Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: Age distribution of HAdV-positive (dark gray) and HAdV-negative (light gray) patients within the digital/virologic surveillance cohort Age groups: Neonates: 0–28 days, infants: 29 days–12 months, toddlers: 13–24 months, pre-school children: 3–5 years, schoolchildren/adolescents: 6–18 years.

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques:

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: Baseline patient characteristics

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques:

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: Descriptive list of co-infections (N = 322)

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques:

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: Scatterplot of ViVI Scores measured in HAdV-positive patients (N = 571) ViVI Score values may range from 0–48, reflecting increasing disease severity with increasing ViVI Scores. The vertical bold black line marks the cohort average ViVI Score of 14.5, i.e. the 50 th percentile in the overall cohort. Dark gray dots indicate cases with above-average ViVI Scores and light gray dots indicate cases with below-average ViVI Scores. Numbers (n) indicate the number of cases below the cohort average ViVI Score and above the cohort average, respectively.

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques:

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: ViVI Score dynamics illustrating disease progression in the HAdV-D80 index case Initial X-ray on hospital day 4 (I) showed diffuse patchy lung infiltrates, corresponding to respiratory distress syndrome grade I. Follow-up imaging on hospital day 10 (II) showed homogenic lung opacity due to diffuse bilateral atelectasis (“white lungs”), corresponding to respiratory distress syndrome grade IV. Follow-up imaging on hospital day 14 (III) revealed generalized compartment syndrome with ongoing abdominal swelling, pleural, and pericardial effusion. (B) Adenovirus load kinetics in different body compartments over time: Cq values (inverted vertical axis) during PCR-testing were used to estimate virus load. Abbreviations: ViVI – Vienna Vaccine Safety Initiative, Cq-Quantitation Cycle.

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques: Biomarker Discovery, Imaging, Virus, Quantitation Assay

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: Relative variable importance analysis for top-5 clinical features of HAdV-positive patients (n = 571) using the permutation feature importance measure The relative feature importance of the most important feature is set to 100. The values of the other features are scaled accordingly relative to the most important feature. Level of importance of top-5 features is reflected as follows: white indicates importance <33, gray indicates importance ≥33 and <66, black indicates importance ≥66.

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques:

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: HAdV-D80 phylogenetic clustering (whole genome, E4, E3) Phylogenetic clustering of the HAdV-D80 (A) whole genome, (B) early gene region 4 (E4), and (C) early gene region 3 (E3) sequence with all other HAdV-D prototype sequences. Bootstrap values > 80% were considered robust. Arrow indicates the clustering position of HAdV-D80.

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques: Sequencing

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet: HAdV-D80 phylogenetic clustering (hexon, fiber, penton) Phylogenetic clustering of the HAdV-D80 (A) hexon gene, (B) fiber gene, and (C) penton base gene sequence with all other HAdV-D prototype sequences. Bootstrap values > 80% were considered robust. Arrow indicates the clustering position of HAdV-D80.

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques: Sequencing

Journal: iScience

Article Title: Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations

doi: 10.1016/j.isci.2022.104276

Figure Lengend Snippet:

Article Snippet: Oligonucleotides for hAdV species genotyping by FMCA , National Reference Center for Influenza , Barbara Chmielewicz, Andreas Nitsche, Brunhilde Schweiger, Heinz Ellerbrok, Development of a PCR-Based Assay for Detection, Quantification, and Genotyping of Human Adenoviruses, Clinical Chemistry, Volume 51, Issue 8, 1 August 2005, Pages 1365–1373, https://doi.org/10.1373/clinchem.2004.045088 , https://academic.oup.com/clinchem/article/51/8/1365/5629946.

Techniques: Virus, Recombinant, DNA Library Preparation, Software, Clinical Proteomics

Journal: PLoS Neglected Tropical Diseases

Article Title: Performance Testing of PCR Assay in Blood Samples for the Diagnosis of Toxoplasmic Encephalitis in AIDS Patients from the French Departments of America and Genetic Diversity of Toxoplasma gondii : A Prospective and Multicentric Study

doi: 10.1371/journal.pntd.0004790

Figure Lengend Snippet: Genotyping analysis with 15 microsatellite markers of 3 reference type I, II, and III strains, the HTI01 strain isolated in the present study, and 43 strains collected in human cases of toxoplasmosis from South America and the Caribbean region by the French national reference center for toxoplasmosis.

Article Snippet: For comparison, we included the genotyping data of three reference strains and of 43 strains collected from human cases of toxoplasmosis in the Caribbean and in South America by the French national reference center for toxoplasmosis ( ).

Techniques: Isolation

Journal: PLoS Neglected Tropical Diseases

Article Title: Performance Testing of PCR Assay in Blood Samples for the Diagnosis of Toxoplasmic Encephalitis in AIDS Patients from the French Departments of America and Genetic Diversity of Toxoplasma gondii : A Prospective and Multicentric Study

doi: 10.1371/journal.pntd.0004790

Figure Lengend Snippet: Squares are for the type I (GT1), II (ME49), and III (VEG) reference strains; the yellow point is for the HTI01 strain isolated in the present study; black points (BRA01–10) are for strains collected in patients infected with imported strains whose epidemiological and genotyping investigation revealed that the origin of infection was likely Brazil; red points (AMZ 1–18) are for strains collected in patients with Amazonian toxoplasmosis who had been infected with wild strains from the rainforest of French Guiana; green points (GUF01–05) are for strains from toxoplasmosis cases diagnosed in babies with congenital toxoplasmosis or immunocompromised patients living in the anthropized areas of French Guiana; blue points are for strains collected in patients infected in Guadeloupe (GLP01–05) and Martinique (MTQ01–05), both in the French West Indies.

Article Snippet: For comparison, we included the genotyping data of three reference strains and of 43 strains collected from human cases of toxoplasmosis in the Caribbean and in South America by the French national reference center for toxoplasmosis ( ).

Techniques: Isolation, Infection