Features of prevalence of ASV types of Cryptosporidium scrofarum in pig farms in the Northwestern of Russia

Abstract

For the first time in the Russian Federation, using the example of the Vologda region of the North-West of the Russian Federation in pig farms by high-performance sequencing of amplicon libraries of fragments of the 18S rRNA gene obtained as a result of nested PCR, we have established parasitization of Cryptosporidium scrofarum in pigs of all age groups. The infection rate of animals kept in pig farms was 34%, in farms – 32.4%. Piglets that are fattening at the age of 13-24 weeks are most susceptible to infection. The analysis of the taxonomic affiliation of ASV carried out using phylogenetic analysis, supplemented by analysis using the blastn algorithm in the GenBank database, showed that in total, 10 ASV types (amplicon sequence variant) with high similarity to sequences deposited in GenBank as fragments of the Cryptosporidium scrofarum 18S rRNA gene are present in all the samples studied. It was found that the ASV1 and ASV2 types detected in various geographical regions of the world from Portugal and Great Britain to China, India and Australia were identified in all surveyed farms, although in significantly different quantities. The remaining ASVS belong to local populations of C. scrofarum subspecies. A unique sequence of the genus Cryptosporidium of type ASV 8 has been discovered, which can later be described as a new species. The nucleotide sequences we have discovered are unique. Each of them was deposited in GenBank with the assignment of identifiers (Sequence ID: OR649139, OR654022, OR654023, OR661243, OR661244, OR654051, OR654052, OR654083, OR654084, OR654106).