Research Project: Intervention Strategies to Predict, Prevent, and Control Emerging Strains of Virulent Newcastle Disease Viruses

Location: Exotic & Emerging Avian Viral Diseases Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Optimization and validation of a universal real-time RT-PCR assay to distinguish between virulent Newcastle disease viruses and viruses of low virulence - (Peer Reviewed Journal)
Alexander Morris, E., Schroeder, M.E., Anderson, P.N., Schroeder, L.J., Monday, N., Gabriel, S., Ficken, M., Ferro, P.J., Suarez, D.L., Dimitrov, K.M. 2025. Optimization and validation of a universal real-time RT-PCR assay to distinguish between virulent Newcastle disease viruses and viruses of low virulence. Viruses. Viruses 2025, 17(5), 670. https://doi.org/10.3390/v17050670.

Nanopore Sequencing in Veterinary Medicine: From Concepts to Clinical Application - (Review Article)
Chaves, M., Hashish, A., Goraichuk, I., Caserta, L.C., Mears, M.C., Gadu, E., Bakre, A.A., Alexander, M.E., Shelkamy, M.M., Nadendla, S., El-Gazzar, M. 2025. Nanopore Sequencing in Veterinary Medicine: From Concepts to Clinical Application. Frontiers in Cellular and Infection Microbiology. 15:1545032. https://doi.org/10.3389/fcimb.2025.1545032.

Age-based host response to turkey arthritis reovirus in commercial turkeys in the presence of maternally derived antibodies - (Peer Reviewed Journal)
Khatiwada, S., Ngunjiri, J., Boley, P.A., Yadav, K.K., Ghorbani, A., Abundo, M., Lee, C.M., Poelstra, J., Lee, C.W., Kenney, S.P., Gharaibeh, S., Rajashekara, G. 2025. Age-based host response to turkey arthritis reovirus in commercial turkeys in the presence of maternally derived antibodies. BMC Veterinary Research. https://doi.org/10.1186/s12917-025-04525-1.

Comparison of direct RNA sequencing of Orthoavulavirus javaense using two different chemistries on the MinION platform - (Peer Reviewed Journal)

Characterizing host microRNA: virus interactions of Orthoavulavirus javaense - (Peer Reviewed Journal)
Bakre, A.A., Mears, M.C. 2024. Characterizing host microRNA: virus interactions of Orthoavulavirus javaense. Viruses. 16(11):1748. https://doi.org/10.3390/v16111748.

Evaluation of commercial RNA extraction protocols for Avian Influenza virus using Nanopore metagenomic sequencing - (Peer Reviewed Journal)
Chaves, M., Hashish, A., Osemeke, O., Sato, Y., Suarez, D.L., El-Gazzar, M. 2024. Evaluation of commercial RNA extraction protocols for Avian Influenza virus using Nanopore metagenomic sequencing. Pathogens. Viruses 2024, 16, 1429. https://doi.org/10.3390/v16091429.

Detection and differentiation of low virulence and virulent avian orthoavulavirus javaense using a molecular beacon with RT-LAMP - (Peer Reviewed Journal)
Mears, M.C., Olivier, T.L., Williams Coplin, T.D., Espinoza, E., Bakre, A.A. 2024. Detection and differentiation of low virulence and virulent avian orthoavulavirus javaense using a molecular beacon with RT-LAMP. Scientific Reports. 2024(14):18047. https://doi.org/10.1038/s41598-024-68816-7.

Introduction of avian metapneumovirus subtype A to the United States: molecular insights and implications - (Peer Reviewed Journal)
Goraichuk, I.V., Torchetti, M., Killian, M., Kapczynski, D.R., Kulkarni, A., Sary, K., Suarez, D.L. 2024. Introduction of avian metapneumovirus subtype A to the United States: molecular insights and implications. Frontiers in Microbiology. 15. https://doi.org/10.3389/fmicb.2024.1428248.

Investigating the uses of machine learning algorithms to inform risk factor analyses: the example of avian infectious bronchitis virus (IBV) in boiler chickens - (Peer Reviewed Journal)
Campler, M.R., Cheng, T., Lee, C.W., Hofacre, C.L., Lossie, G., Silva, G.S., El-Gazzar, M.M., Arruda, A.G. 2024. Investigating the uses of machine learning algorithms to inform risk factor analyses: the example of avian infectious bronchitis virus (IBV) in boiler chickens. Research in Veterinary Science. 171(2024):105201. https://doi.org/10.1016/j.rvsc.2024.105201.

The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in illumina and nanopore sequencing - (Peer Reviewed Journal)
Goraichuk, I.V., Harden, M., Spackman, E., Suarez, D.L. 2023. The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in illumina and nanopore sequencing. Frontiers in Microbiology. Volume 15. https://doi.org/10.3389/fmicb.2024.1328987.

TLR3 and MDA5 knockout DF-1 cells enhance replication of avian orthoavulavirus 1 - (Peer Reviewed Journal)
Lee, C.W., Mahesh, K.C., Ngunjiri, J.M., Ghorbani, A., Lee, K. 2023. TLR3 and MDA5 knockout DF-1 cells enhance replication of avian orthoavulavirus 1. Avian Diseases. 67(1):94-101. https://doi.org/10.1637/aviandiseases-D-22-00065.

Toll-like receptor ligands enhance vaccine efficacy against a virulent Newcastle disease virus challenge in chickens - (Peer Reviewed Journal)
Lee, C.W., Bakre, A.A., Olivier, T.L., Alvarez Narvaez, S., Harrell, T.L., Conrad, S.J. 2023. Toll-like receptor ligands enhance vaccine efficacy against a virulent Newcastle disease virus challenge in chickens. Pathogens. 12(10):1230. https://doi.org/10.3390/pathogens12101230.

Virulent Newcastle disease virus genotypes V.3, VII.2 and XIII.1.1 and their coinfections with infectious bronchitis viruses and other avian pathogens in backyard chickens in Tanzania - (Peer Reviewed Journal)
Kariithi, H.M., Volkening, J.D., Chiwanga, G.H., Goraichuk, I.V., Olivier, T.L., Msoffe, P.M., Suarez, D.L. 2023. Virulent Newcastle disease virus genotypes V.3, VII.2 and XIII.1.1 and their coinfections with infectious bronchitis viruses and other avian pathogens in backyard chickens in Tanzania. Frontiers in Veterinary Science. 10:1272402. https://doi.org/10.3389/fvets.2023.1272402.

Molecular characterization of complete genome sequence of an avian coronavirus identified in a backyard chicken from Tanzania - (Peer Reviewed Journal)
Kariithi, H.M., Volkening, J.D., Chiwanga, G.H., Goraichuk, I.V., Msoffe, P.L., Suarez, D.L. 2023. Molecular characterization of complete genome sequence of an avian coronavirus identified in a backyard chicken from Tanzania. Genes. 14(10):1852. https://doi.org/10.3390/genes14101852.

Complete genome sequence of seven virulent Newcastle disease virus isolates of sub-genotype XIII.1.1 from Tanzania - (Peer Reviewed Journal)
Goraichuk, I.V., Msoffe, P.L., Chiwanga, G.H., Dimitrov, K.M., Afonso, C.L., Suarez, D.L. 2023. Complete genome sequence of seven virulent Newcastle disease virus isolates of sub-genotype XIII.1.1 from Tanzania. Microbiology Resource Announcements. e00405. https://doi.org/10.1128/MRA.00405-23.

Alternative probe hybridization buffers for target RNA depletion and viral sequence recovery in NGS for poultry samples - (Peer Reviewed Journal)
Bakre, A.A., Kariithi, H.M., Suarez, D.L. 2023. Alternative probe hybridization buffers for target RNA depletion and viral sequence recovery in NGS for poultry samples. Journal of Virological Methods. 321:114793. https://doi.org/10.1016/j.jviromet.2023.114793.

Genome sequences and characterization of chicken astrovirus and avian nephritis virus from Tanzanian live bird markets - (Peer Reviewed Journal)
Kariithi, H.M., Volkening, J.D., Chiwanga, G.H., Pantin Jackwood, M.J., Msoffe, P., Suarez, D.L. 2023. Genome sequences and characterization of chicken astrovirus and avian nephritis virus from Tanzanian live bird markets. Viruses. 15(6):1247. https://doi.org/10.3390/v15061247.

Complete genome sequence of an avian orthoavulavirus 13 strain detected in Ukraine - (Peer Reviewed Journal)
Goraichuk, I.V., Muzyka, D., Gaidash, O., Gerilovych, A., Stegniy, B., Pantin Jackwood, M.J., Miller, P.J., Afonso, C.L., Suarez, D.L. 2023. Complete genome sequence of an avian orthoavulavirus 13 strain detected in Ukraine. Microbiology Resource Announcements. 23. Article e00197. https://doi.org/10.1128/mra.00197-23.

Complete genome sequences of avian metapneumovirus subtype B vaccine strains from Brazil - (Peer Reviewed Journal)
Kariithi, H.M., Volkening, J.D., Alves, V.V., Reis-Cunha, J.L., Arantes, L.C., Fernando, F.S., Filho, T.F., Martins, N.R., Lemiere, S., Neto, O.C., Decanini, E.L., Afonso, C.L., Suarez, D.L. 2023. Complete genome sequences of avian metapneumovirus subtype B vaccine strains from Brazil. Microbiology Resource Announcements. 12(6):e00235-23. https://doi.org/10.1128/JVI.01567-16.

Unique variants of avian coronaviruses from indigenous chickens in Kenya - (Peer Reviewed Journal)
Kariithi, H.M., Volkening, J.D., Goraichuk, I.V., Ateya, L.O., Williams Coplin, T.D., Binepal, Y.S., Afonso, C.L., Suarez, D.L. 2023. Unique variants of avian coronaviruses from indigenous chickens in Kenya. Viruses. 15(2):264. https://doi.org/10.3390/v15020264.

Genetic diversity of Newcastle disease viruses circulating in wild and synanthropic birds in Ukraine between 2007 and 2015 - (Peer Reviewed Journal)
Goraichuck, I.V., Gerilovych, A., Bolotin, V., Solodiankin, O., Dimitrov, K.M., Rula, O., Muzyka, N., Mezinov, O., Stegniy, B., Kolesnyk, O., Pantin Jackwood, M.J., Miller, P.J., Afonso, C.L., Muzyka, D. 2023. Genetic diversity of Newcastle disease viruses circulating in wild and synanthropic birds in Ukraine between 2007 and 2015. Frontiers in Veterinary Science. 10:1026296. https://doi.org/10.3389/fvets.2023.1026296.

Genome sequencing and characterization of an avian orthoavulavirus 1 VG/GA-like isolate with a unique fusion cleavage site motif - (Peer Reviewed Journal)
Kariithi, H.M., Suarez, D.L., Davis, J.F., Dufour-Zavala, L., Olivier, T.L., Williams Coplin, T.D., Bakre, A.A., Lee, C.W. 2023. Genome sequencing and characterization of an avian orthoavulavirus 1 VG/GA-like isolate with a unique fusion cleavage site motif. Avian Diseases. 67(1):33-41. https://doi.org/10.1637/aviandiseases-D-22-00064.

Detection and genome sequence analysis of avian metapneumovirus subtype A viruses circulating in commercial chicken flocks in Mexico - (Peer Reviewed Journal)
Kariithi, H.M., Christy, N., Decanini, E.L., Lemiere, S., Volkening, J.D., Afonso, C.L., Suarez, D.L. 2022. Detection and genome sequence analysis of avian metapneumovirus subtype A viruses circulating in commercial chicken flocks in Mexico. Veterinary Sciences. 9(10):579. https://doi.org/10.3390/vetsci9100579.

Genome sequence variations of infectious bronchitis virus serotypes from commercial chickens in Mexico - (Peer Reviewed Journal)
Kariithi, H.M., Volkening, J.D., Leyson, C.M., Alfonso, C.L., Christy, N., Lucio, E.D., Lemiere, S., Suarez, D.L. 2022. Genome sequence variations of infectious bronchitis virus serotypes from commercial chickens in Mexico. Frontiers in Veterinary Science. 9:931272. https://doi.org/10.3389/fvets.2022.931272.

The thermal stability of Newcastle disease virus in poultry litter - (Peer Reviewed Journal)
Mo, J., Stephens, C.B., Spackman, E. 2022. The thermal stability of Newcastle disease virus in poultry litter. Avian Diseases. 66(2):1-4. https://doi.org/10.1637/aviandiseases-D-21-00113.

Evaluation of chickens infected with a recombinant virulent NDV clone expressing chicken IL4 - (Peer Reviewed Journal)
Marcana, V., Susta, L., Diel, D.G., Cardena-Garcia, S., Miller, P.J., Afonso, C.L., Brown, C.C. 2021. Evaluation of chickens infected with a recombinant virulent NDV clone expressing chicken IL4. Microbial Pathogenesis. 159:105116. https://doi.org/10.1016/j.micpath.2021.105116.