Quantifying replication slippage error in Cryptosporidium metabarcoding studies
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Date
2024-02-08
Open Access Location
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press on behalf of the Infectious Diseases Society of America
Rights
(c) 2024 The Author/s
CC BY 4.0
CC BY 4.0
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 synthesised 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%.
Description
Keywords
Cryptosporidium hominis, Cryptosporidium parvum, PCR slippage, STR, dada2, repeat region
Citation
Knox MA, Biggs PJ, Garcia-R JC, Hayman DTS. (2024). Quantifying replication slippage error in Cryptosporidium metabarcoding studies.. J Infect Dis. Accepted manuscript. (pp. jiae065-).