Skip to main content
SpringerLink
Log in

Enhanced phylogenetic resolution of Newcastle disease outbreaks using complete viral genome sequences from formalin-fixed paraffin-embedded tissue samples

  • Original Paper
  • Published:
Virus Genes Aims and scope Submit manuscript

Abstract

Highly virulent Newcastle disease virus (NDV) causes Newcastle disease (ND), which is a threat to poultry production worldwide. Effective disease management requires approaches to accurately determine sources of infection, which involves tracking of closely related viruses. Next-generation sequencing (NGS) has emerged as a research tool for thorough genetic characterization of infectious organisms. Previously formalin-fixed paraffin-embedded (FFPE) tissues have been used to conduct retrospective epidemiological studies of related but genetically distinct viruses. However, this study extends the applicability of NGS for complete genome analysis of viruses from FFPE tissues to track the evolution of closely related viruses. Total RNA was obtained from FFPE spleens, lungs, brains, and small intestines of chickens in 11 poultry flocks during disease outbreaks in Pakistan. The RNA was randomly sequenced on an Illumina MiSeq instrument and the raw data were analyzed using a custom data analysis pipeline that includes de novo assembly. Genomes of virulent NDV were detected in 10/11 birds: eight nearly complete (> 95% coverage of concatenated coding sequence) and two partial genomes. Phylogeny of the NDV complete genome coding sequences was compared to current methods of analysis based on the full and partial fusion genes and determined that the approach provided a better phylogenetic resolution. Two distinct lineages of sub-genotype VIIi NDV were identified to be simultaneously circulating in Pakistani poultry. Non-targeted NGS of total RNA from FFPE tissues coupled with de novo assembly provided a reliable, safe, and affordable method to conduct epidemiological and evolutionary studies to facilitate management of ND in Pakistan.

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. Miller PJ, Koch G (2013) Newcastle disease. In: Swayne DE, Glisson JR, McDougald LR, Nolan LK, Suarez DL, Nair V (eds) Diseases of poultry, 13th edn. Wiley-Blackwell, Hoboken, pp 89–138

    Google Scholar 

  2. Afonso CL, Amarasinghe GK, Banyai K, Bao Y, Basler CF, Bavari S, Bejerman N, Blasdell KR, Briand FX, Briese T et al (2016) Taxonomy of the order Mononegavirales: update 2016. Arch Virol 161(8):2351–2360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Amarasinghe GK, Ceballos NGA, Banyard AC, Basler CF, Bavari S, Bennett AJ, Blasdell KR, Briese T, Bukreyev A, Caì Y (2018) Taxonomy of the order Mononegavirales: update. Arch Virol 2018:1–12

    Google Scholar 

  4. Dimitrov KM, Ramey AM, Qiu X, Bahl J, Afonso CL (2016) Temporal, geographic, and host distribution of avian paramyxovirus 1 (Newcastle disease virus). Infect Genet Evol 2016(39):22–34

    Article  Google Scholar 

  5. Sabouri F, Vasfi Marandi M, Bashashati M (2018) Characterization of a novel VIIl sub-genotype of Newcastle disease virus circulating in Iran. Avian Pathol 47(1):90–99

    Article  CAS  PubMed  Google Scholar 

  6. Gowthaman V, Singh SD, Dhama K, Desingu PA, Kumar A, Malik YS, Munir M (2016) Isolation and characterization of genotype XIII Newcastle disease virus from Emu in India. VirusDisease 27(3):315–318

    Article  PubMed  PubMed Central  Google Scholar 

  7. Chambers P, Millar NS, Bingham RW, Emmerson PT (1986) Molecular cloning of complementary DNA to Newcastle disease virus, and nucleotide sequence analysis of the junction between the genes encoding the haemmaglutinin-neuraminidase and the large protein. J Gen Virol 67:475–486

    Article  CAS  PubMed  Google Scholar 

  8. de Leeuw OS, Koch G, Hartog L, Ravenshorst N, Peeters BPH (2005) Virulence of Newcastle disease virus is determined by the cleavage site of the fusion protein and by both the stem region and globular head of the haemagglutinin-neuraminidase protein. J Gen Virol 86(Pt. 6):1759–1769

    Article  PubMed  CAS  Google Scholar 

  9. Diel DG, da Silva LH, Liu H, Wang Z, Miller PJ, Afonso CL (2012) Genetic diversity of avian paramyxovirus type 1: proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes. Infect Genet Evol 12(8):1770–1779

    Article  PubMed  Google Scholar 

  10. Dimitrov KM, Sharma P, Volkening JD, Goraichuk IV, Wajid A, Rehmani SF, Basharat A, Shittu I, Joannis TM, Miller PJ et al (2017) A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses. Virol J 14(1):72

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P et al (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 437(7062):1162–1166

    Article  CAS  PubMed  Google Scholar 

  12. Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25(4):195–203

    Article  CAS  Google Scholar 

  13. Wakamatsu N, King DJ, Seal BS, Brown CC (2007) Detection of Newcastle disease virus RNA by reverse transcription-polymerase chain reaction using formalin-fixed, paraffin-embedded tissue and comparison with immunohistochemistry and in situ hybridization. J Vet Diagn Invest 19(4):396–400

    Article  PubMed  Google Scholar 

  14. Klopfleisch R, Weiss AT, Gruber AD (2011) Excavation of a buried treasure–DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. Histol Histopathol 26(6):797–810

    CAS  PubMed  Google Scholar 

  15. Perozo F, Villegas P, Estevez C, Alvarado I, Purvis LB (2006) Use of FTA® filter paper for the molecular detection of Newcastle disease virus. Avian Pathol 35(02):93–98

    Article  CAS  PubMed  Google Scholar 

  16. Wakamatsu N, King D, Kapczynski D, Seal B, Brown C (2006) Experimental pathogenesis for chickens, turkeys, and pigeons of exotic Newcastle disease virus from an outbreak in California during 2002-2003. Vet Pathol 43(6):925–933

    Article  CAS  PubMed  Google Scholar 

  17. Boheemen S, Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Osterhaus AD, Haagmans BL, Gorbalenya AE, Snijder EJ et al (2012) Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mBio 3(6):e00473

    PubMed  PubMed Central  Google Scholar 

  18. Carrick DM, Mehaffey MG, Sachs MC, Altekruse S, Camalier C, Chuaqui R, Cozen W, Das B, Hernandez BY, Lih CJ et al (2015) Robustness of next generation sequencing on older formalin-fixed paraffin-embedded tissue. PLoS ONE 10(7):e0127353

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Bodewes R, van Run PR, Schurch AC, Koopmans MP, Osterhaus AD, Baumgartner W, Kuiken T, Smits SL (2015) Virus characterization and discovery in formalin-fixed paraffin-embedded tissues. J Virol Methods 214:54–59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Mubemba B, Thompson PN, Odendaal L, Coetzee P, Venter EH (2017) Evaluation of positive Rift Valley fever virus formalin-fixed paraffin embedded samples as a source of sequence data for retrospective phylogenetic analysis. J Virol Methods 243:10–14

    Article  CAS  PubMed  Google Scholar 

  21. Xiao YL, Kash JC, Beres SB, Sheng ZM, Musser JM, Taubenberger JK (2013) High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic. J Pathol 229(4):535–545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. He Y, Taylor TL, Dimitrov KM, Butt SL, Stanton JB, Goraichuk IV, Fenton H, Poulson R, Zhang J, Brown CC (2018) Whole-genome sequencing of genotype VI Newcastle disease viruses from formalin-fixed paraffin-embedded tissues from wild pigeons reveals continuous evolution and previously unrecognized genetic diversity in the US. Virol J 15(1):9

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Mayahi V, Esmaelizad M (2017) Molecular evolution and epidemiological links study of Newcastle disease virus isolates from 1995 to 2016 in Iran. Arch Virol 162(12):3727–3743

    Article  CAS  PubMed  Google Scholar 

  24. Esmaelizad M, Mayahi V, Pashaei M, Goudarzi H (2017) Identification of novel Newcastle disease virus sub-genotype VII-(j) based on the fusion protein. Arch Virol 162(4):971–978

    Article  CAS  PubMed  Google Scholar 

  25. Bancroft JD, Gamble M (2008) Theory and practice of histological techniques. Elsevier, Amsterdam

    Google Scholar 

  26. Susta L, Miller PJ, Afonso CL, Brown CC (2011) Clinicopathological characterization in poultry of three strains of Newcastle disease virus isolated from recent outbreaks. Vet Pathol 48(2):349–360

    Article  CAS  PubMed  Google Scholar 

  27. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data

  28. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12

    Article  Google Scholar 

  29. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997

  30. Zhang J, Kobert K, Flouri T, Stamatakis A (2013) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30(5):614–620

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, Charbonneau A, Constantinides B, Edvenson G, Fay S (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Research 4

  32. Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information. In: German conference on bioinformatics. Hanover, Germany, pp 45–56

  33. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101(30):11030–11035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3):512–526

    CAS  PubMed  Google Scholar 

  37. Courtney SC, Susta L, Gomez D, Hines NL, Pedersen JC, Brown CC, Miller PJ, Afonso CL (2013) Highly divergent virulent isolates of Newcastle disease virus from the Dominican Republic are members of a new genotype that may have evolved unnoticed for over 2 decades. J Clin Microbiol 51(2):508–517

    Article  PubMed  PubMed Central  Google Scholar 

  38. Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol 9(4):678–687

    CAS  PubMed  Google Scholar 

  39. Dortmans JC, Koch G, Rottier PJ, Peeters BP (2011) Virulence of Newcastle disease virus: what is known so far? Vet Res 42(1):122

    Article  PubMed  PubMed Central  Google Scholar 

  40. Rehmani SF, Wajid A, Bibi T, Nazir B, Mukhtar N, Hussain A, Lone NA, Yaqub T, Afonso CL (2015) Presence of virulent Newcastle disease virus in vaccinated chickens in farms in Pakistan. J Clin Microbiol 53(5):1715–1718

    Article  PubMed  PubMed Central  Google Scholar 

  41. Miller PJ, Haddas R, Simanov L, Lublin A, Rehmani SF, Wajid A, Bibi T, Khan TA, Yaqub T, Setiyaningsih S et al (2015) Identification of new sub-genotypes of virulent Newcastle disease virus with potential panzootic features. Infect Genet Evol 29:216–229

    Article  PubMed  Google Scholar 

  42. Wajid A, Dimitrov KM, Wasim M, Rehmani SF, Basharat A, Bibi T, Arif S, Yaqub T, Tayyab M, Ababneh M et al (2017) Repeated isolation of virulent Newcastle disease viruses in poultry and captive non-poultry avian species in Pakistan from 2011 to 2016. Prev Vet Med 142:1–6

    Article  PubMed  Google Scholar 

  43. Dimitrov KM, Lee D-H, Williams-Coplin D, Olivier TL, Miller PJ, Afonso CL (2016) Newcastle disease viruses causing recent outbreaks worldwide show unexpectedly high genetic similarity to historical virulent isolates from the 1940s. J Clin Microbiol 54(5):1228–1235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Barbezange C, Jestin V (2002) Development of a RT-nested PCR test detecting pigeon Paramyxovirus-1 directly from organs of infected animals. J Virol Methods 106(2):197–207

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Poonam Sharma, Jeremy D. Volkening, and Dawn Williams-Coplin for their technical support during the study. 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. The USDA is an equal opportunity provider and employer.

Funding

This work was supported by the U.S. Department of Agriculture ARS CRIS 6040-32000-072 and the U.S. Department of State BEP/CRDF NDV 31063. Dr. Salman Latif Butt is conducting his PhD research program sponsored by the Fulbright U.S. Student Program.

Author information

Authors and Affiliations

  1. Southeast Poultry Research Laboratory, Exotic and Emerging Avian Viral Diseases Research Unit, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA, USA

    Salman Latif Butt, Kiril M. Dimitrov & Claudio L. Afonso

  2. Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA

    Salman Latif Butt, Jian Zhang, Corrie C. Brown & James B. Stanton

  3. Department of Biotechnology, Virtual University of Pakistan, Lahore, Pakistan

    Abdul Wajid

  4. Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Lahore, Pakistan

    Tasra Bibi, Asma Basharat & Shafqat F. Rehmani

Authors
  1. Salman Latif Butt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kiril M. Dimitrov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jian Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Abdul Wajid
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tasra Bibi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Asma Basharat
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Corrie C. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Shafqat F. Rehmani
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. James B. Stanton
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Claudio L. Afonso
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SLB prepared NGS libraries, performed NGS data analysis, and drafted the manuscript; KMD contributed in NGS data analysis and helped in phylogenetic analysis; JZ conducted IHC; AW, TS, and AB collected clinical tissue samples during disease outbreak and processed for transportation; CCB aided in experimental design and contributed to the drafting of the manuscript; SFR aided in sample collection during disease outbreaks; JBS and CLA designed and oversaw the tissue-based experiments, and aided with analysis of results and with writing of the manuscript.

Corresponding authors

Correspondence to James B. Stanton or Claudio L. Afonso.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving human participants and/or animals

No human subjects were used in this study. This article does not contain any studies with animals performed by any of the authors. Tissues were collected from dead birds being used for diagnostic purposes during disease outbreaks. Sampling was carried out by veterinarian, who took different samples as part of his routine work and under the permission of the farm owner. Since these are diagnostic specimens, sampling did not require the approval of the Ethics Committee.

Additional information

Edited by William Dundon.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

11262_2019_1669_MOESM1_ESM.tif

Supplementary material 1 Fig. S1 A–D: Photomicrographs demonstrating NDV nucleoprotein immunostaining within formalin-fixed paraffin-embedded tissue sections from chicken. Black arrows showing granular staining of viral nucleoprotein in the cytoplasm of cells. A) Brain. B) Spleen. C) Small intestine. D) Lung. Bar = 50 µm. (TIFF 7134 kb)

Supplementary material 2 (DOCX 19 kb)

Supplementary material 3 (DOCX 18 kb)

Supplementary material 4 (DOCX 17 kb)

Supplementary material 5 (DOCX 15 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Butt, S.L., Dimitrov, K.M., Zhang, J. et al. Enhanced phylogenetic resolution of Newcastle disease outbreaks using complete viral genome sequences from formalin-fixed paraffin-embedded tissue samples. Virus Genes 55, 502–512 (2019). https://doi.org/10.1007/s11262-019-01669-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-019-01669-9

Keywords

Search

Navigation