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Abstract

Tick-borne orthoflaviviruses (TBFs) are classified into three conventional groups based on genetics and ecology: mammalian, seabird and probable-TBF group. Recently, a fourth basal group has been identified in ticks from Africa: Mpulungu flavivirus (MPFV) in Zambia and Ngoye virus (NGOV) in Senegal. Despite attempts, isolating these viruses in vertebrate and invertebrate cell lines or intracerebral injection of newborn mice with virus-containing homogenates has remained unsuccessful. In this study, we report the discovery of Xinyang flavivirus (XiFV) in ticks from Xìnyáng, Henan Province, China. Phylogenetic analysis shows that XiFV was most closely related to MPFV and NGOV, marking the first identification of this tick orthoflavivirus group in Asia. We developed a reverse transcriptase quantitative PCR assay to screen wild-collected ticks and egg clutches, with absolute infection rates of 20.75 % in adult females and 15.19 % in egg clutches, suggesting that XiFV could be potentially spread through transovarial transmission. To examine potential host range, dinucleotide composition analyses revealed that XiFV, MPFV and NGOV share a closer composition to classical insect-specific orthoflaviviruses than to vertebrate-infecting TBFs, suggesting that XiFV could be a tick-only orthoflavivirus. Additionally, both XiFV and MPFV lack a furin cleavage site in the prM protein, unlike other TBFs, suggesting these viruses might exist towards a biased immature particle state. To examine this, chimeric Binjari virus with XIFV-prME (bXiFV) was generated, purified and analysed by SDS-PAGE and negative-stain transmission electron microscopy, suggesting prototypical orthoflavivirus size (~50 nm) and bias towards uncleaved prM. structural analyses of the 3′-untranslated regions show that XiFV forms up to five pseudo-knot-containing stem-loops and a prototypical orthoflavivirus dumbbell element, suggesting the potential for multiple exoribonuclease-resistant RNA structures.

Funding
This study was supported by the:
  • Australian Research Council (Award DP190103304)
    • Principle Award Recipient: AlexanderA. Khromykh
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-05-29
2024-06-19
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References

  1. Simmonds P, Becher P, Bukh J, Gould EA, Meyers G et al. ICTV virus taxonomy profile: Flaviviridae. J Gen Virol 2017; 98:2–3 [View Article] [PubMed]
    [Google Scholar]
  2. Pierson TC, Diamond MS. The continued threat of emerging flaviviruses. Nat Microbiol 2020; 5:796–812 [View Article] [PubMed]
    [Google Scholar]
  3. Harrison JJ, Hobson-Peters J, Bielefeldt-Ohmann H, Hall RA. Chimeric vaccines based on novel insect-specific Flaviviruses. Vaccines 2021; 9:1230 [View Article] [PubMed]
    [Google Scholar]
  4. Harrison JJ, Hobson-Peters J, Colmant AMG, Koh J, Newton ND et al. Antigenic characterization of new lineage II insect-specific Flaviviruses in Australian mosquitoes and identification of host restriction factors. mSphere 2020; 5:e00095-20 [View Article] [PubMed]
    [Google Scholar]
  5. Blitvich BJ, Firth AE. A review of Flaviviruses that have no known arthropod vector. Viruses 2017; 9:154 [View Article] [PubMed]
    [Google Scholar]
  6. Roby JA, Setoh YX, Hall RA, Khromykh AA. Post-translational regulation and modifications of flavivirus structural proteins. J Gen Virol 2015; 96:1551–1569 [View Article] [PubMed]
    [Google Scholar]
  7. Roby JA, Funk A, Khromykh AA. Flavivirus replication and assembly. In Shi PY. ed Molecular Virology and Control of Flaviviruses Norfolk, United Kingdom: Caister Academic Press; 2012 pp 21–49
    [Google Scholar]
  8. Slonchak A, Khromykh AA. Subgenomic flaviviral RNAs: what do we know after the first decade of research. Antiviral Res 2018; 159:13–25 [View Article] [PubMed]
    [Google Scholar]
  9. Postler TS, Beer M, Blitvich BJ, Bukh J, de Lamballerie X et al. Renaming of the genus Flavivirus to Orthoflavivirus and extension of binomial species names within the family Flaviviridae. Arch Virol 2023; 168:224 [View Article] [PubMed]
    [Google Scholar]
  10. Harima H, Orba Y, Torii S, Qiu Y, Kajihara M et al. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3’-untranslated region. Sci Rep 2021; 11:4883 [View Article] [PubMed]
    [Google Scholar]
  11. Grard G, Lemasson J-J, Sylla M, Dubot A, Cook S et al. Ngoye virus: a novel evolutionary lineage within the genus Flavivirus. J Gen Virol 2006; 87:3273–3277 [View Article] [PubMed]
    [Google Scholar]
  12. O’Brien CA, Huang B, Warrilow D, Hazlewood JE, Bielefeldt-Ohmann H et al. Extended characterisation of five archival tick-borne viruses provides insights for virus discovery in Australian ticks. Parasit Vectors 2022; 15:59 [View Article] [PubMed]
    [Google Scholar]
  13. Lawrie CH, Uzcátegui NY, Armesto M, Bell-Sakyi L, Gould EA. Susceptibility of mosquito and tick cell lines to infection with various flaviviruses. Med Vet Entomol 2004; 18:268–274 [View Article] [PubMed]
    [Google Scholar]
  14. Mifsud JCO, Costa VA, Petrone ME, Marzinelli EM, Holmes EC et al. Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evol 2023; 9:veac124 [View Article] [PubMed]
    [Google Scholar]
  15. Bamford CGG, de Souza WM, Parry R, Gifford RJ. Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evol 2022; 8:veac085 [View Article] [PubMed]
    [Google Scholar]
  16. Yoshii K, Song JY, Park SB, Yang J, Schmitt HJ. Tick-borne encephalitis in Japan, Republic of Korea and China. Emerg Microbes Infect 2017; 6:e82 [View Article] [PubMed]
    [Google Scholar]
  17. Luan Y, Gou J, Zhong D, Ma L, Yin C et al. The tick-borne pathogens: an overview of China’s situation. Acta Parasitol 2023; 68:1–20 [View Article] [PubMed]
    [Google Scholar]
  18. Lu Z, Bröker M, Liang G. Tick-borne encephalitis in mainland China. Vector Borne Zoonotic Dis 2008; 8:713–720 [View Article] [PubMed]
    [Google Scholar]
  19. Xu L, Guo M, Hu B, Zhou H, Yang W et al. Tick virome diversity in Hubei Province, China, and the influence of host ecology. Virus Evol 2021; 7:veab089 [View Article] [PubMed]
    [Google Scholar]
  20. Kong Y, Zhang G, Jiang L, Wang P, Zhang S et al. Metatranscriptomics reveals the diversity of the tick virome in northwest China. Microbiol Spectr 2022; 10:e0111522 [View Article] [PubMed]
    [Google Scholar]
  21. Guo L, Ma J, Lin J, Chen M, Liu W et al. Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China. Front Microbiol 2022; 13:966735 [View Article] [PubMed]
    [Google Scholar]
  22. Liu Z, Li L, Xu W, Yuan Y, Liang X et al. Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China. PLoS Negl Trop Dis 2022; 16:e0011017 [View Article] [PubMed]
    [Google Scholar]
  23. Zhao T, Gong H, Shen X, Zhang W, Shan T et al. Comparison of viromes in ticks from different domestic animals in China. Virol Sin 2020; 35:398–406 [View Article] [PubMed]
    [Google Scholar]
  24. Shi J, Shen S, Wu H, Zhang Y, Deng F. Metagenomic profiling of viruses associated with Rhipicephalus microplus Ticks in Yunnan Province, China. Virol Sin 2021; 36:623–635 [View Article] [PubMed]
    [Google Scholar]
  25. Kim B-J, Kim H, Won S, Kim H-C, Chong S-T et al. Ticks collected from wild and domestic animals and natural habitats in the Republic of Korea. Korean J Parasitol 2014; 52:281–285 [View Article] [PubMed]
    [Google Scholar]
  26. Cheng W, Zhao G, Jia Y, Bian Q, Du S et al. Characterization of Haemaphysalis flava (Acari: Ixodidae) from Qingling subspecies of giant panda (Ailuropoda melanoleuca qinlingensis) in Qinling Mountains (Central China) by morphology and molecular markers. PLoS One 2013; 8:e69793 [View Article] [PubMed]
    [Google Scholar]
  27. Choi C-Y, Kang C-W, Kim E-M, Lee S, Moon K-H et al. Ticks collected from migratory birds, including a new record of Haemaphysalis formosensis, on Jeju Island, Korea. Exp Appl Acarol 2014; 62:557–566 [View Article] [PubMed]
    [Google Scholar]
  28. Ko S, Kang JG, Kim SY, Kim HC, Klein TA et al. Prevalence of tick-borne encephalitis virus in ticks from southern Korea. J Vet Sci 2010; 11:197–203 [View Article] [PubMed]
    [Google Scholar]
  29. Kim SY, Jeong YE, Yun S-M, Lee IY, Han MG et al. Molecular evidence for tick-borne encephalitis virus in ticks in South Korea. Med Vet Entomol 2009; 23:15–20 [View Article] [PubMed]
    [Google Scholar]
  30. Yun S-M, Song BG, Choi W, Park WI, Kim SY et al. Prevalence of tick-borne encephalitis virus in ixodid ticks collected from the republic of Korea during 2011-2012. Osong Public Health Res Perspect 2012; 3:213–221 [View Article] [PubMed]
    [Google Scholar]
  31. Lee WK, Lim JW, Lee SY, Lee IY. Redescription of Haemaphysalis flava and Ixodes tanuki collected from a raccoon dog in Korea. Korean J Parasitol 1997; 35:1–8 [View Article] [PubMed]
    [Google Scholar]
  32. Yan F, Cheng T. Morphological and molecular identification of Haemaphysalis flava. Chin J Vet Sci 2015; 35:912–916
    [Google Scholar]
  33. Xu XL, Cheng TY, Yang H, Yan F, Yang Y. De novo sequencing, assembly and analysis of salivary gland transcriptome of Haemaphysalis flava and identification of sialoprotein genes. Infect Genet Evol 2015; 32:135–142 [View Article] [PubMed]
    [Google Scholar]
  34. Cheng R, Li D, Duan D-Y, Parry R, Cheng T-Y et al. Egg protein profile and dynamics during embryogenesis in Haemaphysalis flava ticks. Ticks Tick Borne Dis 2023; 14:102180 [View Article] [PubMed]
    [Google Scholar]
  35. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 2011; 17:10 [View Article]
    [Google Scholar]
  36. Bushmanova E, Antipov D, Lapidus A, Prjibelski AD. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. Gigascience 2019; 8:giz100 [View Article] [PubMed]
    [Google Scholar]
  37. Parry R, James ME, Asgari S. Uncovering the worldwide diversity and evolution of the virome of the mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms 2021; 9:1653 [View Article] [PubMed]
    [Google Scholar]
  38. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article] [PubMed]
    [Google Scholar]
  39. Jansen van Vuren P, Parry R, Khromykh AA, Paweska JT. A 1958 isolate of Kedougou virus (KEDV) from Ndumu, South Africa, expands the geographic and temporal range of KEDV in Africa. Viruses 2021; 13:1368 [View Article] [PubMed]
    [Google Scholar]
  40. Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 2019; 20:1160–1166 [View Article] [PubMed]
    [Google Scholar]
  41. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article] [PubMed]
    [Google Scholar]
  42. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
    [Google Scholar]
  43. Blum M, Chang H-Y, Chuguransky S, Grego T, Kandasaamy S et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 2021; 49:D344–D354 [View Article] [PubMed]
    [Google Scholar]
  44. Jeppe H, Konstantinos DT, Mads Damgaard P, José Juan Almagro A, Paolo M et al. Deeptmhmm predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv 2022
    [Google Scholar]
  45. Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 2022; 40:1023–1025 [View Article] [PubMed]
    [Google Scholar]
  46. Parry R, Asgari S. Discovery of novel Crustacean and Cephalopod Flaviviruses: insights into the evolution and circulation of Flaviviruses between marine invertebrate and vertebrate hosts. J Virol 2019; 93:e00432-19 [View Article] [PubMed]
    [Google Scholar]
  47. Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ et al. A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK. J Gen Virol 2023; 104: [View Article]
    [Google Scholar]
  48. Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res 2015; 43:W566–W570 [View Article] [PubMed]
    [Google Scholar]
  49. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S et al. ColabFold: making protein folding accessible to all. Nat Methods 2022; 19:679–682 [View Article] [PubMed]
    [Google Scholar]
  50. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci 2021; 30:70–82 [View Article] [PubMed]
    [Google Scholar]
  51. Amarilla AA, Sng JDJ, Parry R, Deerain JM, Potter JR et al. A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses. Nat Commun 2021; 12:3431 [View Article] [PubMed]
    [Google Scholar]
  52. Hobson-Peters J, Harrison JJ, Watterson D, Hazlewood JE, Vet LJ et al. A recombinant platform for flavivirus vaccines and diagnostics using chimeras of A new insect-specific virus. Sci Transl Med 2019; 11:eaax7888 [View Article] [PubMed]
    [Google Scholar]
  53. Torres FJ, Parry R, Hugo LE, Slonchak A, Newton ND et al. Reporter Flaviviruses as tools to demonstrate homologous and heterologous superinfection exclusion. Viruses 2022; 14:1501 [View Article] [PubMed]
    [Google Scholar]
  54. Piyasena TBH, Setoh YX, Hobson-Peters J, Newton ND, Bielefeldt-Ohmann H et al. Infectious DNAs derived from insect-specific flavivirus genomes enable identification of pre- and post-entry host restrictions in vertebrate cells. Sci Rep 2017; 7:2940 [View Article] [PubMed]
    [Google Scholar]
  55. Hardy JM, Newton ND, Modhiran N, Scott CAP, Venugopal H et al. A unified route for Flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses. Nat Commun 2021; 12:3266 [View Article] [PubMed]
    [Google Scholar]
  56. Scott CAP, Amarilla AA, Bibby S, Newton ND, Hall RA et al. Implications of dengue virus maturation on vaccine induced humoral immunity in mice. Viruses 2021; 13:1843 [View Article] [PubMed]
    [Google Scholar]
  57. Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C et al. ViennaRNA package 2.0. Algorithms Mol Biol 2011; 6:26 [View Article] [PubMed]
    [Google Scholar]
  58. Janssen S, Giegerich R. The RNA shapes studio. Bioinformatics 2015; 31:423–425 [View Article] [PubMed]
    [Google Scholar]
  59. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29:2933–2935 [View Article] [PubMed]
    [Google Scholar]
  60. Ochsenreiter R, Hofacker IL, Wolfinger MT. Functional RNA structures in the 3’UTR of tick-borne, insect-specific and no-known-vector Flaviviruses. Viruses 2019; 11:298 [View Article] [PubMed]
    [Google Scholar]
  61. Kutschera LS, Wolfinger MT. Evolutionary traits of tick-borne encephalitis virus: pervasive non-coding RNA structure conservation and molecular epidemiology. Virus Evol 2022; 8:veac051 [View Article] [PubMed]
    [Google Scholar]
  62. Darty K, Denise A, Ponty Y. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25:1974–1975 [View Article] [PubMed]
    [Google Scholar]
  63. Stadler K, Allison SL, Schalich J, Heinz FX. Proteolytic activation of tick-borne encephalitis virus by furin. J Virol 1997; 71:8475–8481 [View Article] [PubMed]
    [Google Scholar]
  64. Allison SL, Schalich J, Stiasny K, Mandl CW, Heinz FX. Mutational evidence for an internal fusion peptide in Flavivirus envelope protein E. J Virol 2001; 75:4268–4275 [View Article] [PubMed]
    [Google Scholar]
  65. Stiasny K, Allison SL, Schalich J, Heinz FX. Membrane interactions of the tick-borne encephalitis virus fusion protein E at low pH. J Virol 2002; 76:3784–3790 [View Article] [PubMed]
    [Google Scholar]
  66. Rey FA, Stiasny K, Vaney MC, Dellarole M, Heinz FX. The bright and the dark side of human antibody responses to flaviviruses: lessons for vaccine design. EMBO Rep 2018; 19:206–224 [View Article] [PubMed]
    [Google Scholar]
  67. Newton ND, Hardy JM, Modhiran N, Hugo LE, Amarilla AA et al. The structure of an infectious immature flavivirus redefines viral architecture and maturation. Sci Adv 2021; 7:eabe4507 [View Article] [PubMed]
    [Google Scholar]
  68. Slonchak A, Parry R, Pullinger B, Sng JDJ, Wang X et al. Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinants of sfRNA biogenesis and provides new insights into flavivirus evolution. Nat Commun 2022; 13:1279 [View Article] [PubMed]
    [Google Scholar]
  69. Gao G, Guo X, Goff SP. Inhibition of retroviral RNA production by ZAP, a CCCH-type zinc finger protein. Science 2002; 297:1703–1706 [View Article] [PubMed]
    [Google Scholar]
  70. Lobo FP, Mota BEF, Pena SDJ, Azevedo V, Macedo AM et al. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS One 2009; 4:e6282 [View Article] [PubMed]
    [Google Scholar]
  71. Pijlman GP, Funk A, Kondratieva N, Leung J, Torres S et al. A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity. Cell Host Microbe 2008; 4:579–591 [View Article] [PubMed]
    [Google Scholar]
  72. MacFadden A, O’Donoghue Z, Silva PAGC, Chapman EG, Olsthoorn RC et al. Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs. Nat Commun 2018; 9:119 [View Article] [PubMed]
    [Google Scholar]
  73. Akiyama BM, Graham ME, O Donoghue Z, Beckham JD, Kieft JS. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res 2021; 49:7122–7138 [View Article] [PubMed]
    [Google Scholar]
  74. Dobler G. Zoonotic tick-borne flaviviruses. Vet Microbiol 2010; 140:221–228 [View Article] [PubMed]
    [Google Scholar]
  75. Baidaliuk A, Miot EF, Lequime S, Moltini-Conclois I, Delaigue F et al. Cell-fusing agent virus reduces Arbovirus dissemination in Aedes aegypti mosquitoes In Vivo. J Virol 2019; 93:e00705-19 [View Article] [PubMed]
    [Google Scholar]
  76. Parry R, Asgari S. Aedes Anphevirus: an insect-specific virus distributed worldwide in Aedes aegypti mosquitoes that has complex interplays with Wolbachia and Dengue virus infection in cells. J Virol 2018; 92:e00224-18 [View Article] [PubMed]
    [Google Scholar]
  77. Agboli E, Leggewie M, Altinli M, Schnettler E. Mosquito-specific viruses-transmission and interaction. Viruses 2019; 11:873 [View Article] [PubMed]
    [Google Scholar]
  78. Di Giallonardo F, Schlub TE, Shi M, Holmes EC. Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species. J Virol 2017; 91:e02381-16 [View Article] [PubMed]
    [Google Scholar]
  79. Nuttall PA, Labuda M. Dynamics of infection in tick vectors and at the tick-host interface. Adv Virus Res 2003; 60:233–272 [View Article] [PubMed]
    [Google Scholar]
  80. Lequime S, Lambrechts L. Vertical transmission of arboviruses in mosquitoes: a historical perspective. Infect Genet Evol 2014; 28:681–690 [View Article] [PubMed]
    [Google Scholar]
  81. Rodenhuis-Zybert IA, van der Schaar HM, da Silva Voorham JM, van der Ende-Metselaar H, Lei H-Y et al. Immature dengue virus: a veiled pathogen?. PLoS Pathog 2010; 6:e1000718 [View Article] [PubMed]
    [Google Scholar]
  82. Zhang Y, Liang D, Yuan F, Yan Y, Wang Z et al. Replication is the key barrier during the dual-host adaptation of mosquito-borne flaviviruses. Proc Natl Acad Sci U S A 2022; 119:e2110491119 [View Article] [PubMed]
    [Google Scholar]
  83. Barbosa AD, Long M, Lee W, Austen JM, Cunneen M et al. The troublesome ticks research protocol: developing a comprehensive, multidiscipline research plan for investigating human tick-associated disease in Australia. Pathogens 2022; 11:1290 [View Article] [PubMed]
    [Google Scholar]
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