OPEN ACCESS | Published on : 23-Mar-2026 | Pages: 94-110 | Doi : 10.37446/volbook022025/94-110
Livestock Infectious diseases in animals impose substantial economic and public health burdens on livestock, poultry, and aquaculture systems. Conventional diagnostic methods, including PCR and immunoassays, are limited by high cost, operational complexity, and long turnaround times. The CRISPR-Cas system provides a rapid sensitive detection platform for diagnostics utilizing the collateral cleavage activity. This chapter examines CRISPR diagnostics platforms, their mechanisms, and integration with amplification-free assays, and the point of care application which includes, Cas12a fluorometric/LFA detection of canine tick-borne pathogens (Ehrlichia, Babesia with 100% sensitivity and specificity), Cas14a paper-based ASFV biosensors (LOD 5copies/µL), Multiplex RT-RPA-Cas13a for AIV subtypes (LOD 1-10 copies/µL), RPA-Cas12a for Brucella (LOD 1copy/µL), and RPA-Cas12a for lumpy skin disease virus with 96% sensitivity. These technologies are particularly suited for deployment in resource-limited settings, enabling rapid on-site surveillance and disease control, these tools enable on-farm surveillance, variant differentiation, preventive measures and food security.
CRISPR, Veterinary science, Diagnostics, LFA, Fluorescence, Cas system
Al-Ouqaili, M. T., Ahmad, A., Jwair, N. A., & Al-Marzooq, F. (2025). Harnessing bacterial immunity: CRISPR-Cas system as a versatile tool in combating pathogens and revolutionizing medicine. Frontiers in Cellular and Infection Microbiology, 15, 1588446. https://doi.org/10.3389/fcimb.2025.1588446
Azeem, S., & Yoon, K. J. (2025). Diagnostic assays for avian influenza virus surveillance and monitoring in poultry. Viruses, 17(2), 228. https://doi.org/10.3390/v17020228
Badawi, N. M., & Yousif, A. A. (2020). Babesia canis spp. in dogs in Baghdad Province, Iraq: First molecular identification and clinical and epidemiological study. Veterinary World, 13(3), 579–584. https://doi.org/10.14202/vetworld.2020.579-584
Bagi, M., Jamalzadegan, S., Steksova, A., & Wei, Q. (2025). CRISPR–Cas based platforms for RNA detection: Fundamentals and applications. Chemical Communications, 61(72), 13571–13600. https://doi.org/10.1039/D5CC02045A
Bayyappa, M. R. G., Uma, C. R., Bijalwan, S., Tadakod, S., Nagaraj, S., Naragund, M., & Gulati, B. R.
(2025). Molecular epidemiological and spatiotemporal analysis of lumpy skin disease outbreaks in cattle from Karnataka, India. Frontiers in Cellular and Infection Microbiology, 15, 1596973. https://doi.org/10.3389/fcimb.2025.1596973
Bora, D. P., Borah, B., Bora, M., Kakati, P., Nehar, S., Dutta, L. J., & Das, S. K. (2018). Detection and characterization of Swinepox virus from pig population of Assam, a North Eastern state of India. Indian Journal of Animal Research, 52(9), 1337–1342. https://doi.org/10.18805/ijar.B-3427
Broughton, J. P., Deng, X., Yu, G., Fasching, C. L., Servellita, V., Singh, J., & Chiu, C. Y. (2020). CRISPR–Cas12-based detection of SARS-CoV-2. Nature Biotechnology, 38(7), 870–874. https://doi.org/10.1038/s41587-020-0513-4
Burranboina, K., Abraham, S., Murugan, K., Bayyappa, M. R., Yogisharadhya, R., & Raghavendra, G. (2018). Genome wide identification and analysis of microsatellite repeats in the largest DNA viruses (Poxviridae Family): An in silico approach. Annual Research & Review in Biology, 22(1), 1–11. https://doi.org/10.9734/ARRB/2018/39242
Cao, S., Ma, D., Xie, J., Wu, Z., Yan, H., Ji, S., & Zhu, S. (2024). Point-of-care testing diagnosis of African swine fever virus by targeting multiple genes with enzymatic recombinase amplification and CRISPR/Cas12a system. Frontiers in Cellular and Infection Microbiology, 14, 1474825. https://doi.org/10.3389/fcimb.2024.1474825
Charostad, J., Rukerd, M. R. Z., Mahmoudvand, S., Bashash, D., Hashemi, S. M. A., Nakhaie, M., & Zandi, K. (2023). A comprehensive review of highly pathogenic avian influenza (HPAI) H5N1: An imminent threat at doorstep. Travel Medicine and Infectious Disease, 55, 102638. https://doi.org/10.1016/j.tmaid.2023.102638
Chen, F., Zhang, C., Xue, J., Wang, F., & Li, Z. (2024). Molecular mechanism for target RNA recognition and cleavage of Cas13h. Nucleic Acids Research, 52(12), 7279–7291. https://doi.org/10.1093/nar/gkae430
Chen, H., Song, F., Wang, B., Huang, H., Luo, Y., Han, X., & Mao, C. (2025). Ultrasensitive detection of clinical pathogens through a target-amplification-free collateral-cleavage-enhancing CRISPR-CasΦ tool. Nature Communications, 16(1), 3929.
Constable, P. D., Hinchcliff, K. W., Done, S. H., & Grünberg, W. (2016). Veterinary medicine: A textbook of the diseases of cattle, horses, sheep, pigs and goats (11th ed.). Elsevier Health Sciences.
Dang, S., Sui, H., Zhang, S., Wu, D., Chen, Z., Zhai, J., & Bai, M. (2023). CRISPR-Cas12a test strip (CRISPR/CAST) package: In-situ detection of Brucella from infected livestock. BMC Veterinary Research, 19(1), 202. https://doi.org/10.1186/s12917-023-03702-1
Fu, X., Wang, Q., Ma, B., Zhang, B., Sun, K., Yu, X., & Zhang, M. (2023). Advances in detection techniques for the H5N1 avian influenza virus. International Journal of Molecular Sciences, 24(24), 17157. https://doi.org/10.3390/ijms242417157
Ghouneimy, A., Mahas, A., Marsic, T., Aman, R., & Mahfouz, M. (2022). CRISPR-based diagnostics: Challenges and potential solutions toward point-of-care applications. ACS Synthetic Biology, 12(1), 1–16. https://doi.org/10.1021/acssynbio.2c00410
Ghssein, G., Ezzeddine, Z., Tokajian, S., Khoury, C. A., Kobeissy, H., Ibrahim, J. N., & Hassan, H. F. (2025). Brucellosis: Bacteriology, pathogenesis, epidemiology and role of the metallophores in virulence: A review. Frontiers in Cellular and Infection Microbiology, 15, 1621230. https://doi.org/10.3389/fcimb.2025.1621230
Gootenberg, J. S., Abudayyeh, O. O., Kellner, M. J., Joung, J., Collins, J. J., & Zhang, F. (2018). Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science, 360(6387), 439–444. https://doi.org/10.1126/science.aaq0179.
He, J., & Kam, Y. W. (2024). Insights from avian influenza: A review of its multifaceted nature and future pandemic preparedness. Viruses, 16(3), 458. https://doi.org/10.3390/v16030458.
Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., & Nakata, A. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology, 169(12), 5429–5433. https://doi.org/10.1128/jb.169.12.5429-5433.1987
Jacob, S. S., Sengupta, P. P., Kumar, H. B. C., Maharana, S. M., Goudar, A., Chandu, A. G. S., & Reddy, G. B. M. (2024). Unveiling genotypic diversity of Theileria orientalis in lethal outbreaks among bovines in Karnataka, India. Parasitology Research, 123(5), 202. https://doi.org/10.1007/s00436-024-08156-4
Jiang, C., Tao, D., Geng, Y., Yang, H., Xu, B., Chen, Y., & Guo, A. (2022). Sensitive and specific detection of lumpy skin disease virus in cattle by CRISPR-Cas12a fluorescent assay coupled with recombinase polymerase amplification. Genes, 13(5), 734. https://doi.org/10.3390/genes13050734.
Kruszyński, M., Śróda, K., Juszkiewicz, M., Siuda, D., Olszewska, M., & Woźniakowski, G. (2023). Nine years of African swine fever in Poland. Viruses, 15(12), 2325. https://doi.org/10.3390/v15122325.
Lesinski, J. M., Khosla, N. K., Paganini, C., Verberckmoes, B., Vermandere, H., deMello, A. J., & Richards, D. A. (2024). FRETting about CRISPR-Cas assays: Dual-channel reporting lowers detection limits and times-to-result. ACS Sensors, 9(7), 3616–3624. https://doi.org/10.1021/acssensors.4c00981.
Lobato, I. M., & O'Sullivan, C. K. (2018). Recombinase polymerase amplification: Basics, applications and recent advances. TrAC Trends in Analytical Chemistry, 98, 19–35. https://doi.org/10.1016/j.trac.2017.10.015.
Makarova, K. S., Shmakov, S. A., Wolf, Y. I., Mutz, P., Altae-Tran, H., Beisel, C. L., & Koonin, E. V. (2025). An updated evolutionary classification of CRISPR–Cas systems including rare variants. Nature Microbiology, 1–16. https://doi.org/10.1038/s41564-025-01982-2.
Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J., ... & Koonin, E. V. (2020). Evolutionary classification of CRISPR–Cas systems: A burst of class 2 and derived variants. Nature Reviews Microbiology, 18(2), 67–83. https://doi.org/10.1038/s41579-019-0299-x
Manjunatha Reddy, G. B., Krishnappa, V. K., Siddalingaiah, C. D., Rao, S., Nayakvadi, S., Harlipura Basavarajappa, C. K., & Gulati, B. R. (2024). Epidemiological, pathological, and molecular studies on sheeppox disease outbreaks in Karnataka, India. Microorganisms, 12(7), 1373. https://doi.org/10.3390/microorganisms12071373
Manjunatha Reddy, G. B., Pabbineedi, S. M., Nagaraj, S., Bijalwan, S., Tadakod, S., Bhutia, Z., & Gulati, B. R. (2023). Lumpy skin disease (LSD) in yak (Bos grunniens): An evidence of species spillover from cattle in India. Microorganisms, 11(12), 2823. https://doi.org/10.3390/microorganisms11122823
Manjunathareddy, G. B., Sumana, K., Yogisharadhya, R., Cherian, S., Prajapati, A., Patil, S. S., & Rahman, H. (2016). Diagnosis of animal rabies: Comparison of direct fluorescent antibody test (dFAT), reverse transcriptase-PCR and real-time PCR. Veterinary World, 9(8), 867–870. https://doi.org/10.14202/vetworld.2016.867-870
Meng, S., Zhao, Z., Huang, L., Peng, X., Chen, H., & Tang, X. (2025). CRISPR/Cas technology for the diagnosis of animal infectious diseases. Microorganisms, 13(9), 2006. https://doi.org/10.3390/microorganisms13092006
Palavesam, A., Karthik Raj, B. N., Madan, N., Sri, S. S. L., Babitha, R., & Tirumurugaan, K. G. (2025). CRISPR-Cas12a-based rapid detection of Babesia gibsoni and Ehrlichia canis in dogs using fluorometer platform. Scientific Reports, 15, Article number pending.
Pan, Z., Xu, L., Fan, Z., Cao, Y., & Ren, F. (2026). CRISPR-based diagnostics for infectious diseases: Mechanisms, advancements and clinical transformation prospects. Frontiers in Cellular and Infection Microbiology, 16, 1769226. https://doi.org/10.3389/fcimb.2026.1769226
Park, S. J., Lee, G. E., Cho, S. M., & Choi, E. H. (2025). Recent applications, future perspectives, and limitations of the CRISPR-Cas system. Molecular Therapy Nucleic Acids. Advance online publication. https://doi.org/10.1016/j.omtn.2025.102345
Paul, S., Emmadi, V., Saxena, S., Sarkar, M., Mandal, B., Kumar, R., & Roy, A. (2025). RPA-assisted CRISPR-Cas12a-enabled point-of-care diagnostic platform for chili leaf curl virus with fluorescent and colorimetric readouts. Frontiers in Microbiology, 16, 1644322. https://doi.org/10.3389/fmicb.2025.1644322
Pausch, P., Al-Shayeb, B., Bisom-Rapp, E., Tsuchida, C. A., Li, Z., Cress, B. F., & Doudna, J. A. (2020). CRISPR-CasΦ from huge phages is a hypercompact genome editor. Science, 369(6501), 333–337. https://doi.org/10.1126/science.abb1400
Quak, S., Moonen-Leusen, H. W., & Loeffen, W. L. (2019). Transmission of African swine fever virus via carrier (survivor) pigs does occur. Veterinary Microbiology, 237, 108345. https://doi.org/10.1016/j.vetmic.2019.108345
Rasool, H. M. H., Chen, R. 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. https://doi.org/10.1096/fj.202401234R
Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015). The CRISPR-Cas immune system: Biology, mechanisms and applications. Biochimie, 117, 119–128. https://doi.org/10.1016/j.biochi.2015.03.025
Reddy, G., Kumari, A., Mishra, A., Shivashanarappa, N., Paul, S., Gupta, V., & Sharma, D. K. (2014). Prevalence of group A rotavirus in diarrhoeic goat kids from organized goat farms. Indian Journal of Comparative Microbiology, Immunology and Infectious Diseases, 35(1), 9–12.
Ren, M., Mei, H., Zhou, J., Zhou, M., Han, H., & Zhao, L. (2021). Early diagnosis of rabies virus infection by RPA-CRISPR techniques in a rat model. Archives of Virology, 166(4), 1083–1092. https://doi.org/10.1007/s00705-021-04970-x
Saeed, K., Ayub, F., Durrani, M. A., & Mujahid, M. (2025). CRISPR Cas systems: From bacterial defense mechanisms to revolutionary tools reshaping genetic research and translation therapeutics. The Microbe, 7, 100344. https://doi.org/10.1016/j.microb.2025.100344
Shen, Y., Yi, C., Wang, H., Tang, Y., & Li, J. (2025). Development of a rapid and sensitive RPA-CRISPR/Cas12a-based assay for the detection of Brucella melitensis. Microbiology Spectrum, 13(10), e00998-25. https://doi.org/10.1128/spectrum.00998-25
Shivasharanappa, N., Gururaj, K., Sharma, D. K., Reddy, G. M., & Vihan, V. S. (2011). Acute hepatic and pneumonic cysticercosis in Barbari goats. Indian Journal of Veterinary Pathology, 35(1), 80–81.
Solikhah, T. I., Rostiani, F., Nanra, A. F. P., Dewi, A. D. P. P., Nurbadri, P. H., Agustin, Q. A. D., & Solikhah, G. P. (2025). African swine fever virus: Virology, pathogenesis, clinical impact, and global control strategies. Veterinary World, 18(6), 1599–1612. https://doi.org/10.14202/vetworld.2025.1599-1612
Soroka, M., Wasowicz, B., & Rymaszewska, A. (2021). Loop-mediated isothermal amplification (LAMP): The better sibling of PCR? Cells, 10(8), 1931. https://doi.org/10.3390/cells10081931
Strich, J. R., & Chertow, D. S. (2019). CRISPR-Cas biology and its application to infectious diseases. Journal of Clinical Microbiology, 57(4), e01307-18. https://doi.org/10.1128/JCM.01307-18
Tang, Z., Gao, M., Gong, F., Shan, X., Yang, Y., Zhang, Y., & He, Z. (2024). Quantum dot reporters designed for CRISPR-based detection of viral nucleic acids. Analytical Chemistry, 96(40), 16017–16026. https://doi.org/10.1021/acs.analchem.4c02851
Teffera, M., & Babiuk, S. (2019). Potential of using capripoxvirus vectored vaccines against arboviruses in sheep, goats, and cattle. Frontiers in Veterinary Science, 6, 450. https://doi.org/10.3389/fvets.2019.00450
Tripathi, A. K., Sendor, A. B., & Sapra, A. (2025). Avian influenza. In StatPearls. StatPearls Publishing. https://www.ncbi.nlm.nih.gov/books/NBK541123/
Venkatesan, G., Balamurugan, V., Yogisharadhya, R., Kumar, A., & Bhanuprakash, V. (2012). Differentiation of sheeppox and goatpox viruses by polymerase chain reaction-restriction fragment length polymorphism. Virologica Sinica, 27(6), 353–359. https://doi.org/10.1007/s12250-012-3277-2
Wang, Z., Wang, Q., Zhang, J., Li, B., Li, Y., Chen, Z., & Feng, S. (2025). CRISPR-driven diagnostics: Molecular mechanisms, clinical efficacy and translational challenges. Clinical and Translational Medicine, 15(10), e70482. https://doi.org/10.1002/ctm2.70482
Wang, Z., Wang, Y., Zhang, Y., Qin, G., Sun, W., Wang, A., & Zhao, J. (2024). On-site detection and differentiation of African swine fever virus variants using an orthogonal CRISPR-Cas12b/Cas13a-based assay. iScience, 27(4), 109411. https://doi.org/10.1016/j.isci.2024.109411
Wu, Y., Zhan, J., Shan, Z., Li, Y., Liu, Y., Li, Y., & Wang, X. (2023). CRISPR-Cas13a-based detection method for avian influenza virus. Frontiers in Microbiology, 14, 1288951. https://doi.org/10.3389/fmicb.2023.1288951
Xu, D., Wu, Q., Yang, F., Zhang, Q., Jiang, Q., Zeng, X., & Li, F. (2025). Fast-Flu: RT-RPA-CRISPR/Cas12a assisted one-step platform for rapid influenza B virus detection. Microbiology Spectrum, 13(6), e00365-25. https://doi.org/10.1128/spectrum.00365-25
Xu, Y., Le, H., Wu, Q., Wang, N., & Gong, C. (2025). Advancements in CRISPR/Cas systems for disease treatment. Acta Pharmaceutica Sinica B, 15(6), 2818–2844. https://doi.org/10.1016/j.apsb.2025.02.014
Yang, Y., Yang, Z., Zhang, X., Niu, B., Huang, Q., Li, Y., & Jia, W. (2025). Rapid detection of pan-avian influenza virus and H5, H7, H9 subtypes of avian influenza virus using CRISPR/Cas13a and lateral flow assay. Poultry Science, 104(2), 104745. https://doi.org/10.1016/j.psj.2024.104745
Yin, C., Yang, C., Wu, Y., Di, J., Bai, T., Wang, Y., & Li, Z. (2025). Molecular epidemiology of Brucella spp. in aborted livestock in the Ningxia Hui Autonomous Region, China. Veterinary Sciences, 12(8), 702. https://doi.org/10.3390/vetsci12080702
Zhang, J., Li, J., Zhou, J., Zhong, J., Xu, Y., Mao, X., & Li, X. (2025). A critical review of the CRISPR-Cas technology in the detection of SARS-CoV-2 variants. Canadian Journal of Infectious Diseases and Medical Microbiology, 2025(1), 9107724. https://doi.org/10.1155/2025/9107724
Zhang, X., Ma, D., & Liu, F. (2025). CRISPR technology and its emerging applications. Genomics, Proteomics & Bioinformatics, 23(3), qzaf034. https://doi.org/10.1093/gpbjnl/qzaf034
Zhang, Z., Wang, C., Chen, X., Zhang, Z., Shi, G., Zhai, X., & Zhang, T. (2024). Based on CRISPR-Cas13a system, to establish a rapid visual detection method for avian influenza viruses. Frontiers in Veterinary Science, 10, 1272612. https://doi.org/10.3389/fvets.2023.1272612
Zhao, X., He, Y., Shao, S., Ci, Q., Chen, L., Lu,X., & Chen, J. (2024). CRISPR/Cas14 and G-quadruplex DNAzyme-driven biosensor for paper-based colorimetric detection of African swine fever virus. ACS Sensors, 9(5), 2413–2420. https://doi.org/10.1021/acssensors.4c00374
Zhou, X., Wang, S., Ma, Y., Jiang, Y., Li, Y., Shi, J., & Wang, X. (2024). On-site and visual detection of the H5 subtype avian influenza virus based on RT-RPA and CRISPR/Cas12a. Viruses, 16(5), 753. https://doi.org/10.3390/v16050753
Zhou, Z., Cho, I. H., & Kadam, U. S. (2025). CRISPR-Cas-based diagnostics in biomedicine: Principles, applications, and future trajectories. Biosensors, 15(10), 660. https://doi.org/10.3390/bios15100660.