CRISPR-Cas-Based Diagnostic Tools for Companion Birds: An Overview
DOI:
https://doi.org/10.48165/ijvsbt.22.4.1Keywords:
Avian medicine, Companion birds, CRISPR-Cas, Point-of-care diagnostics, Zoonotic diseasesAbstract
Though pet bird ownership is increasing substantially, avian medicine faces a unique diagnostic challenge as birds often conceal signs of illness until the disease has progressed beyond treatment possibilities. Current diagnostic tools, such as qPCR and ELISA, are promising but rely heavily on expensive equipment and trained personnel. This results in long turn-around times, which makes them unsuitable for rapidly progressing avian diseases. This review evaluates the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems to overcome these limitations. By utilizing the "collateral cleavage" activity of Cas12 and Cas13 nucleases, these platforms offer the sensitivity of qPCR with the speed and portability of point-of-care tools. The review also describes recently validated CRISPR-Cas-based models for poultry diseases such as Avian Leukosis Virus, Infectious Bronchitis Virus, and Duck Hepatitis A Virus and analyses their potential for translation into companion bird diseases. Further, the possibility of CRISPR-Cas to aid in detection of zoonotic threats like Psittacosis and Avian Influenza, alongside a few other critical avian pathogens is described. Despite challenges such as aerosol contamination and sample preparation, CRISPR-Cas systems combined with isothermal amplification represent a significant step toward accessible, lab-quality diagnostics for veterinarians, pet owners, and breeders.
Downloads
References
Angamuthu, R., Baskaran, S., Gopal, D. R., Devarajan, J., & Kathaperumal, K. (2012). Rapid detection of the Marek’s disease viral genome in chicken feathers by loop-mediated isothermal amplification. Journal of Clinical Microbiology, 50(3), 961–965.
Ayuti, S. R., Khairullah, A. R., Lamid, M., Al-Arif, M. A., Warsito, S. H., Silaen, O. S. M., Moses, I. B., Hermawan, I. P., Yanestria, S. M., Delima, M., Ferasyi, T. R., & Aryaloka, S. (2024). Avian influenza in birds: Insights from a comprehensive review. Veterinary World, 17, 2544–2555.
Chandrasekar, A., Raja, A., Dhinakar Raj, G., Thangavelu, A., & Kumanan, K. (2015). Rapid detection of avian infectious bronchitis virus by reverse transcriptase-loop mediated isothermal amplification. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 85(3), 815–820.
Chen, J. S., Ma, E., Harrington, L. B., Da Costa, M., Tian, X., Palefsky, J. M., & Doudna, J. A. (2018). CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 360(6387), 436–439.
Chen, S., Li, Y., Liao, R., Liu, C., Zhou, X., Wang, H., Wang, Q., & Lan, X. (2024). Detection of avian leukosis virus subgroup J (ALV-J) using RAA and CRISPR-Cas13a combined with fluorescence and lateral flow assay. International Journal of Molecular Sciences, 25(19), 10780.
Chen, S., Wang, S., Cheng, X., Xiao, S., Zhu, X., Lin, F., Wu, N., Wang, J., Huang, M., Zheng, M., Chen, S., & Yu, F. (2016). Isolation and characterization of a distinct duck-origin goose parvovirus causing an outbreak of duckling short beak and dwarfism syndrome in China. Archives of Virology, 161(9), 2407–2416.
Chen, X., Zhang, S., Lin, S., Huang, M., Chen, S., & Wang, S. (2025). From lab to field: Innovative RPA–CRISPR-Cas12a platform for early short-beak and dwarfism syndrome virus nucleic acids detection. Poultry Science, 104(7), 105191.
Chitradevi, S., Sukumar, K., Suresh, P., Balasubramaniam, G. A., Kannan, D., & Raja, A. (2024). Quantitative profiling of fowl adenoviral load in experimentally infected chicken using SYBR Green real-time PCR. Veterinarski Arhiv, 95(1), 39–50.
Chitradevi, S., Sukumar, K., Suresh, P., Balasubramaniam, G. A., Kannan, D., & Raja, A. (2018). Concurrent infections associated with fowl adenovirus in commercial broiler chicken. Indian Journal of Comparative Microbiology, Immunology and Infectious Diseases, 39(1), 20.
Dembek, Z. F., Mothershead, J. L., Owens, A. N., Chekol, T., & Wu, A. (2023). Psittacosis: An underappreciated and often undiagnosed disease. Pathogens, 12(9), 1165.
Esmaeelzadeh-Dizaji, R., Molouki, A., Hosseini, H., Fallah-Mehrabadi, M. H., Ziafati-Kafi, Z., Takalou, A., Eram, N., Kumar, N., Ashuri, A., Sadri, N., & Ghalyanchi-Langeroudi, A. (2022). Molecular characterization of a pigeon paramyxovirus type 1 virus isolated from Eurasian collared doves in Iran, 2017. Journal of Veterinary Science, 23(3), e29.
Fenton, S. P., Reddy, M. R., & Bagust, T. J. (2005). Single and concurrent avian leukosis virus infections with avian leukosis virus-J and avian leukosis virus A in Australian meat-type chickens. Avian Pathology, 34(1), 48–54.
Gootenberg, J. S., Abudayyeh, O. O., Lee, J. W., Essletzbichler, P., Dy, A. J., et al. (2017). Nucleic acid detection with CRISPR-Cas13a/C2c2. Science, 356(6336), 438–442.
Hidalgo-Cantabrana, C., & Barrangou, R. (2020). Characterization and applications of Type I CRISPR-Cas systems. Biochemical Society Transactions, 48(1), 15–23.
Hu, F., Liu, Y., Zhao, S., Zhang, Z., Li, X., Peng, N., & Jiang, Z. (2022). A one-pot CRISPR-Cas13a-based contamination-free biosensor for low-cost and rapid nucleic acid diagnostics. Biosensors and Bioelectronics, 202, 113994.
Kang, E. G., Han, J. H., Shim, Y. J., Lee, D. N., Choi, K. S., & Yeon, S. C. (2025). Psittacine beak and feather disease: Global spread, international trade, and conservation challenges. Animals, 15(20), 2947.
Khudeir, M. A., Alsultan, A. S., & Khudhair, Y. I. (2024). Novel CRISPR Cas13-based assay for diagnosis of avian infectious bronchitis. Iraqi Journal of Veterinary Sciences, 38(1), 63–69.
Korteweg, C., & Gu, J. (2008). Pathology, molecular biology, and pathogenesis of avian influenza A (H5N1) infection in humans. The American Journal of Pathology, 172(5), 1155–1170.
Li, K. P., Hsu, Y. C., Lin, C. A., Chang, P. C., Shien, J. H., Liu, H. Y., Yen, H., & Ou, S. C. (2021). Molecular characterization and pathogenicity of the novel recombinant Muscovy duck parvovirus isolated from geese. Animals, 11(11), 3211.
Li, S. Y., Cheng, Q. X., Liu, J. K., Nie, X. Q., Zhao, G. P., & Wang, J. (2018). CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA. Cell Research, 28(4), 491–493.
Li, Y., Li, S., Wang, J., & Liu, G. (2019). CRISPR-Cas systems towards next-generation biosensing. Trends in Biotechnology, 37(7), 730–743.
Li, Y., Shang, J., Luo, J., Zhang, F., Meng, G., Feng, Y., Jiang, W., Yu, X., Deng, C., Liu, G., & Liu, H. (2023). Rapid detection of H5 subtype avian influenza virus using CRISPR Cas13a based-lateral flow dipstick. Frontiers in Microbiology, 14, 1283210.
Liang, L., Wang, D., Gao, Z., Tang, J., Li, X., Ren, P., Wang, Y., Gao, S., Wu, X., Guo, Y., Yang, B., & Li, J. (2024). RAA-CRISPR-Cas12a mediated rapid, sensitive, and onsite detection of Newcastle disease in pigeons. Veterinary Sciences, 11(10), 473.
Liang, Q., Chen, W., Wang, W., Liu, R., Fu, Q., Fu, G., Cheng, L., Jiang, N., Chen, H., & Huang, Y. (2025). Development of a rapid on-site nucleic acid detection method for new genotype Muscovy duck parvovirus based on RPA-CRISPR-Cas12a. Frontiers in Veterinary Science, 12.
Madani, S. A., & Peighambari, S. M. (2012). PCR-based diagnosis, molecular characterization and detection of atypical strains of avian Chlamydia psittaci in companion and wild birds. Avian Pathology, 42(1), 38–44.
Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., et al. (2019). Evolutionary classification of CRISPR-Cas systems: A burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2), 67–83.
Mao, X., Xu, M., Luo, S., Yang, Y., Zhong, J., Zhou, J., Fan, H., Li, X., & Chen, Z. (2023). Advancements in the synergy of isothermal amplification and CRISPR-Cas technologies for pathogen detection. Frontiers in Bioengineering and Biotechnology, 11, 1273988.
Matczuk, A. K., Chmielewska-Władyka, M., Siedlecka, M., Bednarek, K. J., & Wieliczko, A. (2020). Short beak and dwarfism syndrome in ducks in Poland caused by novel goose parvovirus. Animals, 10(12), 2397.
Miao, J., Zuo, L., He, D., Fang, Z., Berthet, N., Yu, C., & Wong, G. (2023). Rapid detection of Nipah virus using the one-pot RPA-CRISPR Cas13a assay. Virus Research, 332, 199130.
Padzil, F., Mariatulqabtiah, A. R., & Abu, J. (2017). Avian polyoma virus: A recent update. Journal Veterinary Malaysia, 9–13.
Peiris, J. S. M., de Jong, M. D., & Guan, Y. (2007). Avian influenza virus (H5N1): A threat to human health. Clinical Microbiology Reviews, 20(2), 243–267.
Piepenbring, A. K., Enderlein, D., Herzog, S., Al-Ibadi, B., Heffels Redmann, U., Heckmann, J., Lange-Herbst, H., Herden, C., & Lierz, M. (2016). Parrot Bornavirus (PaBV)-2 isolate causes different disease patterns in cockatiels than PaBV-4. Avian Pathology, 45(2), 156–168.
Ponnusamy, P., Sukumar, K., Raja, A., Saravanan, S., Srinivasan, P., & Thangavelu, A. (2022). Characterization of infectious laryngotracheitis virus isolates from laying hens during 2019–2020 outbreaks in Tamil Nadu, India. Archives of Virology, 167(9), 1819–1829.
Raja, A., Dhinakar Raj, G., & Kumanan, K. (2020). Emergence of variant avian infectious bronchitis virus in India. Iranian Journal of Veterinary Research, 21(1), 33–39.
Rasool, H. M. H., Chen, Q., Gong, X., & Zhou, J. (2024). CRISPR/Cas system and its application in the diagnosis of animal infectious diseases. The FASEB Journal, 38(24), e70252.
Rubbenstroth, D. (2022). Avian bornavirus research—A comprehensive review. Viruses, 14(7), 1513.
Sambandam, R., Angamuthu, R., Kanagaraj, V., Kathaperumal, K., Chothe, S. K., Nissly, R. H., Barry, R. M., Jayarao, B. M., & Kuchipudi, S. V. (2017). An immuno-chromatographic lateral flow assay (LFA) for rapid on-the-farm detection of classical swine fever virus (CSFV). Archives of Virology, 162(10), 3045–3050.
Shi, Y., Chen, J., Shi, X., Hu, J., Li, H., Li, X., Wang, Y., & Wu, B. (2021). A case of Chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: A case report and literature review. BMC Infectious Diseases, 21(1), 621.
Sigrist, B., Geers, J., Albini, S., Rubbenstroth, D., & Wolfrum, N. (2021). A new multiplex real-time RT-PCR for simultaneous detection and differentiation of avian bornaviruses. Viruses, 13(7), 1358.
Sun, D., Zhu, Y., Wang, M., Wang, J., Cheng, W., Li, Z., Deng, Y., Ou, X., Jia, R., Chen, S., Zhu, D., Liu, M., Zhao, X., Yang, Q., Wu, Y., Zhang, S., Huang, J., He, Y., Wu, Z., & Cheng, A. (2025). A RT-ERA CRISPR-Cas12a assay for rapid point-of-care duck hepatitis A virus detection. Poultry Science, 104(8), 105316.
Suohu, S., Balasubramaniam, G. A., Arulmozhi, A., Gopalakrishnamurthy, T. R., & Raja, A. (2025). Determination of tissue tropism of chicken anaemia virus on chicken embryos: A molecular insight. Journal of Veterinary Science, 26(3), e17.
Wang, R., Mao, X., Xu, J., Yao, P., Jiang, J., Li, Q., & Wang, F. (2023). Engineering of the LAMP-CRISPR-Cas12b platform for Chlamydia psittaci detection. Journal of Medical Microbiology, 72(12), 1781.
Yang, H., Zhang, Y., Teng, X., Hou, H., Deng, R., & Li, J. (2023). CRISPR-based nucleic acid diagnostics for pathogens. TrAC Trends in Analytical Chemistry, 160, 116980.
Zhang, S., Yang, J., Wang, Z., Chen, L., Diao, Y., & Tang, Y. (2020). Research Note: Development of an ELISA to distinguish between goose parvovirus infection and vaccine immunization antibodies. Poultry Science, 99(3), 1332–1340.
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Indian Journal of Veterinary Sciences and Biotechnology
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
