Background: Tropheryma whipplei is the causative pathogen of Whipple’s disease and other acute and chronic manifestations. Children have been identified as reservoirs of this bacterium especially in low-middle income countries. No information is currently available on the dissemination of T. whipplei in Iran. Therefore, the aim of this study was to investigate the presence of T. whipplei in children with immunodeficiency. Methods: This cross-sectional study was performed from July 2018 to February 2019 in Qom province (central Iran). Stool samples were collected from immuno-compromised children. T. whipplei was tested by SYBR Green and Taq-Man Real-time PCR assays. For confirmation, sequencing of the isolated bacteria was done. Results: One hundred and 30 children with a mean age of 56.7 months were enrolled. Acute lymphocytic leukemia was the most reported immunodeficient disease (77%), followed by non-Hodgkin lymphoma and retinoblastoma. The majority of the children were undergoing chemotherapy during the study. Thirteen (10%) children had T. whipplei DNA in the collected stools. Sequencing results confirmed T. whipplei identification in all the cases. Eight out of 70 (11.4%) children under 5 years old resulted positive. Conclusion: This is the first study showing the circulation of T. whipplei among immunocompromised children in Iran. More epidemiological studies are needed to evaluate the prevalence of this pathogen in different risk groups in Iran and to increase the knowledge of its rare clinical manifestations.

Background: The reference test for SARS-CoV-2 detection is the reverse transcriptase real time PCR (real time RT-PCR). However, evidences reported that real time RT-PCR has a lower sensitivity compared with the droplet digital PCR (ddPCR) leading to possible false negative in low viral load cases. Methods: We used ddPCR for viral genes N1 and N2 on 20 negative (no detection) samples from symptomatic hospitalized COVID-patients presenting fluctuating real time RT-PCR results and 10 suspected samples (Ct value>35) from asymptomatic not hospitalized subjects. Results: ddPCR performed on RNA revealed 65% of positivity for at least one viral target in the hospitalized patients group of samples (35% for N1 and N2, 10% only for N1 and 20% only for N2) and 50% in the suspected cases (30% for N1 and N2, while 20% only for N2). On hospitalized patients’ samples, we applied also a direct ddPCR approach on the swab material, achieving an overall positivity of 83%. Conclusion: ddPCR, in particular the direct quantitation on swabs, shows a sensitivity advantage for the SARS-CoV-2 identification and may be useful to reduce the false negative diagnosis, especially for low viral load suspected samples.

Background: the devastating outbreak of COVID-19 poses serious challenges for the diagnostics laboratories, which are often facing global shortage of reagents and equipment. With the aim of increasing the diagnostic throughput for SARS-CoV-2 molecular test, the purpose of this study was to validate an additional RNA extraction method respect to those already recommended by WHO and the US Centers for Disease Control and Prevention (CDC). Methods: a new protocol for RNA extraction from nasopharyngeal swab was set up, adapting the Qiagen RNeasy 96 plate and validated on a set of 100 clinical samples analyzed in parallel by Roche-Magnapure method (already recommended by CDC guidelines). Results: the internal control and target genes analysis showed a good agreement between the two extraction methods indicating that the two methods can be considered equivalent and that the RNeasy-adapted method can be applied for the SARS-CoV-2 diagnostics. The addition of this new extraction method resulted in a throughput increase for SARS-CoV-2 molecular test of about 2000 samples/month during the initial months of the pandemic emergency in which the lack of reagents for the extraction led to an insufficient sample processing throughput of the analysis of the swabs.