title: Reconstruction of the Evolutionary History and Dispersal of Usutu Virus, a Neglected Emerging Arbovirus in Europe and Africa.
abstract: Usutu virus (USUV), one of the most neglected Old World encephalitic flaviviruses, causes epizootics among wild and captive birds and sporadic infection in humans. The dynamics of USUV spread and evolution in its natural hosts are unknown. Here, we present the phylogeny and evolutionary history of all available USUV strains, including 77 newly sequenced complete genomes from a variety of host species at a temporal and spatial scaled resolution. The results showed that USUV can be classified into six distinct lineages and that the most recent common ancestor of the recent European epizootics emerged in Africa at least 500 years ago. We demonstrated that USUV was introduced regularly from Africa into Europe in the last 50 years, and the genetic diversity of European lineages is shaped primarily by in situ evolution, while the African lineages have been driven by extensive gene flow. Most of the amino acid changes are deleterious polymorphisms removed by purifying selection, with adaptive evolution restricted to the NS5 gene and several others evolving under episodic directional selection, indicating that the ecological or immunological factors were mostly the key determinants of USUV dispersal and outbreaks. Host-specific mutations have been detected, while the host transition analysis identified mosquitoes as the most likely origin of the common ancestor and birds as the source of the recent European USUV lineages. Our results suggest that the major migratory bird flyways could predict the continental and intercontinental dispersal patterns of USUV and that migratory birds might act as potential long-distance dispersal vehicles.
  
  
  OBJECTIVE
  Usutu virus (USUV), a mosquito-borne flavivirus of the Japanese encephalitis virus antigenic group, caused massive bird die-offs, mostly in Europe. There is increasing evidence that USUV appears to be pathogenic for humans, becoming a potential public health problem. The emergence of USUV in Europe allows us to understand how an arbovirus spreads, adapts, and evolves in a naive environment. Thus, understanding the epidemiological and evolutionary processes that contribute to the emergence, maintenance, and further spread of viral diseases is the sine qua non to develop and implement surveillance strategies for their control. In this work, we performed an expansive phylogeographic and evolutionary analysis of USUV using all published sequences and those generated during this study. Subsequently, we described the genetic traits, reconstructed the potential pattern of geographic spread between continents/countries of the identified viral lineages and the drivers of viral migration, and traced the origin of outbreaks and transition events between different hosts.
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Engel
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany.
authors.forename: Hanna
authors.initials: H
authors.lastname: Jöst
authors.affiliation: Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Wink
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany.
authors.forename: Jessica
authors.initials: J
authors.lastname: Börstler
authors.affiliation: Nature and Biodiversity Conservation Union (NABU), Stuttgart, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bosch
authors.affiliation: Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
authors.forename: Mutien-Marie
authors.initials: MM
authors.lastname: Garigliany
authors.affiliation: German Mosquito Control Association (KABSeV), Speyer, Germany.
authors.forename: Artur
authors.initials: A
authors.lastname: Jöst
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany German Mosquito Control Association (KABSeV), Speyer, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Czajka
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany.
authors.forename: Renke
authors.initials: R
authors.lastname: Lühken
authors.affiliation: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany.
authors.forename: Ute
authors.initials: U
authors.lastname: Ziegler
authors.affiliation: Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany.
authors.forename: Martin H
authors.initials: MH
authors.lastname: Groschup
authors.affiliation: Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Pfeffer
authors.affiliation: German Mosquito Control Association (KABSeV), Speyer, Germany.
authors.forename: Norbert
authors.initials: N
authors.lastname: Becker
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany danielcadar@gmail.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: Cadar
authors.affiliation: Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany.
authors.forename: Jonas
authors.initials: J
authors.lastname: Schmidt-Chanasit
mesh_terms: D000220:Adaptation, Biological; D000349:Africa / Q000453:epidemiology; D000818:Animals; D001102:Arbovirus Infections / Q000453:epidemiology / Q000662:veterinary / Q000821:virology; D001103:Arboviruses / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D001717:Birds; D016000:Cluster Analysis; D005060:Europe / Q000453:epidemiology; D019143:Evolution, Molecular; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral
references.citation: Clin Infect Dis. 2007 Oct 15;45(8):1039-46
references.pmid: 17879923
references.citation: J Clin Microbiol. 2007 Dec;45(12):3870-4
references.pmid: 17913929
references.citation: Vet Microbiol. 2011 Mar 24;148(2-4):207-12
references.pmid: 20980109
references.citation: Am J Trop Med Hyg. 2011 Jul;85(1):178-81
references.pmid: 21734145
references.citation: Virology. 2011 Aug 15;417(1):203-10
references.pmid: 21723580
references.citation: Am J Trop Med Hyg. 2011 Sep;85(3):551-3
references.pmid: 21896821
references.citation: Mol Biol Evol. 2011 Nov;28(11):3033-43
references.pmid: 21670087
references.citation: Vector Borne Zoonotic Dis. 2011 Nov;11(11):1417-23
references.pmid: 21767160
references.citation: PLoS One. 2012;7(2):e32604
references.pmid: 22389712
references.citation: Virology. 2012 May 25;427(1):18-24
references.pmid: 22365326
references.citation: Vector Borne Zoonotic Dis. 2012 May;12(5):431-3
references.pmid: 22217176
references.citation: J Math Biol. 2008 Mar;56(3):391-412
references.pmid: 17874105
references.citation: Vet Microbiol. 2008 Mar 18;127(3-4):237-48
references.pmid: 17869454
references.citation: BMC Evol Biol. 2007;7:214
references.pmid: 17996036
references.citation: Emerg Infect Dis. 2008 May;14(5):861-3
references.pmid: 18439389
references.citation: Infect Genet Evol. 2008 May;8(3):239-46
references.pmid: 17921073
references.citation: Prev Vet Med. 2008 Jul 15;85(3-4):166-86
references.pmid: 18314208
references.citation: Viral Immunol. 2008 Jun;21(2):247-53
references.pmid: 18433332
references.citation: Transbound Emerg Dis. 2014 Jun;61(3):273-6
references.pmid: 23095331
references.citation: Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2014 May;57(5):531-40
references.pmid: 24781910
references.citation: Infection. 2014 Aug;42(4):689-95
references.pmid: 24793998
references.citation: Emerg Infect Dis. 2014 Oct;20(10):1771-3
references.pmid: 25271769
references.citation: J Neurovirol. 2015 Feb;21(1):92-7
references.pmid: 25361698
references.citation: PLoS One. 2015;10(2):e0117849
references.pmid: 25719412
references.citation: Infect Genet Evol. 2015 Jun;32:292-7
references.pmid: 25818400
references.citation: J Virol. 2016 Jan;90(2):862-72
references.pmid: 26512086
references.citation: Bioinformatics. 2000 Jun;16(6):562-3
references.pmid: 10980155
references.citation: Virology. 2001 Mar 1;281(1):75-87
references.pmid: 11222098
references.citation: Emerg Infect Dis. 2002 Jul;8(7):652-6
references.pmid: 12095429
references.citation: Infect Genet Evol. 2003 Jul;3(2):87-95
references.pmid: 12809802
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: J Gen Virol. 2003 Oct;84(Pt 10):2807-17
references.pmid: 13679615
references.citation: J Virol. 2003 Oct;77(20):11296-8
references.pmid: 14512579
references.citation: J Comput Chem. 2004 Oct;25(13):1605-12
references.pmid: 15264254
references.citation: Nat Rev Microbiol. 2004 Oct;2(10):789-801
references.pmid: 15378043
references.citation: J Virol. 2004 Nov;78(22):12225-35
references.pmid: 15507609
references.citation: Ann Trop Med Parasitol. 1964 Sep;58:367-74
references.pmid: 14212897
references.citation: Virology. 2004 Dec 5;330(1):342-50
references.pmid: 15527859
references.citation: J Gen Virol. 2005 Feb;86(Pt 2):405-12
references.pmid: 15659760
references.citation: Virol J. 2006;3:71
references.pmid: 16952307
references.citation: Microbes Infect. 2007 Jan;9(1):1-6
references.pmid: 17196419
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: PLoS Comput Biol. 2009 Sep;5(9):e1000520
references.pmid: 19779555
references.citation: Euro Surveill. 2009;14(50). pii: 19448
references.pmid: 20070935
references.citation: Euro Surveill. 2009;14(50). pii: 19446
references.pmid: 20070936
references.citation: Vet Microbiol. 2010 Feb 24;141(1-2):159-63
references.pmid: 19720475
references.citation: Syst Biol. 2010 May;59(3):307-21
references.pmid: 20525638
references.citation: J Virol. 2011 Mar;85(6):2964-74
references.pmid: 21159871
references.citation: PLoS Genet. 2012;8(7):e1002764
references.pmid: 22807683
references.citation: Mol Biol Evol. 2012 Aug;29(8):1969-73
references.pmid: 22367748
references.citation: Nat Methods. 2012 Aug;9(8):772
references.pmid: 22847109
references.citation: Euro Surveill. 2012;17(50). pii: 20341
references.pmid: 23241231
references.citation: J Gen Virol. 2013 Feb;94(Pt 2):318-25
references.pmid: 23136360
references.citation: Emerg Infect Dis. 2013 Feb;19(2):274-7
references.pmid: 23347844
references.citation: PLoS Negl Trop Dis. 2013;7(5):e2245
references.pmid: 23738027
references.citation: PLoS One. 2013;8(5):e64761
references.pmid: 23741387
references.citation: Emerg Infect Dis. 2013 Jul;19(7):1173-5
references.pmid: 23764143
references.citation: Virol J. 2013;10:217
references.pmid: 23816256
references.citation: Emerg Infect Dis. 2013;19(9):1418-27
references.pmid: 23965756
references.citation: PLoS Negl Trop Dis. 2013;7(8):e2411
references.pmid: 24009790
references.citation: Vet J. 2014 Jan;199(1):191-3
references.pmid: 24268481
references.citation: Comp Immunol Microbiol Infect Dis. 2014 Mar;37(2):131-41
references.pmid: 24503179