Top

Published in:

01-11-2018 | Original Article

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

Authors: 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

Published in: Archives of Virology | Issue 11/2018

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.

Available only for authorised users

Mankertz A, Hattermann K, Ehlers B, Soike D (2000) Cloning and sequencing of columbid circovirus (CoCV), a new circovirus from pigeons. Arch Virol 145:2469–2479. https://doi.org/10.1007/s007050070002 CrossRefPubMed

Duchatel JP, Todd D, Curry A et al (2005) New data on the transmission of pigeon circovirus. Vet Rec 157:413–415. https://doi.org/10.1136/vr.157.14.413 CrossRefPubMed

Rosario K, Breitbart M, Harrach B et al (2017) Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus. Arch Virol 162:1447–1463. https://doi.org/10.1007/s00705-017-3247-y CrossRefPubMed

Stenzel T, Farkas K, Varsani A (2015) Genome sequence of a diverse goose circovirus recovered from greylag goose. Genome Announc. https://doi.org/10.1128/genomeA.00767-15 CrossRefPubMedPubMedCentral

Cságola A, Lőrincz M, Tombácz K et al (2012) Genetic diversity of pigeon circovirus in Hungary. Virus Genes 44:75–79. https://doi.org/10.1007/s11262-011-0669-6 CrossRefPubMed

Yamamoto E, Ito H, Kitamoto E et al (2015) Complete genome sequence of pigeon circovirus detected in racing pigeons in western Japan. Virus Genes 51:140–143. https://doi.org/10.1007/s11262-015-1211-z CrossRefPubMed

Delwart E, Li L (2012) Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res 164:114–121. https://doi.org/10.1016/j.virusres.2011.11.021 CrossRefPubMed

Todd D, Weston JH, Soike D, Smyth JA (2001) Genome sequence determinations and analyses of novel circoviruses from goose and pigeon. Virology 286:354–362. https://doi.org/10.1006/viro.2001.0985 CrossRefPubMed

Woods LW, Latimer KS, Niagro FD et al (1994) A retrospective study of circovirus infection in pigeons: nine cases (1986–1993). J Vet Diagn Invest 6:156–164. https://doi.org/10.1177/104063879400600205 CrossRefPubMed

10.

Julian L, Piasecki T, Chrzastek K et al (2013) Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland. J Gen Virol 94:1086–1095. https://doi.org/10.1099/vir.0.050179-0 CrossRefPubMed

11.

Ng TFF, Willner DL, Lim YW et al (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS ONE. https://doi.org/10.1371/journal.pone.0020579 CrossRefPubMedPubMedCentral

12.

Dean FB (2001) Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11:1095–1099. https://doi.org/10.1101/gr.180501 CrossRefPubMedPubMedCentral

13.

Lasken RS (2009) Genomic DNA amplification by the multiple displacement amplification (MDA) method: figure 1. Biochem Soc Trans 37:450–453. https://doi.org/10.1042/BST0370450 CrossRefPubMed

14.

Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340 CrossRefPubMedPubMedCentral

15.

Schmidt HA, Petzold E, Vingron M, von Haeseler A (2003) Molecular phylogenetics: parallelized parameter estimation and quartet puzzling. J Parallel Distrib Comput 63:719–727. https://doi.org/10.1016/S0743-7315(03)00129-1 CrossRef

16.

Guindon S, Dufayard J-F, Lefort V et al (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321. https://doi.org/10.1093/sysbio/syq010 CrossRefPubMed

17.

Lefort V, Longueville J-E, Gascuel O (2017) SMS: smart model selection in PhyML. Mol Biol Evol 34:2422–2424. https://doi.org/10.1093/molbev/msx149 CrossRefPubMedPubMedCentral

18.

Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55:539–552. https://doi.org/10.1080/10635150600755453 CrossRefPubMed

19.

Rambaut A (2009) FigTree v1.4: tree figure drawing tool [Internet]

20.

Yu G, Smith DK, Zhu H et al (2017) GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol 8:28–36. https://doi.org/10.1111/2041-210X.12628 CrossRef

21.

Muhire B, Martin DP, Brown JK et al (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424. https://doi.org/10.1007/s00705-012-1601-7 CrossRefPubMed

22.

Lole KS, Bollinger RC, Paranjape RS et al (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160PubMedPubMedCentral

23.

Sambrook J, Russel DW (2001) Molecular cloning—a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York

24.

Stenzel T, Piasecki T, Chrzstek K et al (2014) Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses. J Gen Virol 95:1338–1351. https://doi.org/10.1099/vir.0.063917-0 CrossRefPubMed

25.

Bencke GA (2007) POMBOS-DOMÉSTICOS Sugestões para o controle em escolas públicas estaduais. http://www.FzbRsGovBr/Upload/20150514114242Pombos_DomesticosPdf. 23

26.

Fontoura PM, Dyer E, Blackburn TM, Orsi ML (2013) Non-native bird species in Brazil Espécies. Neotrop Biol Conserv 8:165–175. https://doi.org/10.4013/nbc.2013.83.07 CrossRef

27.

Duchatel JP, Todd D, Smyth JA et al (2006) Observations on detection, excretion and transmission of pigeon circovirus in adult, young and embryonic pigeons. Avian Pathol 35:30–34. https://doi.org/10.1080/03079450500465692 CrossRefPubMed

28.

Stenzel TA, Pestka D, Tykałowski B et al (2012) Epidemiological investigation of selected pigeon viral infections in Poland. Vet Rec 171:562. https://doi.org/10.1136/vr.100932 CrossRefPubMed

29.

Wang K-C, Zhuang Q, Qiu Y et al (2017) Genome sequence characterization of pigeon circoviruses in China. Virus Res 233:1–7. https://doi.org/10.1016/j.virusres.2017.03.007 CrossRefPubMed

30.

Lefeuvre P, Lett J-M, Varsani A, Martin DP (2009) Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83:2697–2707. https://doi.org/10.1128/JVI.02152-08 CrossRefPubMed

31.

Varsani A, de Villiers GK, Regnard GL et al (2010) A unique isolate of beak and feather disease virus isolated from budgerigars (Melopsittacus undulatus) in South Africa. Arch Virol 155:435–439. https://doi.org/10.1007/s00705-010-0589-0 CrossRefPubMed

32.

Lemey P, Posada D (2009) Introduction to recombination detection. In: Lemey P, Salemi M, Vandamme A-M (eds) The phylogenetic handbook, 2nd edn. Cambridge University Press, Cambridge, pp 493–517CrossRef

Title: Columbid circoviruses detected in free ranging pigeons from Southern Brazil: insights on PiCV evolution
Authors: 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
Publication date: 01-11-2018
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 11/2018
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-018-3990-8

Live Webinar | 27-06-2024 | 18:00 (CEST)

Keynote webinar | Spotlight on medication adherence

Reserve your place

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

WHO estimates that half of all patients worldwide are non-adherent to their prescribed medication. The consequences of poor adherence can be catastrophic, on both the individual and population level.

Join our expert panel to discover why you need to understand the drivers of non-adherence in your patients, and how you can optimize medication adherence in your clinics to drastically improve patient outcomes.

Prof. Kevin Dolgin

Prof. Florian Limbourg

Prof. Anoop Chauhan

Developed by: Springer Medicine

Obesity Clinical Trial Summary

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 11/2018

Full genome sequence of a polyvalent bacteriophage infecting strains of Shigella, Salmonella, and Escherichia

Genetic characterization of a novel HIV-1 CRF01_AE/CRF07_BC recombinant form among men who have sex with men in Guangdong, China

Acipenser iridovirus-European encodes a replication factor C (RFC) sub-unit

Genetic diversity and phylogenetic analysis of newly discovered bat astroviruses in Korea

Genetic characterization of chikungunya viruses isolated during the 2015-2017 outbreaks in different states of India, based on their E1 and E2 genes

A genome-wide diversity study of grapevine rupestris stem pitting-associated virus

Keynote webinar | Spotlight on medication adherence

Live: Thursday 27th June 2024, 18:00-19:30 (CEST)

At a glance: The STEP trials