Skip to main content
SpringerLink
Log in

Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3’UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. de Souza Lopes O, Coimbra TL, de Abreu Sacchetta L, Calisher CH (1978) Emergence of a new arbovirus disease in Brazil. I. Isolation and characterization of the etiologic agent, Rocio virus. Am J Epidemiol 107(5):444–449

    Article  PubMed  Google Scholar 

  2. de Souza Lopes O, de Abreu Sacchetta L, Coimbra TL, Pinto GH, Glasser CM (1978) Emergence of a new arbovirus disease in Brazil. II. Epidemiologic studies on 1975 epidemic. Am J Epidemiol 108(5):394–401

    Article  PubMed  Google Scholar 

  3. Straatmann A, Santos-Torres S, Vasconcelos PF, da Rosa AP, Rodrigues SG, Tavares-Neto J (1997) Serological evidence of the circulation of the Rocio arbovirus (Flaviviridae) in Bahia. Rev Soc Bras Med Trop 30(6):511–515

    Article  CAS  PubMed  Google Scholar 

  4. Ferreira IB, Pereira LE, Rocco IM, Marti AT, Souza L, Iversson LB (1994) Surveillance of arbovirus infections in the atlantic forest region, State of São Paulo, Brazil: I. detection of hemagglutination-inhibition antibodies in wild birds between 1978 and 1990. Revista do Instituto de Medicina Tropical de São Paulo 36(3):265–274

    Article  CAS  PubMed  Google Scholar 

  5. Pauvolid-Correa A, Campos Z, Juliano R, Velez J, Nogueira RM, Komar N (2014) Serological evidence of widespread circulation of West Nile virus and other flaviviruses in equines of the Pantanal, Brazil. PLoS Negl Trop Dis 8(2):e2706. doi:10.1371/journal.pntd.0002706

    Article  PubMed  PubMed Central  Google Scholar 

  6. Silva JR, Romeiro MF, Souza WM, Munhoz TD, Borges GP, Soares OA, Campos CH, Machado RZ, Silva ML, Faria JL, Chavez JH, Figueiredo LT (2014) A Saint Louis encephalitis and Rocio virus serosurvey in Brazilian horses. Rev Soc Bras Med Trop 47(4):414–417

    Article  PubMed  Google Scholar 

  7. Casseb AR, Cruz AV, Jesus IS, Chiang JO, Martins LC, Silva SP, Henriques DF, Casseb LM, Vasconcelos PF (2014) Seroprevalence of flaviviruses antibodies in water buffaloes (Bubalus bubalis) in Brazilian Amazon. J Venom Anim Toxins Incl Trop Dis 20(1):9. doi:10.1186/1678-9199-20-9

    Article  PubMed  PubMed Central  Google Scholar 

  8. Duffy MR, Chen TH, Hancock WT, Powers AM, Kool JL, Lanciotti RS, Pretrick M, Marfel M, Holzbauer S, Dubray C, Guillaumot L, Griggs A, Bel M, Lambert AJ, Laven J, Kosoy O, Panella A, Biggerstaff BJ, Fischer M, Hayes EB (2009) Zika virus outbreak on Yap Island, Federated States of Micronesia. N Engl J Med 360(24):2536–2543. doi:10.1056/NEJMoa0805715

    Article  CAS  PubMed  Google Scholar 

  9. Hancock WT, Marfel M, Bel M (2014) Zika virus, French Polynesia, South Pacific, 2013. Emerg Infect Dis 20(11):1960. doi:10.3201/eid2011.141380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Campos GS, Bandeira AC, Sardi SI (2015) Zika virus outbreak, Bahia, Brazil. Emerg Infect Dis 21(10):1885–1886. doi:10.3201/eid2110.150847

    Article  PubMed  PubMed Central  Google Scholar 

  11. Tiriba AC, Miziara AM, Lorenco R, da Costa RB, Costa CS, Pinto GH (1976) Primary human epidemic encephalitis induced by Arbovirus found at the sea shore south of the State of Sao Paulo. Clinical study in an emergency hospital. AMB Rev Assoc Med Bras 22(11):415–420

    CAS  PubMed  Google Scholar 

  12. Medeiros DB, Nunes MR, Vasconcelos PF, Chang GJ, Kuno G (2007) Complete genome characterization of Rocio virus (Flavivirus: Flaviviridae), a Brazilian flavivirus isolated from a fatal case of encephalitis during an epidemic in Sao Paulo state. J Gen Virol 88(Pt 8):2237–2246. doi:10.1099/vir.0.82883-0

    Article  CAS  PubMed  Google Scholar 

  13. Chambers TJ, Hahn CS, Galler R, Rice CM (1990) Flavivirus genome organization, expression, and replication. Annu Rev Microbiol 44:649–688. doi:10.1146/annurev.mi.44.100190.003245

    Article  CAS  PubMed  Google Scholar 

  14. Roby JA, Funk A, Khromykh AA (2012) Flavivirus replication and assembly. In: Shi PY (ed) Molecular virology and control of flaviviruses. Caister Academic Press, Wymondham, pp 21–49

  15. Amarilla AA, Setoh YX, Periasamy P, Peng NY, Pali G, Figueiredo LT, Khromykh AA, Aquino VH (2017) Chimeric viruses between Rocio and West Nile: the role for Rocio prM-E proteins in virulence and inhibition of interferon-alpha/beta signaling. Sci Rep 7:44642. doi:10.1038/srep44642

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Author notes

  1. Yin Xiang Setoh and Alberto A. Amarilla contributed equally to this manuscript, and should be considered equal first authors.

Authors and Affiliations

  1. Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia

    Yin Xiang Setoh, Alberto A. Amarilla, Nias Y. Peng, Andrii Slonchak, Parthiban Periasamy & Alexander A. Khromykh

  2. Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil

    Victor H. Aquino

  3. Virology Research Center, School of Medicine of Ribeirao Preto, University of de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil

    Luiz T. M. Figueiredo

Authors
  1. Yin Xiang Setoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alberto A. Amarilla
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nias Y. Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrii Slonchak
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Parthiban Periasamy
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Luiz T. M. Figueiredo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Victor H. Aquino
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Alexander A. Khromykh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alexander A. Khromykh.

Ethics declarations

Funding

This work was supported by the National Health and Medical Research Council of Australia (Grant nos. APP1059794 and APP1045188).

Conflict of interest

The authors declare that they have no competing interests.

Ethical approval

This article does not contain any studies with animals performed by any of the authors. This study was approved by the Australian Office of the Gene Technology Regulator (License no. DNIR 472).

Additional information

Handling Editor: Patricia Aguilar.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Setoh, Y.X., Amarilla, A.A., Peng, N.Y. et al. Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence. Arch Virol 163, 255–258 (2018). https://doi.org/10.1007/s00705-017-3561-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-017-3561-4

Search

Navigation