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Archives of Virology

, Volume 163, Issue 11, pp 3083–3090 | Cite as

Columbid circoviruses detected in free ranging pigeons from Southern Brazil: insights on PiCV evolution

  • M. R. Loiko
  • D. M. Junqueira
  • A. P. M. Varela
  • C. Tochetto
  • C. M. Scheffer
  • D. A. Lima
  • A. P. Morel
  • C. Cerva
  • W. P. Paim
  • Fabiana Quoos Mayer
  • P. M. Roehe
Original Article

Abstract

Pigeon circovirus (PiCV) is taxonomically classified as a member of the Circovirus genus, family Circoviridae. The virus contains a single stranded DNA genome of approximately 2 kb, with minor length variations among different isolates. The occurrence of PiCV infections in pigeons (Columba livia) has been documented worldwide over the past 20 years; however, in Brazil there were still no reports on PiCV detection. This study identifies seven PiCV genomes recovered from domestic pigeons of South Brazil through high-throughput sequencing and shows a high frequency of PiCV infection, through quantitative real-time PCR. Phylogenetic classification was performed by maximum likelihood analysis of the full genomes, ORF V1 (Rep) and ORF C1 (Cap). The results show that either full genome or Cap based analysis allowed PiCV classification into five major clades (groups A to E), where Brazilian sequences were classified as A, C or D. Recombination analyses were carried out with Simplot and RDP4 and the results show that both Rep and Cap ORFs contain several recombination hotspots, pointing to an important role for such events in PiCV evolution.

Notes

Acknowledgements

The authors are grateful to Mr. Luis Gustavo Trainini, who kindly gave access to the samples. This work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Financiadora de Estudos e Projetos (FINEP, contract 01.10.0783.00). P.M.R. has a CNPq 1A research fellow. This work was carried out as part of the doctoral studies of M.R.L (Programa de Pós-graduação em Ciências Veterinárias, UFRGS).

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

705_2018_3990_MOESM1_ESM.docx (68 kb)
Supplementary material 1 (DOCX 67 kb)
705_2018_3990_MOESM2_ESM.docx (202 kb)
Fig.S1. Place of origin of the free-living pigeons used in this study. The points marked on the map are the cities where the pigeons were captured. (DOCX 201 kb)
705_2018_3990_MOESM3_ESM.docx (396 kb)
Fig.S2. Likelihood mapping of five datasets comprising 82 PiCV sequences. A) Complete genome nucleotide sequences, B) Cap nucleotide sequences, C) Cap amino acid sequences, D) Rep nucleotide sequences, and E) Rep amino acid sequences. (DOCX 395 kb)
705_2018_3990_MOESM4_ESM.docx (818 kb)
Fig. S3. Bootscanning plots of six PiCV recombinant sequences. Bootscan analyses were performed on a sliding window of 200 nt by increments of 20 nt. A) Genotype A sequence showing no recombination profile; B) Genotype A (Table S1) sequence showing a recombination pattern around positions 1619-1826; C) Genotype A, break point positions around 1480-1826; D) Genotype C sequence presenting no recombination profile; E) and F) Recombination profiles of the sequences from Brazil in this study (genotype C*). (DOCX 818 kb)
705_2018_3990_MOESM5_ESM.docx (137 kb)
Fig.S4. Box plot of PiCV viral genome loads and the city of origin of sampled pigeons. (DOCX 136 kb)

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018
corrected publication August 2018

Authors and Affiliations

  • M. R. Loiko
    • 1
    • 2
  • D. M. Junqueira
    • 3
  • A. P. M. Varela
    • 1
    • 2
  • C. Tochetto
    • 1
    • 2
  • C. M. Scheffer
    • 1
  • D. A. Lima
    • 1
    • 2
  • A. P. Morel
    • 4
  • C. Cerva
    • 1
    • 2
  • W. P. Paim
    • 1
    • 2
  • Fabiana Quoos Mayer
    • 2
  • P. M. Roehe
    • 1
  1. 1.Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da SaúdeUFRGSPorto AlegreBrazil
  2. 2.Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Secretaria Estadual de Agricultura, Pecuária e IrrigaçãoEldorado do SulBrazil
  3. 3.Centro Universitário Ritter dos Reis-UniRitterLaureate International UniversitiesPorto AlegreBrazil
  4. 4.Falcoaria e Consultoria Ambiental-HAYABUSASão Francisco de PaulaBrazil

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