School of Veterinary Science.
School of Natural Sciences, Massey University, Palmerston North, Manawatu-Wanganui, New Zealand.
J Infect Dis. 2024 Jul 25;230(1):e144-e148. doi: 10.1093/infdis/jiae065.
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%.
人类肠道寄生虫隐孢子虫的遗传变异通常基于包含三核苷酸重复的标记基因，这些重复区分了亚型并追踪了暴发。然而，重复区域的复制滑动率很高，使得难以从错误中辨别生物多样性。在这里，我们在克隆质粒载体中合成了隐孢子虫 DNA，在不同的模拟群落比例中扩增它们，并使用下一代测序通过 dada2 来确定复制滑动的速率。我们的结果表明，滑动率随重复区域的长度而增加，并可能导致高达 20%的错误率。
