Molecular characteristics of Cryptosporidium scrofarum in pig farms of the Vologda region of the Northwestern Federal District of the Russian Federation

The purpose of these studies was to identify, identify, analyze and study the distribution of Cryptosporidium scrofarum in pigs in the  farms  of  the  Vologda  Region  of  the Northwestern Federal District of the Russian Federation.For the first time in the Russian Federation, using the example of the Vologda Oblast of the Northwestern Federal District in pig  farms  of  various  types  using  the  latest molecular  genetic  methods,  namely  using high-throughput  sequencing  of  amplicon libraries of fragments of the 18S rRNA gene obtained  because  of  nested  PCR,  we  have established the infection of C. scrofarum in all  age  groups  of  examined  animals.  The contamination of animals kept in pig farms was 34%, in farms - 32.4%. Animals that are fattened at the age of 13-24 weeks are most susceptible to infection.Analysis  of  ASV  taxonomic  affiliation using  phylogenetic  analysis,  supplemented by analysis using the blastn algorithm in the GenBank database, showed that a total of 10 ASV types (amplicon sequence variant) are present  in  all  tested  samples,  which  have high  similarity  to  sequences  deposited  in GenBank  as  fragments  of  the  18S  p  gene Cryptosporidium  scrofarum  RNA.  It  has been established that the types of ASV1 and ASV2  detected  in  various  geographical  regions of the world from Portugal and Great Britain  to  China,  India  and  Australia  are identified in all examined farms, although in significantly  different  quantities.  The  remaining ASVs are present in much smaller numbers  and  do  not  repeat  from  farm  to farm.  These  sequences  probably  belong  to local populations of subspecies Cryptosporidium scrofarum.  It  is  interesting  to  find  a unique sequence of the genus Cryptosporidium  of  type  ASV8,  which  can  later  be  described as a new species.