| Summary: | While hybridization probe-based real-time PCR assays targeting highly repetitive multi-copy genome sequences for the diagnosis of <i>S. mansoni</i> complex or <i>S. haematobium</i> complex from human serum are well established, reports on the evaluation of respective assays for the identification of <i>S. japonicum</i> complex DNA in human serum are scarce. Here, we assessed the potential use of the retrotransposon sequences <i>SjR2</i> and <i>SjCHGCS19</i> from <i>S. japonicum</i>, <i>S. mekongi</i> and <i>S. malayensis</i> for the diagnosis of Asian <i>Schistosoma</i> infections. Based on available <i>S. japonicum</i> sequences and newly provided <i>S. mekongi</i> and <i>S. malayensis</i> sequences, hybridization probe-based real-time PCRs targeting <i>SjR2</i> and <i>SjCHGCS19</i> of the <i>S. japonicum</i> complex were designed both as consensus primer assays as well as multi-primer assays for the coverage of multiple variants of the target sequences. The assays were established using plasmids and <i>S. mekongi</i> DNA. While the consensus primer assays failed to detect <i>S. mekongi</i> DNA in human serum samples, the multi-primer assays showed positive or borderline positive results but only in 9.8% (6/61) of serum samples from patients with confirmed <i>S. mekongi</i> infections. Some cross-reactions with samples positive for <i>S. mansoni</i> or <i>S. haematobium</i> were observed but with the <i>SjCHGCS19</i>-PCR only. In spite of the low sensitivity, the presented experience may guide future evaluations of <i>S. japonicum-</i>complex-specific PCRs from human serum.
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