doi-asserted-by":"crossref","unstructured":"Conrad, K.D., Giering, F., Erfurth, C., Neumann, A., Fehr, C., Meister, G., and Niepmann, M. (2013). microRNA-122 Dependent Binding of Ago2 Protein to Hepatitis C Virus RNA Is Associated with Enhanced RNA Stability and Translation Stimulation. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0056272"},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1126\/science.1113329","article-title":"Modulation of Hepatitis C Virus RNA Abundance by a Liver-Specific MicroRNA","volume":"309","author":"Jopling","year":"2005","journal-title":"Science"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/6\/540\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:57:23Z","timestamp":1760187443000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/11\/6\/540"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6,10]]},"references-count":117,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2019,6]]}},"alternative-id":["v11060540"],"URL":"https:\/\/doi.org\/10.3390\/v11060540","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6,10]]}}}