Next-generation sequencing in tick-borne apicomplexan parasites: approaches for Theileria and Babesia, a systematic review.

Abstract

BACKGROUND: Tick-borne apicomplexan parasites are a threat to livestock health and human life, underscoring parasite significance within the One Health Framework. Advances in sequencing provide vital insights into parasite diversity, genetic composition, and behavior, supporting improved prevention and control strategies. This review synthesizes sequencing approaches applied to Theileria and Babesia, highlighting how evolving technologies are reshaping comprehension of parasite variation and gene function. METHODS: A systematic analysis was conducted using five databases -Wiley Online Library, ScienceDirect, SpringerLink, PubMed, and the Africa Online Journals (AJOL), and Google Scholar. The Joanna Briggs Institute critical appraisal checklist was used for managing data bias and the PRISMA guidelines flow diagram summarized the data selection criteria. RESULTS: A total of 127 articles (1995 to 2025) were synthesized, representing the first systematic synthesis of sequencing approaches for Theileria and Babesia. The review highlights three sampling approaches used in sequencing; infected host tissue, parasite culture and questing ticks. Emerging sequencing technologies such as Oxford Nanopore present promising opportunities for direct RNA sequencing, complementing existing platforms. Sequencing advances have revealed hypervariable genetic regions with direct implications for improved variant detection and surveillance, and vaccine target discovery. Whole-genome and transcriptome sequencing have uncovered key gene families essential for host specificity and parasite survival, paving way for potential targets for parasite control strategies in livestock and human health, while reassembly of older genomes has enhanced resolution of genetic variation. CONCLUSION: Advances in genome sequencing have enhanced our understanding of parasite biology and reshaped parasite detection, surveillance, and vaccine development. CLINICAL TRIAL NUMBER: Not applicable.