1. Quantifying Replication Slippage Error in Cryptosporidium Metabarcoding Studies.
- Author
-
Knox MA, Biggs PJ, Garcia-R JC, and Hayman DTS
- Subjects
- Humans, DNA, Protozoan genetics, High-Throughput Nucleotide Sequencing, DNA Barcoding, Taxonomic methods, Cryptosporidiosis parasitology, Genetic Variation, Cryptosporidium genetics, Cryptosporidium classification, DNA Replication
- Abstract
Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesized Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios, and sequenced them using next-generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%., Competing Interests: Potential conflicts of interest . All authors: No reported conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)
- Published
- 2024
- Full Text
- View/download PDF