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Virus Genes

pp 1–11 | Cite as

Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017

  • H. L. Ferreira
  • T. L. Taylor
  • A. E. Absalon
  • K. M. Dimitrov
  • D. V. Cortés-Espinosa
  • S. L. Butt
  • J. L. Marín-Cruz
  • I. V. Goraichuk
  • J. D. Volkening
  • D. L. Suarez
  • C. L. AfonsoEmail author
Original Paper

Abstract

Virulent Newcastle disease viruses (NDV) have been present in Mexico since 1946, and recently, multiple outbreaks have been reported in the country. Here, we characterized eleven NDV isolated from apparently healthy wild birds and backyard chickens in three different locations of Jalisco, Mexico in 2017. Total RNA from NDV was reverse-transcribed, and 1285 nucleotides, which includes 3/4 of the fusion gene, was amplified and sequenced using a long-read MinION sequencing method. The sequences were 99.99–100% identical to the corresponding region obtained using the Illumina MiSeq. Phylogenetic analysis using MinION sequences demonstrated that nine virulent NDV from wild birds belonged to sub-genotypes Vc and VIn, and two backyard chicken isolates were of sub-genotype Vc. The sub-genotype Vc viruses had nucleotide sequence identity that ranged from 97.7 to 98% to a virus of the same sub-genotype isolated from a chicken in Mexico in 2010. Three viruses from pigeons had 96.3–98.7% nucleotide identity to sub-genotype VIn pigeon viruses, commonly referred to as pigeon paramyxovirus, isolated in the USA during 2000–2016. This study demonstrates that viruses of sub-genotype Vc are still present in Mexico, and the detection of this sub-genotype in both chickens and wild birds suggests that transmission among these species may represent a biosecurity risk. This is the first detection and complete genome sequencing of genotype VI NDV from Mexico. In addition, the utilization of an optimized long-read sequencing method for rapid virulence and genotype identification using the Oxford nanopore MinION system is demonstrated.

Keywords

Newcastle Virus Wild birds MinION MiSeq Genotype 

Notes

Acknowledgements

We are grateful to Dawn Williams-Coplin and Timothy L. Olivier for their technical assistance. The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture, ARS, or ORAU/ORISE. The USDA is an equal opportunity provider and employer.

Author Contributions

Conceived of or designed study: HLF, TLT, CLF; performed research: HLF, TLT, AEA, DVC-E, SLB, JLM-C, IVG, JDV; analyzed data: HLF, TLT, KDM; contributed new methods or models: HLF, TLT; wrote the paper: HLF, TLT, KDM; funding acquisition, DLS and CLA.

Funding

This work was supported by USDA funding. This research was supported in part by an appointment to the Agricultural Research Service (ARS) Research Participation Program. This research was supported by the Agricultural Research Service (ARS), USDA CRIS (6612-32000-072-00D) and by an appointment to the ORAU/ORISE.

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest regarding the publication of this article.

Ethical approval

All procedures performed in the present study involving sample collection and virus isolation in chicken embryonated eggs followed the applicable international, national, and/or institutional guidelines for the care and use of animals by the authors.

Supplementary material

11262_2019_1663_MOESM1_ESM.pdf (369 kb)
Supplementary Fig. 1 Phylogenetic analysis of NDV concatenated complete genome coding sequences. The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time Reversible model. The tree with the highest log likelihood (-78416.35) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Joining and BioNJ algorithms to a matrix of pairwise distances, estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with a superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites [five categories (+G, parameter = 0.4623)]. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 51 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 13,746 positions in the final dataset. Evolutionary analyses were conducted in MEGA7. The sequences from Mexico from 2017 are highlighted in red and blue and are classified into sub-genotypes VIn and Vc, respectively. Supplementary material 1 (PDF 368 kb)
11262_2019_1663_MOESM2_ESM.xlsx (14 kb)
Supplementary Table 1 Evolutionary divergence between nucleotide sequences obtained by MinION and the most closely related sequences available in GenBank. Analyses were conducted using the Maximum Composite Likelihood model. The analysis involved 95 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1229 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 (41). Supplementary material 2 (XLSX 14 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • H. L. Ferreira
    • 1
    • 2
  • T. L. Taylor
    • 1
  • A. E. Absalon
    • 3
  • K. M. Dimitrov
    • 1
  • D. V. Cortés-Espinosa
    • 4
  • S. L. Butt
    • 1
    • 5
  • J. L. Marín-Cruz
    • 6
  • I. V. Goraichuk
    • 1
    • 7
  • J. D. Volkening
    • 8
  • D. L. Suarez
    • 1
  • C. L. Afonso
    • 1
    Email author
  1. 1.Southeast Poultry Research LaboratoryUS National Poultry Research CenterAthensUSA
  2. 2.University of Sao Paulo, ZMV- FZEAPirassunungaBrazil
  3. 3.Vaxbiotek S.CCuautlancingoMexico
  4. 4.Instituto Politécnico Nacional/CIBA-TlaxcalaTepetitlaMexico
  5. 5.Department of Pathology, College of Veterinary MedicineUniversity of GeorgiaAthensUSA
  6. 6.Consorcio consultivo empresarial S.C.San Juan De Los LagosMexico
  7. 7.National Scientific Center Institute of Experimental and Clinical Veterinary MedicineKharkivUkraine
  8. 8.BASE2BIOOshkoshUSA

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