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Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology.

Taylor TL, Volkening JD, DeJesus E, Simmons M, Dimitrov KM, Tillman GE, Suarez DL, Afonso CL.

Sci Rep. 2019 Nov 8;9(1):16350. doi: 10.1038/s41598-019-52424-x.


Pathobiology and innate immune responses of gallinaceous poultry to clade H5Nx highly pathogenic avian influenza virus infection.

Bertran K, Pantin-Jackwood MJ, Criado MF, Lee DH, Balzli CL, Spackman E, Suarez DL, Swayne DE.

Vet Res. 2019 Nov 1;50(1):89. doi: 10.1186/s13567-019-0704-5.


Biosafety risk assessment for production of candidate vaccine viruses to protect humans from zoonotic highly pathogenic avian influenza viruses.

Chen LM, Donis RO, Suarez DL, Wentworth DE, Webby R, Engelhardt OG, Swayne DE.

Influenza Other Respir Viruses. 2019 Oct 28. doi: 10.1111/irv.12698. [Epub ahead of print]


Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets.

Kariithi HM, Welch CN, Ferreira HL, Pusch EA, Ateya LO, Binepal YS, Apopo AA, Dulu TD, Afonso CL, Suarez DL.

Infect Genet Evol. 2019 Oct 18:104074. doi: 10.1016/j.meegid.2019.104074. [Epub ahead of print]


Rapid evolution of Mexican H7N3 highly pathogenic avian influenza viruses in poultry.

Youk S, Lee DH, Ferreira HL, Afonso CL, Absalon AE, Swayne DE, Suarez DL, Pantin-Jackwood MJ.

PLoS One. 2019 Sep 12;14(9):e0222457. doi: 10.1371/journal.pone.0222457. eCollection 2019.


First Complete Genome Sequence of Currently Circulating Infectious Bronchitis Virus Strain DMV/1639 of the GI-17 Lineage.

Goraichuk IV, Kulkarni AB, Williams-Coplin D, Suarez DL, Afonso CL.

Microbiol Resour Announc. 2019 Aug 22;8(34). pii: e00840-19. doi: 10.1128/MRA.00840-19.


Virulent Newcastle disease viruses from chicken origin are more pathogenic and transmissible to chickens than viruses normally maintained in wild birds.

Ferreira HL, Taylor TL, Dimitrov KM, Sabra M, Afonso CL, Suarez DL.

Vet Microbiol. 2019 Aug;235:25-34. doi: 10.1016/j.vetmic.2019.06.004. Epub 2019 Jun 5.


First Complete Genome Sequence of a Subgenotype Vd Newcastle Disease Virus Isolate.

Goraichuk IV, Msoffe PLM, Chiwanga GH, Dimitrov KM, Afonso CL, Suarez DL.

Microbiol Resour Announc. 2019 Jul 3;8(27). pii: e00436-19. doi: 10.1128/MRA.00436-19.


Efficacy of Two Licensed Avian Influenza H5 Vaccines Against Challenge with a 2015 U.S. H5N2 clade Highly Pathogenic Avian Influenza Virus in Domestic Ducks.

Pantin-Jackwood MJ, DeJesus E, Costa-Hurtado M, Smith D, Chrzastek K, Kapczynski DR, Suarez DL.

Avian Dis. 2019 Mar 1;63(1):90-96. doi: 10.1637/11895-050918-Reg.1.


Armoured exogenous internal control for real-time PCR diagnosis of avian influenza.

Andreychuk DB, Andriyasov AV, Nikonova ZB, Kozlov АА, Suarez DL, Chvala IA.

Avian Pathol. 2019 Oct;48(5):492-498. doi: 10.1080/03079457.2019.1628918. Epub 2019 Jul 8.


Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus.

Dimitrov KM, Abolnik C, Afonso CL, Albina E, Bahl J, Berg M, Briand FX, Brown IH, Choi KS, Chvala I, Diel DG, Durr PA, Ferreira HL, Fusaro A, Gil P, Goujgoulova GV, Grund C, Hicks JT, Joannis TM, Torchetti MK, Kolosov S, Lambrecht B, Lewis NS, Liu H, Liu H, McCullough S, Miller PJ, Monne I, Muller CP, Munir M, Reischak D, Sabra M, Samal SK, Servan de Almeida R, Shittu I, Snoeck CJ, Suarez DL, Van Borm S, Wang Z, Wong FYK.

Infect Genet Evol. 2019 Oct;74:103917. doi: 10.1016/j.meegid.2019.103917. Epub 2019 Jun 11.


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

Ferreira HL, Taylor TL, Absalon AE, Dimitrov KM, Cortés-Espinosa DV, Butt SL, Marín-Cruz JL, Goraichuk IV, Volkening JD, Suarez DL, Afonso CL.

Virus Genes. 2019 Aug;55(4):479-489. doi: 10.1007/s11262-019-01663-1. Epub 2019 Apr 12.


Age-dependent pathogenesis of clade H5N2 HPAIV in experimentally infected Broad Breasted White turkeys.

Carnaccini S, Santos JJS, Obadan AO, Pantin-Jackwood MJ, Suarez DL, Rajão DS, Perez DR.

Vet Microbiol. 2019 Apr;231:183-190. doi: 10.1016/j.vetmic.2019.03.011. Epub 2019 Mar 12.


Pathogenicity and transmission of virulent Newcastle disease virus from the 2018-2019 California outbreak and related viruses in young and adult chickens.

Dimitrov KM, Ferreira HL, Pantin-Jackwood MJ, Taylor TL, Goraichuk IV, Crossley BM, Killian ML, Bergeson NH, Torchetti MK, Afonso CL, Suarez DL.

Virology. 2019 May;531:203-218. doi: 10.1016/j.virol.2019.03.010. Epub 2019 Mar 22.


First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan.

Ababneh M, Ferreira HL, Khalifeh M, Suarez DL, Afonso CL.

Microbiol Resour Announc. 2018 Dec 13;7(23). pii: e01136-18. doi: 10.1128/MRA.01136-18. eCollection 2018 Dec.


Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing.

Butt SL, Taylor TL, Volkening JD, Dimitrov KM, Williams-Coplin D, Lahmers KK, Miller PJ, Rana AM, Suarez DL, Afonso CL, Stanton JB.

Virol J. 2018 Nov 22;15(1):179. doi: 10.1186/s12985-018-1077-5.


The Multifaceted Zoonotic Risk of H9N2 Avian Influenza.

Pusch EA, Suarez DL.

Vet Sci. 2018 Sep 21;5(4). pii: E82. doi: 10.3390/vetsci5040082. Review.


Attenuation of highly pathogenic avian influenza A(H5N1) viruses in Indonesia following the reassortment and acquisition of genes from low pathogenicity avian influenza A virus progenitors.

Dharmayanti NLPI, Thor SW, Zanders N, Hartawan R, Ratnawati A, Jang Y, Rodriguez M, Suarez DL, Samaan G, Pudjiatmoko, Davis CT.

Emerg Microbes Infect. 2018 Aug 22;7(1):147. doi: 10.1038/s41426-018-0147-5.


Sugar yield and composition of tubers from Jerusalem Artichoke (Helianthus tuberosus) irrigated with saline waters.

Bhagia S, Ferreira JFS, Kothari N, Nunez A, Liu X, da Silva Dias N, Suarez DL, Kumar R, Wyman CE.

Biotechnol Bioeng. 2018 Jun;115(6):1475-1484. doi: 10.1002/bit.26582. Epub 2018 Mar 15.


Molecular characterization and expression analysis of the Na+/H+ exchanger gene family in Medicago truncatula.

Sandhu D, Pudussery MV, Kaundal R, Suarez DL, Kaundal A, Sekhon RS.

Funct Integr Genomics. 2018 Mar;18(2):141-153. doi: 10.1007/s10142-017-0581-9. Epub 2017 Dec 26.


Characterization of a Feline Influenza A(H7N2) Virus.

Hatta M, Zhong G, Gao Y, Nakajima N, Fan S, Chiba S, Deering KM, Ito M, Imai M, Kiso M, Nakatsu S, Lopes TJ, Thompson AJ, McBride R, Suarez DL, Macken CA, Sugita S, Neumann G, Hasegawa H, Paulson JC, Toohey-Kurth KL, Kawaoka Y.

Emerg Infect Dis. 2018 Jan;24(1):75-86. doi: 10.3201/eid2401.171240.


Impact of treated wastewater for irrigation on soil microbial communities.

Ibekwe AM, Gonzalez-Rubio A, Suarez DL.

Sci Total Environ. 2018 May 1;622-623:1603-1610. doi: 10.1016/j.scitotenv.2017.10.039. Epub 2017 Oct 18.


Protection of commercial turkeys following inactivated or recombinant H5 vaccine application against the 2015U.S. H5N2 clade highly pathogenic avian influenza virus.

Kapczynski DR, Sylte MJ, Killian ML, Torchetti MK, Chrzastek K, Suarez DL.

Vet Immunol Immunopathol. 2017 Sep;191:74-79. doi: 10.1016/j.vetimm.2017.08.001. Epub 2017 Aug 10.


Short- and long-term protective efficacy against clade H5N2 highly pathogenic avian influenza virus following prime-boost vaccination in turkeys.

Santos JJS, Obadan AO, Garcia SC, Carnaccini S, Kapczynski DR, Pantin-Jackwood M, Suarez DL, Perez DR.

Vaccine. 2017 Oct 9;35(42):5637-5643. doi: 10.1016/j.vaccine.2017.08.059. Epub 2017 Sep 6.


Pathobiology of Clade H5Nx High-Pathogenicity Avian Influenza Virus Infections in Minor Gallinaceous Poultry Supports Early Backyard Flock Introductions in the Western United States in 2014-2015.

Bertran K, Lee DH, Pantin-Jackwood MJ, Spackman E, Balzli C, Suarez DL, Swayne DE.

J Virol. 2017 Oct 13;91(21). pii: e00960-17. doi: 10.1128/JVI.00960-17. Print 2017 Nov 1.


Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses.

Chrzastek K, Lee DH, Smith D, Sharma P, Suarez DL, Pantin-Jackwood M, Kapczynski DR.

Virology. 2017 Sep;509:159-166. doi: 10.1016/j.virol.2017.06.019. Epub 2017 Jun 21.


First Detection of Avian Lineage H7N2 in Felis catus.

Newbury SP, Cigel F, Killian ML, Leutenegger CM, Seguin MA, Crossley B, Brennen R, Suarez DL, Torchetti M, Toohey-Kurth K.

Genome Announc. 2017 Jun 8;5(23). pii: e00457-17. doi: 10.1128/genomeA.00457-17.


Complete Genome Sequences of Four Avian Paramyxoviruses of Serotype 10 Isolated from Rockhopper Penguins on the Falkland Islands.

Goraichuk IV, Dimitrov KM, Sharma P, Miller PJ, Swayne DE, Suarez DL, Afonso CL.

Genome Announc. 2017 Jun 1;5(22). pii: e00472-17. doi: 10.1128/genomeA.00472-17.


Protection of White Leghorn chickens by U.S. emergency H5 vaccination against clade H5N2 high pathogenicity avian influenza virus.

Bertran K, Balzli C, Lee DH, Suarez DL, Kapczynski DR, Swayne DE.

Vaccine. 2017 Nov 1;35(46):6336-6344. doi: 10.1016/j.vaccine.2017.05.051. Epub 2017 May 26.


Homologous and heterologous antigenic matched vaccines containing different H5 hemagglutinins provide variable protection of chickens from the 2014 U.S. H5N8 and H5N2 clade highly pathogenic avian influenza viruses.

Kapczynski DR, Pantin-Jackwood MJ, Spackman E, Chrzastek K, Suarez DL, Swayne DE.

Vaccine. 2017 Nov 1;35(46):6345-6353. doi: 10.1016/j.vaccine.2017.04.042. Epub 2017 Apr 26.


Reassortment of Influenza A Viruses in Wild Birds in Alaska before H5 Clade Outbreaks.

Hill NJ, Hussein IT, Davis KR, Ma EJ, Spivey TJ, Ramey AM, Puryear WB, Das SR, Halpin RA, Lin X, Fedorova NB, Suarez DL, Boyce WM, Runstadler JA.

Emerg Infect Dis. 2017 Apr;23(4):654-657. doi: 10.3201/eid2304.161668.


Variable salinity responses of 12 alfalfa genotypes and comparative expression analyses of salt-response genes.

Sandhu D, Cornacchione MV, Ferreira JF, Suarez DL.

Sci Rep. 2017 Feb 22;7:42958. doi: 10.1038/srep42958.


Recombinant viral-vectored vaccines for the control of avian influenza in poultry.

Suarez DL, Pantin-Jackwood MJ.

Vet Microbiol. 2017 Jul;206:144-151. doi: 10.1016/j.vetmic.2016.11.025. Epub 2016 Nov 24. Review.


Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

Mark Ibekwe A, Ors S, Ferreira JFS, Liu X, Suarez DL.

Sci Total Environ. 2017 Feb 1;579:1485-1495. doi: 10.1016/j.scitotenv.2016.11.151. Epub 2016 Dec 1.


H5N2 Highly Pathogenic Avian Influenza Viruses from the US 2014-2015 outbreak have an unusually long pre-clinical period in turkeys.

Spackman E, Pantin-Jackwood MJ, Kapczynski DR, Swayne DE, Suarez DL.

BMC Vet Res. 2016 Nov 22;12(1):260.


Changes in adaptation of H5N2 highly pathogenic avian influenza H5 clade viruses in chickens and mallards.

DeJesus E, Costa-Hurtado M, Smith D, Lee DH, Spackman E, Kapczynski DR, Torchetti MK, Killian ML, Suarez DL, Swayne DE, Pantin-Jackwood MJ.

Virology. 2016 Dec;499:52-64. doi: 10.1016/j.virol.2016.08.036. Epub 2016 Sep 12.


Pathogenicity and Transmission of H5 and H7 Highly Pathogenic Avian Influenza Viruses in Mallards.

Pantin-Jackwood MJ, Costa-Hurtado M, Shepherd E, DeJesus E, Smith D, Spackman E, Kapczynski DR, Suarez DL, Stallknecht DE, Swayne DE.

J Virol. 2016 Oct 14;90(21):9967-9982. doi: 10.1128/JVI.01165-16. Print 2016 Nov 1.


H9N2 low pathogenic avian influenza in Pakistan (2012-2015).

Lee DH, Swayne DE, Sharma P, Rehmani SF, Wajid A, Suarez DL, Afonso C.

Vet Rec Open. 2016 Jun 27;3(1):e000171. doi: 10.1136/vetreco-2016-000171. eCollection 2016.


Histopathologic Characterization and Shedding Dynamics of Guineafowl (Numida meleagris) Intravenously Infected with a H6N2 Low Pathogenicity Avian Influenza Virus.

Dimitrov KM, Zarkov IS, Dinev I, Goujgoulova GV, Miller PJ, Suarez DL.

Avian Dis. 2016 May;60(1 Suppl):279-85. doi: 10.1637/11141-050815-Reg.


Introduction: Ninth International Symposium on Avian Influenza Introduction.

Suarez DL, Pantin-Jackwood M.

Avian Dis. 2016 May;60(1 Suppl):102-3. doi: 10.1637/10000-042216-INT. No abstract available.


Lack of chicken adaptation of newly emergent Eurasian H5N8 and reassortant H5N2 high pathogenicity avian influenza viruses in the U.S. is consistent with restricted poultry outbreaks in the Pacific flyway during 2014-2015.

Bertran K, Swayne DE, Pantin-Jackwood MJ, Kapczynski DR, Spackman E, Suarez DL.

Virology. 2016 Jul;494:190-7. doi: 10.1016/j.virol.2016.04.019. Epub 2016 Apr 26.


Poultry vaccination directed evolution of H9N2 low pathogenicity avian influenza viruses in Korea.

Lee DH, Fusaro A, Song CS, Suarez DL, Swayne DE.

Virology. 2016 Jan 15;488:225-31. doi: 10.1016/j.virol.2015.11.023. Epub 2015 Dec 3.


International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies.

Miller PJ, Dimitrov KM, Williams-Coplin D, Peterson MP, Pantin-Jackwood MJ, Swayne DE, Suarez DL, Afonso CL.

Front Public Health. 2015 Oct 19;3:235. doi: 10.3389/fpubh.2015.00235. eCollection 2015. Review.


Previous infection with virulent strains of Newcastle disease virus reduces highly pathogenic avian influenza virus replication, disease, and mortality in chickens.

Costa-Hurtado M, Afonso CL, Miller PJ, Shepherd E, Cha RM, Smith D, Spackman E, Kapczynski DR, Suarez DL, Swayne DE, Pantin-Jackwood MJ.

Vet Res. 2015 Sep 23;46:97. doi: 10.1186/s13567-015-0237-5.


Impact of route of exposure and challenge dose on the pathogenesis of H7N9 low pathogenicity avian influenza virus in chickens.

Spackman E, Pantin-Jackwood M, Swayne DE, Suarez DL, Kapczynski DR.

Virology. 2015 Mar;477:72-81. doi: 10.1016/j.virol.2015.01.013. Epub 2015 Feb 6.


Antibody titer has positive predictive value for vaccine protection against challenge with natural antigenic-drift variants of H5N1 high-pathogenicity avian influenza viruses from Indonesia.

Swayne DE, Suarez DL, Spackman E, Jadhao S, Dauphin G, Kim-Torchetti M, McGrane J, Weaver J, Daniels P, Wong F, Selleck P, Wiyono A, Indriani R, Yupiana Y, Sawitri Siregar E, Prajitno T, Smith D, Fouchier R.

J Virol. 2015 Apr;89(7):3746-62. doi: 10.1128/JVI.00025-15. Epub 2015 Jan 21.


Potency, efficacy, and antigenic mapping of H7 avian influenza virus vaccines against the 2012 H7N3 highly pathogenic avian influenza virus from Mexico.

Spackman E, Wan XF, Kapczynski D, Xu Y, Pantin-Jackwood M, Suarez DL, Swayne D.

Avian Dis. 2014 Sep;58(3):359-66.


Improving pandemic influenza risk assessment.

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JD.

Elife. 2014 Oct 16;3:e03883. doi: 10.7554/eLife.03883.


Variation in protection of four divergent avian influenza virus vaccine seed strains against eight clade 2.2.1 and Egyptian H5N1 high pathogenicity variants in poultry.

Spackman E, Swayne DE, Pantin-Jackwood MJ, Wan XF, Torchetti MK, Hassan M, Suarez DL, Sá e Silva M.

Influenza Other Respir Viruses. 2014 Nov;8(6):654-62. doi: 10.1111/irv.12290. Epub 2014 Oct 3.


Role of poultry in the spread of novel H7N9 influenza virus in China.

Pantin-Jackwood MJ, Miller PJ, Spackman E, Swayne DE, Susta L, Costa-Hurtado M, Suarez DL.

J Virol. 2014 May;88(10):5381-90. doi: 10.1128/JVI.03689-13. Epub 2014 Feb 26.

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