**1. Introduction**

*Trypanosoma cruzi (T. cruzi)* is a heterogeneous parasite, in which strains are composed of different sub-populations or clones that circulate in nature between triatomine vectors, wild and domestic mammals, including man. The need for adaptation and survival in different hosts appears to be responsible for the high genetic diversity of the parasite [1] and the various clinical manifestations observed in Chagas' disease [2, 3].

The heterogeneity of strains of this parasite has been demonstrated using different markers: morphological, biological susceptibility to chemotherapeutic agents, immunological, biochemical and molecular [4–13].

Considerable advances have been made to understand the genetic makeup of *T. cruzi* and the process that involves the control of gene expression of the parasite. Molecular genetic markers have been used to correlate different strains with their different biological properties, clinical and epidemiological characteristics [14].

Ribosomal gene sequences have been widely used to infer phylogenetic relationships among the trypanosomatids and representatives of other families of the order Kinetoplastida and phylum Euglenozoa. In trypanosomes, the sequence of the 24S subunit is interrupted by an internal spacer generating two molecules, 24Sα and 24Sβ.

The conserved non-transcribed regions of the pre-rRNA correspond to the internal transcribed spacer (ITS) and external (ETS). The presence of several regions, transcribed or not, that display varying degrees of variability, entail a high degree of polymorphism of the ribosomal cistrons and for this reason, have proved to be excellent as a tool for identification and phylogenetic studies of trypanosomes [15]. The ITS spacers are highly variable compared with ITS which, in turn, are much more variable regions of the Small Sub Unit (SSU) and Large Sub Unit (LSU). Analysis of polymorphism of ribosomal sequences has been used in the identification and genotyping of strains.

Souto and cols. [16] standardized a marker based on the region of the LSU 24Sα, which distinguishes the *T. cruzi* I and *T. cruzi* II strains. Another excellent marker for the study of diversity in *T. cruzi* gene is the Mini-Exon. The identification of strains (genotyping) using PCR methods based on gene sequences of mini-exon has been widely used [16–20].

Due to its organization comprising regions with differing degrees of conservation of the mini-exon genes have been used for diagnosis purposes and taxonomic. Each repeating unit of the Spliced Leader (SL) gene can be basically divided into three parts: a highly conserved exon of 39 nucleotides, an intron moderately conserved nucleotides 50–100 and an intergenic spacer region, which varies in size and sequence among trypanosomes species and strains. There are about 200 repeated copies of the SL gene "in tandem" in the trypanosomes genome which are therefore a good target for diagnosis [21–23]. The use of PCR methods for genotyping based on the miniexon and ribosomal genes segregates this parasite into three major lineages: *T. cruzi* I, *T. cruzi* II and Z3 [16, 20, 24].

Augusto-Pinto and cols [25] demonstrated that *T. cruzi* can be divided into three distinct haplogroups called A, B and C, based on an analysis of polymorphisms in the MSH2 gene of several strains of this parasite. It was subsequently found that strains of haplogroups B and C have a lower efficiency of the mismatching error repair (MMR) compared to strains of haplogroup A after treatment with cisplatin hydroxide and hydrogen [26].

These results suggested that the lower efficiency of MMR of haplogroups B and C could be associated with an increased generation of genetic variability in these strains. Thus an analysis of genetic variability by targeting the gene encoding the *T. cruzi* called TcAg48 is present in a large number of copies in the genome of this parasite. Digestion of the amplified product of a region of this gene with the restriction enzyme *Hha*I allowed by the group 35 strains in the same haplogroups already described for the analysis of MSH2. It was found even greater genetic variability of this antigen in strains belonging to haplogroups B and C, which showed a less efficient MMR. Some of the haplogroup B strains have a digestion pattern with characteristics of both strains of haplogroup B and C, indicating a hybrid character.

*Evaluation of Molecular Variability of Isolates of* Trypanosoma cruzi *in the State… DOI: http://dx.doi.org/10.5772/intechopen.104498*

Zingales and cols [13] standardized nomenclature into six groups (*T. cruzi* I-VI), each group termed DTU ("discrete typing unit"), where DTU is defined by a set of strains that are genetically similar, and that can be identified by molecular markers common or immunological [27]; DTUs *T. cruzi* I and *T. cruzi* II respond to two groups originally defined at the first meeting [28]. Although it was evident that the V-VI DTUs correspond to hybrid organisms, their origin swims from different events of genetic exchange.

This study aimed to evaluate the genetic diversity of 14 isolates of specimens of *Triatoma vitticeps* collected from the locality of Triunfo, 2nd District of the municipality of Santa Maria Madalena and Conceição Macabu from Rio de Janeiro State.
