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

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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.

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References

  1. Amarasinghe GK, Bao Y, Basler CF, Bavari S, Beer M, Bejerman N, Blasdell KR, Bochnowski A, Briese T, Bukreyev A, Calisher CH, Chandran K, Collins PL, Dietzgen RG, Dolnik O, Durrwald R, Dye JM, Easton AJ, Ebihara H, Fang Q, Formenty P, Fouchier RA, Ghedin E, Harding RM, Hewson R, Higgins CM, Hong J, Horie M, James AP, Jiang D, Kobinger GP, Kondo H, Kurath G, Kurath G, Lamb RA, Lee B, Leroy EM, Li M, Maisner A, Muhlberger E, Netesov SV, Nowotny N, Patterson JL, Payne SL, Paweska JT, Pearson MN, Randall RE, Revill PA, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Smither SJ, Song Q, Stone DM, Takada A, Terregino C, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang B, Wang D, Wang F, Wang LF, Werren JH, Whitfield AE, Yan Z, Ye G, Kuhn JH (2017) Taxonomy of the order Mononegavirales: update 2017. Arch Virol. https://doi.org/10.1007/s00705-017-3311-7

    Article  PubMed  PubMed Central  Google Scholar 

  2. Lamb RA, Parks G (2013) Paramyxoviridae. In: Knipe DM, Howley PM (eds) Fields virology. Lippincott Williams & Wilkins, Philadelphia, pp 957–995

    Google Scholar 

  3. Miller PJ, Koch G (2013) Newcastle disease. In: Swayne D (ed) Diseases of poultry. Wiley, Ames, IA, pp. 89–107; 120–130

  4. Czegledi A, Ujvari D, Somogyi E, Wehmann E, Werner O, Lomniczi B (2006) Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications. Virus Res 120:36–48. https://doi.org/10.1016/j.virusres.2005.11.009

    Article  CAS  PubMed  Google Scholar 

  5. 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 12:1770–1779. https://doi.org/10.1016/j.meegid.2012.07.012

    Article  PubMed  Google Scholar 

  6. de Almeida RS, Hammoumi S, Gil P, Briand FX, Molia S, Gaidet N, Cappelle J, Chevalier V, Balanca G, Traore A, Grillet C, Maminiaina OF, Guendouz S, Dakouo M, Samake K, Bezeid Oel M, Diarra A, Chaka H, Goutard F, Thompson P, Martinez D, Jestin V, Albina E (2013) New avian paramyxoviruses type I strains identified in Africa provide new outcomes for phylogeny reconstruction and genotype classification. PLoS ONE 8:e76413. https://doi.org/10.1371/journal.pone.0076413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Snoeck CJ, Owoade AA, Couacy-Hymann E, Alkali BR, Okwen MP, Adeyanju AT, Komoyo GF, Nakoune E, Le Faou A, Muller CP (2013) High genetic diversity of newcastle disease virus in poultry in West and Central Africa: cocirculation of genotype XIV and newly defined genotypes XVII and XVIII. J Clin Microbiol 51:2250–2260. https://doi.org/10.1128/Jcm.00684-13

    Article  PubMed  PubMed Central  Google Scholar 

  8. 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 39:22–34. https://doi.org/10.1016/j.meegid.2016.01.008

    Article  PubMed  Google Scholar 

  9. Villegas P (1998) Viral diseases of the respiratory system. Poult Sci 77:1143–1145. https://doi.org/10.1093/ps/77.8.1143

    Article  CAS  PubMed  Google Scholar 

  10. OIE (2018) Detailed country (ies) disease incidence. http://www.oie.int/wahis_2/public/wahid.php/Diseaseinformation/statusdetail

  11. Cardenas Garcia S, Navarro Lopez R, Morales R, Olvera MA, Marquez MA, Merino R, Miller PJ, Afonso CL (2013) Molecular epidemiology of Newcastle disease in Mexico and the potential spillover of viruses from poultry into wild bird species. Appl Environ Microbiol 79:4985–4992. https://doi.org/10.1128/AEM.00993-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. 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 51:508–517. https://doi.org/10.1128/JCM.02393-12

    Article  PubMed  PubMed Central  Google Scholar 

  13. Absalon AE, Mariano-Matias A, Garcia LJ, Morales-Garzon A, Toscano-Contreras A, Lucio-Decanini E, Cortes-Espinosa DV (2014) Complete genome analysis of velogenic Newcastle disease virus reference strain “Chimalhuacan”: evolution of viral lineages in Mexico. Virus Genes 49:233–236. https://doi.org/10.1007/s11262-014-1082-8

    Article  CAS  PubMed  Google Scholar 

  14. Fernandes CC, Varani AM, Lemos EG, de Miranda VF, Silva KR, Fernando FS, Montassier MF, Montassier HJ (2014) Molecular and phylogenetic characterization based on the complete genome of a virulent pathotype of Newcastle disease virus isolated in the 1970s in Brazil. Infect Genet Evol. https://doi.org/10.1016/j.meegid.2014.05.014

    Article  PubMed  Google Scholar 

  15. Walker JW, Heron BR, Mixon MA (1973) Exotic Newcastle disease eradication program in the United States. Avian Diseases 17:486–503

    Article  CAS  PubMed  Google Scholar 

  16. Pedersen JC, Senne DA, Woolcock PR, Kinde H, King DJ, Wise MG, Panigrahy B, Seal BS (2004) Phylogenetic relationships among virulent Newcastle disease virus isolates from the 2002-2003 outbreak in California and other recent outbreaks in North America. J Clin Microbiol 42:2329–2334. https://doi.org/10.1128/Jcm.42.5.2329-2334.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Perozo F, Merino R, Afonso CL, Villegas P, Calderon N (2008) Biological and phylogenetic characterization of virulent Newcastle disease virus circulating in Mexico. Avian Dis 52:472–479. https://doi.org/10.1637/8276-022908-Reg.1

    Article  CAS  PubMed  Google Scholar 

  18. Xiao S, Paldurai A, Nayak B, Mirande A, Collins PL, Samal SK (2013) Complete genome sequence of a highly virulent newcastle disease virus currently circulating in Mexico. Genome Announc 1:e00177-00112. https://doi.org/10.1128/genomeA.00177-12

    Article  Google Scholar 

  19. Absalon AE, Mariano-Matias A, Vasquez-Marquez A, Morales-Garzon A, Cortes-Espinosa DV, Ortega-Garcia R, Lucio-Decanini E (2012) Complete genome sequence of a velogenic Newcastle disease virus isolated in Mexico. Virus Genes 45:304–310. https://doi.org/10.1007/s11262-012-0782-1

    Article  CAS  PubMed  Google Scholar 

  20. SAGARPA SdA, Ganadería, Desarrollo Rural, Pesca y Alimentación (2016) Acuerdo mediante el cual se enlistan las enfermedades y plagas de los animales, exóticas y endémicas de notificación obligatoria en los Estados Unidos Mexicanos. Diario Oficial 4 de mayo de 2016.

  21. Ayala AJ, Dimitrov KM, Becker CR, Goraichuk IV, Arns CW, Bolotin VI, Ferreira HL, Gerilovych AP, Goujgoulova GV, Martini MC, Muzyka DV, Orsi MA, Scagion GP, Silva RK, Solodiankin OS, Stegnigy BT, Miller PJ, Afonso CL (2016) Presence of Live Newcastle Disease Vaccines in Wild Birds. PLoS One. https://doi.org/10.1371/journal.pone.0162484

    Article  PubMed  PubMed Central  Google Scholar 

  22. Devlin JM, Vaz PK, Coppo MJ, Browning GF (2016) Impacts of poultry vaccination on viruses of wild bird. Curr Opin Virol 19:23–29. https://doi.org/10.1016/j.coviro.2016.06.007

    Article  PubMed  Google Scholar 

  23. Kaleta EF, Alexander DJ, Russell PH (1985) The first isolation of the avian PMV-1 virus responsible for the current panzootic in pigeons ? Avian Pathol 14:553–557. https://doi.org/10.1080/03079458508436258

    Article  CAS  PubMed  Google Scholar 

  24. He Y, Taylor TL, Dimitrov KM, Butt SL, Stanton JB, Goraichuk IV, Fenton H, Poulson R, Zhang J, Brown CC, Ip HS, Isidoro-Ayza M, Afonso CL (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 U.S. Virol J. https://doi.org/10.1186/s12985-017-0914-2

    Article  PubMed  PubMed Central  Google Scholar 

  25. Alexander DJ (2011) Newcastle disease in the European Union 2000 to 2009. Avian Pathol 40:547–558. https://doi.org/10.1080/03079457.2011.618823

    Article  PubMed  Google Scholar 

  26. Chong YL, Lam TT, Kim O, Lu H, Dunn P, Poss M (2013) Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission. Infect Genet Evol 17:260–268. https://doi.org/10.1016/j.meegid.2013.04.025

    Article  PubMed  Google Scholar 

  27. Souza S, Fredo G, Dupont P, Leite-Filho R, Pavarini SC, Canal C, Driemeier D (2018) Pathological and molecular findings of avian avulavirus Type 1 outbreak in pigeons (Columba livia) of southern Brazil. Pesq Vet Bras. https://doi.org/10.1590/1678-5150-pvb-5528

    Article  Google Scholar 

  28. Zanetti F, Mattiello R, Garbino C, Kaloghlian A, Terrera MV, Boviez J, Palma E, Carrillo E, Berinstein A (2001) Biological and molecular characterization of a pigeon paramyxovirus type-1 isolate found in Argentina. Avian Dis 45:567–571. https://doi.org/10.2307/1592896

    Article  CAS  PubMed  Google Scholar 

  29. Castro ER, Zanetti F, Arbiza J (2012) Genetic characterization of a pigeon paramyxovirus type 1 isolated from Columba livia in Uruguay. Avian Dis 56:243–248. https://doi.org/10.1637/9835-061611-Case.1

    Article  CAS  PubMed  Google Scholar 

  30. Dortmans JC, Rottier PJ, Koch G, Peeters BP (2011) Passaging of a Newcastle disease virus pigeon variant in chickens results in selection of viruses with mutations in the polymerase complex enhancing virus replication and virulence. J Gen Virol 92:336–345. https://doi.org/10.1099/vir.0.026344-0

    Article  CAS  PubMed  Google Scholar 

  31. Dortmans JCFM, Koch G, Rottier PJM, Peeters BPH (2009) Virulence of pigeon paramyxovirus type 1 does not always correlate with the cleavability of its fusion protein. J Gen Virol 90:2746–2750. https://doi.org/10.1099/vir.0.014118-0

    Article  CAS  PubMed  Google Scholar 

  32. Dortmans JCFM, Rottier PJM, Koch G, Peeters BPH (2010) The viral replication complex is associated with the virulence of Newcastle disease virus. J Virol 84:10113–10120. https://doi.org/10.1128/Jvi.00097-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Munir M, Linde AM, Zohari S, Stahl K, Baule C, Engstrom B, M Renström LH, Berg M (2011) Whole genome sequencing and characterization of a virulent Newcastle disease virus isolated from an outbreak in Sweden. Virus Genes 43:261–271. https://doi.org/10.1007/s11262-011-0636-2

    Article  CAS  PubMed  Google Scholar 

  34. Hanson RP, Spalatin J, Jacobson GS (1973) The viscerotropic pathotype of Newcastle disease virus. Avian Dis 17:354–361. https://doi.org/10.2307/1589219

    Article  CAS  PubMed  Google Scholar 

  35. Alexander DJ, Wilson GW, Russell PH, Lister SA, Parsons G (1985) Newcastle disease outbreaks in fowl in Great Britain during 1984. Vet Rec 117:429–434

    Article  CAS  PubMed  Google Scholar 

  36. Damena D, Fusaro A, Sombo M, Belaineh R, Heidari A, Kebede A, Kidane M, Chaka H (2016) Characterization of Newcastle disease virus isolates obtained from outbreak cases in commercial chickens and wild pigeons in Ethiopia. Springerplus 5:476. https://doi.org/10.1186/s40064-016-2114-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Wise MG, Suarez DL, Seal BS, Pedersen JC, Senne DA, King DJ, Kapczynski DR, Spackman E (2004) Development of a real-time reverse-transcription PCR for detection of newcastle disease virus RNA in clinical samples. J Clin Microbiol 42:329–338. https://doi.org/10.1128/JCM.42.1.329-338.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Butt SL, Taylor TL, Volkening JD, Dimitrov KM, Williams-Coplin D, Lahmers KK, Rana AM, Miller PJ, Suarez DL, Afonso CL, Stanton JB (2018) Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing. Virol J. https://doi.org/10.1101/349159

    Article  PubMed  PubMed Central  Google Scholar 

  39. Dimitrov KM, Sharma P, Volkening JD, Goraichuk IV, Wajid A, Rehmani SF, Basharat A, Shittu I, Joannis TM, Miller PJ, Afonso CL (2017) A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses. Virol J 14:72. https://doi.org/10.1186/s12985-017-0741-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030–11035. https://doi.org/10.1073/pnas.0404206101

    Article  CAS  PubMed  Google Scholar 

  41. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  CAS  Google Scholar 

  42. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York

    Google Scholar 

  43. OIE (2012) Newcastle Disease (infection with Newcastle disease virus). In: OIE (ed) Manual of diagnostic tests and vaccines for terrestrial animals: mammals, birds and bees. Biological Standards Commission, World Organization for Animal Health, Paris, pp 555–574

    Google Scholar 

  44. Merino R, Villegas H, Quintana JA, Calderon N (2009) Characterization of Newcastle disease viruses isolated from chicken, gamefowl, pigeon and quail in Mexico. Vet Res Commun 33:1023–1030. https://doi.org/10.1007/s11259-009-9321-5

    Article  PubMed  Google Scholar 

  45. Sabra M, Dimitrov KM, Goraichuk IV, Wajid A, Sharma P, Williams-Coplin D, Basharat A, Rehmani SF, Muzyka DV, Miller PJ, Afonso CL (2017) Phylogenetic assessment reveals continuous evolution and circulation of pigeon-derived virulent avian avulaviruses 1 in Eastern Europe, Asia, and Africa. BMC Vet Res 13:291. https://doi.org/10.1186/s12917-017-1211-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Aldous EW, Fuller CM, Ridgeon JH, Irvine RM, Alexander DJ, Brown IH (2014) The evolution of pigeon paramyxovirus type 1 (PPMV-1) in Great Britain: a molecular epidemiological study. Transbound Emerg Dis 61:134–139. https://doi.org/10.1111/tbed.12006

    Article  CAS  PubMed  Google Scholar 

  47. Alexander DJ, Parsons G, Marshall R (1984) Infection of fowls with Newcastle disease virus by food contaminated with pigeon faeces. Vet Rec 115:601–602

    Article  CAS  PubMed  Google Scholar 

  48. Abolnik C, Gerdes GH, Kitching J, Swanepoel S, Romito M, Bisschop SP (2008) Characterization of pigeon paramyxoviruses (Newcastle disease virus) isolated in South Africa from 2001 to 2006. Onderstepoort J Vet Res 75:147–152. https://doi.org/10.4102/ojvr.v75i2.13

    Article  CAS  PubMed  Google Scholar 

  49. Gardy J, Loman NJ, Rambaut A (2015) Real-time digital pathogen surveillance - the time is now. Genome Biol 16:155. https://doi.org/10.1186/s13059-015-0726-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Boza V, Brejova B, Vinar T (2017) DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLoS ONE 12:e0178751. https://doi.org/10.1371/journal.pone.0178751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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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.

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.

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Author notes

  1. H. L. Ferreira and T. L. Taylor have contributed equally to this work.

Authors and Affiliations

  1. Southeast Poultry Research Laboratory, US National Poultry Research Center, 934 College Station Rd, Athens, GA, 30605, USA

    H. L. Ferreira, T. L. Taylor, K. M. Dimitrov, S. L. Butt, I. V. Goraichuk, D. L. Suarez & C. L. Afonso

  2. University of Sao Paulo, ZMV- FZEA, Pirassununga, 13635900, Brazil

    H. L. Ferreira

  3. Vaxbiotek S.C, San Lorenzo No. 122-7, CP. 72700, Cuautlancingo, Puebla, Mexico

    A. E. Absalon

  4. Instituto Politécnico Nacional/CIBA-Tlaxcala, Carr. Est. Santa Ines Tecuexcomac Km 1.5, Tepetitla, Tlaxcala, Mexico

    D. V. Cortés-Espinosa

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

    S. L. Butt

  6. Consorcio consultivo empresarial S.C., Lasallistas No. 120 Col. Rosario, San Juan De Los Lagos, Jalisco, Mexico

    J. L. Marín-Cruz

  7. National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83, Pushkinska Street, Kharkiv, 61023, Ukraine

    I. V. Goraichuk

  8. BASE2BIO, 1945, Arlington Drive, Oshkosh, WI, 54904, USA

    J. D. Volkening

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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.

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Correspondence to C. L. Afonso.

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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.

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11262_2019_1663_MOESM1_ESM.pdf

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

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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Ferreira, H.L., Taylor, T.L., Absalon, A.E. et al. Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017. Virus Genes 55, 479–489 (2019). https://doi.org/10.1007/s11262-019-01663-1

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