Validation of GeneFinder COVID-19 Ag Plus Rapid Test and Its Potential Utility to Slowing Infection Waves: A Single-Center Laboratory Evaluation Study.

Diagnostic laboratory tools are essential to keep everyone safe and track newly emerging variants; on the other hand, "filter" screening tests recognizing positivity are valuable tools to avoid hectic laboratory work that, besides COVID-19, are also part of the routine. Therefore, complementary assays, such as rapid antigen tests (RATs), are essential in controlling and monitoring virus spread within the community, especially in the asymptomatic population. A subset of nasopharyngeal swab specimens resulted in SARS-CoV-2 positive and investigated for genomic characterization were used for RAT validation. RATs were performed immediately after sampling, following the manufacturer's instructions (reading at 15 min). RT-PCRs were carried out within 24 h of specimens' collection. Out of 603 patients, 145 (24.05%) tested positive by RT-PCR and RAT and 451 (74.79%) tested negative by both methods; discordant results (RT-PCR+/RAT- or RT-PCR-/RAT+) were obtained in 7 patients (1.16%). RATs' overall specificity and sensitivity were 96.03% (95%CI: 91.55-98.53%) and 99.78% (95%CI: 98.77-99.99%), respectively, taking RT-PCR as the reference. Overall, RAT negative predictive value was 98.69% (95%CI 97.17-99.40%). The GeneFinder COVID-19 Ag Plus Rapid Test performed well as a screening test for early diagnosis of COVID-19, especially in asymptomatic subjects. The data suggested that patients with RT-PCR-proven COVID-19 testing negative by RAT are unlikely to be infectious. GeneFinder COVID-19 Ag Plus Rapid Test also works on variants of concern (VOC) delta and omicron BA.1 and BA.2.

Proof of Concept for a Portable Platform for Molecular Diagnosis of Tropical Diseases: On-Chip Ready-to-Use Real-Time Quantitative PCR for Detection of Trypanosoma cruzi or Plasmodium spp.

Although molecular diagnostics is well established in clinical laboratories, its full potential has not been extended to field settings. Typically, diagnostic real-time quantitative PCR (qPCR) reagents require temperature-controlled transportation and storage. Furthermore, thermocyclers are bulky and fragile, requiring good infrastructure for optimal operation. These major hurdles strongly limit use of molecular-based tests in low-resource scenarios. Herein, Trypanosoma cruzi or Plasmodium spp. DNA were detected with qPCR using commercial equipment (ABI7500 instrument) and a prototype platform comprising a portable device and a silicon chip, named Q3-Plus. In addition, a ready-to-use reaction format, where all qPCR reagents are stored on plate or on chip, was compared with the traditional freezer-stored format. No significant differences were observed in detecting T. cruzi or Plasmodium spp. DNA between thermocyclers, as well as between reagents' formats, for storage periods of up to 28 days (at 2°C to 8°C or 21°C to 23°C, respectively). When challenged with patients' samples, the Q3-Plus system performed as efficiently as the standard equipment for Plasmodium spp. DNA detection, showing it to be a valuable solution to malaria point-of-care diagnostics. Detection of T. cruzi DNA in chronic patients' samples using the Q3-Plus system yielded approximately 50% efficiency relative to the ABI7500. These results are essential to support future endeavors to bring molecular diagnostics to the point of care, where most needed.

Enabling heterogeneous data integration and biomedical event prediction through ICT: the test case of cancer reoccurrence.

Early prediction of cancer reoccurrence constitutes a challenge for oncologists and surgeons. This chapter describes one ongoing experience, the EU-Project NeoMark, where scientists from different medical and biology research fields joined efforts with Information Technology experts to identify methods and algorithms that are able to early predict the reoccurrence risk for one of the most devastating tumors, the oral cavity squamous cell carcinoma (OSCC). The challenge of NeoMark is to develop algorithms able to identify a "signature" or bio-profile of the disease, by integrating multiscale and multivariate data from medical images, genomic profile from tissue and circulating cells RNA, and other medical parameters collected from patients before and after treatment. A limited number of relevant biomarkers will be identified and used in a real-time PCR device for early detection of disease reoccurrence.

Polymerase chain reaction of 2-kb cyanobacterial gene and human anti-alpha1-chymotrypsin gene from genomic DNA on the In-Check single-use microfabricated silicon chip.

The microfabricated chip is a promising format for automating and miniaturizing the multiple steps of genotyping. We tested an innovative silicon biochip (In-Check Lab-on-Chip; STMicroelectronics, Agrate Brianza, Italy) designed for polymerase chain reaction (PCR) analysis of complex biological samples. The chip is mounted on a 1x3-in(2). plastic slide that provides the necessary mechanical, thermal, electrical, and fluidic connections. A temperature control system drives the chip to the desired temperatures, and a graphical user interface allows experimenters to define cycling conditions and monitor reactions in real time. During thermal cycling, we recorded a cooling rate of 3.2 degrees C/s and a heating rate of 11 degrees C/s. The temperature maintained at each thermal plateau was within 0.13 degrees C of the programmed temperature at three sensors. From 0.5 ng/microl genomic DNA, the In-Check device successfully amplified the 2060-bp cyanobacterial 16S rRNA gene and the 330-bp human anti-alpha(1)-chymotrypsin gene. The shortest PCR protocol that produced an amplicon by capillary electrophoresis comprised 30 cycles and was 22.5 min long. These thermal cycling characteristics suggest that the In-Check device will permit future development of a genotyping lab-on-a-chip device, yielding results in a short time from a limited amount of biological starting material.