Designing and conducting in silico analysis for identifying of Echinococcus spp. with discrimination of novel haplotypes: an approach to better understanding of parasite taxonomic

Abstract

The definitive identification of Echinococcus species is currently carried out by sequencing and phylogenetic strategies. However, the application of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns is not broadly used as a result of heterogeneity traits of Echinococcus genome in different regions of the world. Therefore, designing and conducting a standardized pattern should indigenously be considered in under-studied areas. In this investigation, an in silico mapping was designed and developed for eight Echinococcus spp. on the basis of regional sequences in Iran and the world. The numbers of 60 Echinococcus isolates were collected from the liver and lungs of 15 human, 15 sheep, 15 cattle, and 15 camel cases in Semnan province, Central Iran. DNA samples were extracted and examined by polymerase chain reaction of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and PCR-RFLP via Rsa1 endonuclease enzyme. Moreover, 15 amplicons of cytochrome oxidase 1 (Cox1) were directly sequenced in order to identify the strains/haplotypes. PCR-RFLP and phylogenetic analyses revealed firmly the presence of the G1 and G6 genotypes with heterogeneity (three novel haplotypes) of Cox1 gene although no other expected genotypes were found in the region. Finding shows that the identification of novel haplotypes along with discrimination of Echinococcus spp. through regional patterns can unambiguously illustrate the real taxonomic status of parasite in Central Iran.

Genetic variability and discrimination of low doses of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification assay as a field-friendly molecular tool

“…Low genetic diversity (HD; 0.295) of T. canis isolates can explain to be conserved the nature of ITS2 gene and its high copy number or small effective sample size [35]. In addition, this may be related to fertilization of Toxocara adult worm and/or to the longevity of the parasite in the stray dogs [36].…”

Echinococcus granulosus genotypes in Iran: a systematic review

“…;Pestechian et al, 2014;Sharafi et al, 2014;Vahedi et al, 2014;Fadakar et al, 2015;Farhadi et al, 2015;Rostami et al, 2015;Spotin et al, 2015;Oskouei et al, 2016;Maldonado et al, 2017 …”

Discrimination of Mixed Infections of Echinococcus Species Based on in Silico Sequence Analysis: A New Way of Reflecting Overlapped Strains in Indigenous Areas

“…Interestingly, the following taxonomic positions of these genotypes are defined based on an extensive revision: E. granulosus sensu stricto (G1 -G3), E. equines (G4) that are classified as non-zoonotic strains, and E. ortleppi (G5), E. canadensis (G6-G10) and E. felidis ('lion strain') as zoonotic strains (4-7). However, some genotypes have remained unknown in the consequence of overlapping cycles among various intermediate -definitive hosts (8,9). actions, the occurrence of mixed (dual/triple) infections would not be unexpected.…”

“…So far, at least four genotypes (G1, G2, G3, and G6) of E. granulosus have been reported in different parts of Iran (9,(18)(19)(20) where according to the circulation of a variety of intermediate hosts, this seems to be underestimated. However, many Iranian researchers are focusing on genotyping of E. granulosus in different regions of Iran and among populations of sheep, cattle, goat, and camel (19)(20)(21)(22)(23)(24).…”