Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. Refer to individual Series

Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v2 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4943 viral probes for the detection of 416 viruses (112 viruses transmitted by small mammals and 304 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

Project description:Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n= 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods. The SMAvirusChip v1 microarray includes more than 15,000 oligonucleotide probes (60-mers long) for the detection of viruses transmitted by small mammals and arthropods. The sequences of 4209 viral probes for the detection of 409 viruses (109 viruses transmitted by small mammals and 300 arboviruses) were included in this platform. Positive and negative control oligonucleotide probes were also included in the design.

Project description:Colorectal cancer (CRC) is the third leading cause of cancer mortality in Switzerland, and kills 1600 people annually. Most deaths could be prevented by screening, but the 2012 Swiss national health survey found that only 40% of 50-75-year-olds had been tested within recommended intervals (26% with colonoscopy in the last 10 year, 7% with fecal occult blood test [FOBT] in the last 2 years, and 7% with both). If screening starts at age 50, in the average risk population absolute risk of dying from CRC at age 80 can be cut from 2% to 1%, reducing relative risk by 50%. Since 2013, Switzerland has reimbursed screening by colonoscopy every 10 years or FOBT every 2 years for adults 50-69 years old. Conforming to current recommendations, the Federal Office of Public Health (FOPH) officially recognizes both screening modalities. When patients are offered a choice of screening test (colonoscopy vs. FOBT), they are as likely to opt for one as the other. Patient preferences are unlikely to vary much between PCP practices, so distribution of colonoscopy and FOBT within each practice should also be roughly equal. Family physicians are recognized as the most trusted professional to discuss CRC screening in Switzerland. However, many primary care physicians (PCPs) prefer prescribing colonoscopy over FOBT, but physician preference for method seems to vary widely between regions. If physician preferences and local medical culture currently influence choice of method more strongly than patient preferences, encouraging PCPs to diagnose patient preferences for screening method may reduce the number of PCPs who prescribe only one method. An earlier study in Switzerland showed that training PCPs and giving them educational support and decision aids raised the number who intend to prescribe colonoscopy and FOBT in equal proportions. A randomized controlled trial in the US showed that when patients were offered both FOBT and colonoscopy rather than only colonoscopy alone, more patients were screened for CRC. Offering choice of method may thus increase overall screening rates. The Swiss Sentinel Surveillance Network (Sentinella) is a cooperative surveillance project including the Federal Office of Public Health (FOPH), PCPs representatives and the five Swiss institutes of family medicine. A sample of 150 to 250 general practitioners, internists and pediatricians in private practices from all regions of Switzerland report weekly morbidity data to the network using irreversibly anonymized patient data collected during consultations. In 2017, 91 out of 129 eligible PCPs of the Sentinella network participated in a cross-sectional data collection on CRC screening. The Sentinella network appears ideally suited to perform an intervention in order to modify screening practices and measure outcomes using the same collection form as in 2017. This study will test the benefits of a prepackaged training program in participatory medicine sent by post to PCPs in Switzerland. The package is designed to improve their diagnoses of patient preferences for screening and screening method (colonoscopy or FOBT). The study begins with the hypothesis that giving PCPs evidence summaries on CRC screening, decision aids for patients, and performance feedback on the 2017 data collection will increase the number of PCPs whose patients include at least one screened with FOBT, and who will prescribe at least one FOBT/FIT (Fecal Immunochemical Test) instead of prescribing only colonoscopy. This might reduce variation in care between PCP practices by increasing variation in methods of screening prescribed within each PCP practices. Analyses from the 2017 data collection suggest that fewer patients refused CRC testing in practices that offered both methods than in practices that offered only colonoscopy. This intervention might increase screening rates overall, while respecting patient’s autonomy to refuse the test and to be prescribed the test they prefer. The study will compare outcomes among PCPs allocated to the intervention group to those in the control group, and will be measured by collecting anonymous structured patient data on 40 consecutive patients by PCPs and questionnaires filled by PCPs. The study is designed to fit within the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework for structuring data collection. RE-AIM ensures that a study’s outcomes for future implementation and dissemination works are collected. The RE-AIM criteria will be used to identify the translatability and public health impact of this intervention, and for making clear to future stakeholders the internal and external validity of study results.

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Swiss Viral variants Wastewater Surveillance

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