Deep sequencing to detect diversity of Trypanosoma cruzi infection in patients co-infected with HIV and Chagas disease.

Chagas disease, caused by Trypanosoma cruzi, can reactivate and cause severe acute disease in immunocompromised patients such as those infected with HIV. We conducted amplicon deep sequencing of a 327-base pair fragment of the tcscd5 gene using an Ion Torrent PGM directly from clinical samples from HIV patients with high parasitemia. We describe the within host diversity, both characterizing the discrete typing unit (DTUs) of the infections and confirming the presence of multi-strain infections, directly from clinical samples. This method can rapidly provide information on the genetic diversity of T. cruzi infection, which can have direct impacts on clinical disease.