Understanding pathogen transmission is key to effective infection prevention. From February to December 2021, we implemented genomics-enhanced contact tracing for SARS-CoV-2 in Düsseldorf, Germany, integrating data on 32,380 cases, 49,906 contact tracing records, 162 outbreaks, and 8,028 viral genomes (sequencing coverage 24.5%). Combining epidemiological and genetic data, we found a putative infection source for 19% of sequenced and 44% of all cases. Household-associated transmission accounted for up to 40% of all cases; genetic links for epidemiologically unexplained cases suggested limited sensitivity of classical contact tracing for non-household links. Outbreaks were associated with 8% of cases; school, kindergarten and nightlife outbreaks were strongly connected to the community, with nightlife outbreaks showing a strong post-outbreak increase in genetically associated cases. Sequencing detected previously unrecognized links between school outbreaks and 18% additional outbreak-associated sequenced cases. Across analyses, schools, kindergartens and gastronomy and nightlife settings were consistently identified as important contributors to transmission dynamics. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement We acknowledge funding by the Ministry for Work, Health and Social Affairs of the State of North Rhine-Westphalia ("24.04.01 Gen. u. IKA" and CPS-1-1A); the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung; Netzwerk Universitätsmedizin, GenSurv/MolTraX), award number 01KX2021; by the Jürgen Manchot Foundation; and by the Deutsche Forschungsgemeinschaft (DFG) award 428994620. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The ethics committee of the Medical Faculty of Heinrich Heine University Düsseldorf gave ethical approval for this work (#2020-839). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Code developed during the present study is available upon request to the authors.

Abstract Background Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmission networks by integration of molecular epidemiology into classical contact tracing. Methods In collaboration with local public health authorities, we set up an integrated system of genomic surveillance in an urban setting, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) integration of public health authority contact tracing data, and d) a user-friendly dashboard application as a central data analysis platform. Results Application of the integrated system from August to December 2020 enabled a characterization of viral population structure, analysis of 4 outbreaks at a maximum care hospital, and genetically based identification of 5 putative population infection clusters, all of which were confirmed by contact tracing. The system contributed to the development of improved hospital infection control and prevention measures and enabled the identification of previously unrecognized transmission chains, involving a martial arts gym and establishing a link between the hospital to the local population. Conclusions Integrated systems of genomic surveillance could contribute to the monitoring and, potentially, improved management of SARS-CoV-2 transmission in the population.

BackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.AimWe demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.MethodsGenomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.ResultsCluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.ConclusionIGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.

Viral genome sequencing can address key questions about SARS-CoV-2 evolution and viral transmission. Here, we present an integrated system of genomic surveillance in the German city of Dusseldorf, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) analysis of hospital outbreaks, d) integration of public health authority contact tracing data, and e) a user-friendly dashboard application as a central data analysis platform. The generated surveillance sequencing data (n = 320 SARS-CoV-2 genomes) showed that the development of the local viral population structure from August to December 2020 was consistent with European trends, with the notable absence of SARS-CoV-2 variants 20I/501Y.V1/B.1.1.7 and B.1.351 until the end of the local sampling period. Against a background of local surveillance and other publicly available SARS-CoV-2 data, four putative SARS-CoV-2 outbreaks at Dusseldorf University Hospital between October and December 2020 (n = 44 viral genomes) were investigated and confirmed as clonal, contributing to the development of improved infection control and prevention measures. An analysis of the generated surveillance sequencing data with respect to infection clusters in the population based on a greedy clustering algorithm identified five candidate clusters, all of which were subsequently confirmed by the integration of public health authority contact tracing data and shown to be represent transmission settings of particular relevance (schools, care homes). A joint analysis of outbreak and surveillance data identified a potential transmission of an outbreak strain from the local population into the hospital and back; and an in-depth analysis of one population infection cluster combining genetic with contact tracing data enabled the identification of a previously unrecognized population transmission chain involving a martial arts gym. Based on these results and a real-time sequencing experiment in which we demonstrated the feasibility of achieving sample-to-turnaround times of <30 hours with the Oxford Nanopore technology, we discuss the potential benefits of routine ultra-fast sequencing of all detected infections for contact tracing, infection cluster detection, and, ultimately, improved management of the SARS-CoV-2 pandemic.

Integration of genomic surveillance with contact tracing provides a powerful tool for the reconstruction of person-to-person pathogen transmission chains. We report two large clusters of SARS-CoV-2 cases ("Delta" clade, 110 cases combined) detected in July 2021 by Integrated Genomic Surveillance in Dusseldorf. Structured interviews and deep contact tracing demonstrated an association to a single SARS-CoV-2 infected return traveller (Cluster 1) and to return travel from Catalonia and other European countries (Cluster 2), highlighting the importance of containing travel-imported SARS-CoV-2 infections.

BACKGROUND:Fuchs endothelial corneal dystrophy (FECD) is one of the most common indications for corneal transplants. FECD is associated with various genes, e.g., COL8A2 or SLC4A11. Among other things a TGC trinucleotide repeat expansion in intron 2 of the TCF4 gene has been characterised in FECD patients and the allele G of the polymorphism rs613872 in intron 3 of the same gene has been associated with this disease. Our intention was to investigate sources in molecular genetics in the German population and to calculate the odds ratio as indicator for the chance to suffer from FECD.PATIENTS AND METHOD:42 unrelated FECD patients, 93 unrelated controls and 17 members of a family with four FECD affected patients have been examined for the described changes in the TCF4 gene. After amplification of the TGC repeats with specific PCR the obtained products were electrophoretically divided according to their length and investigated with a triplet-primed PCR. Polymorphism rs613872 was analysed by Sanger sequencing. All coding exons of the adjacent genes TCF4 and LOXHD1 were sequenced in six patients in order to exclude potential disease associated mutations.RESULTS:33 out of 42 unrelated analysed patients (79 %) had a TGC repeat expansion (> 50 TGC repeats) in intron 2 of the TCF4 gene. Out of 93 controls only 10 (10.8 %) showed an expanded allele. In the family the four diseased and four healthy subjects of the 17 examined family members had an expanded allele. Analysis of the polymorphism rs613872 in intron 3 of the TCF4 gene exhibited 33 of 42 unrelated patients (78.6 %) heterozygous TG and four homozygous GG (9.5 %). 65 of 93 controls were homozygous TT (69.9 %) and only 21 heterozygous TG (22.6 %). Of the 17 family members nine had the genotype TG, including the four FECD patients. Sequencing of the coding exons of TCF4 and LOXHD1 in six patients showed no variant described with FECD. The odds ratio as indicator for being affected by FECD in our data for the expanded TGC allele is 30. The chance of being affected is thus 30 times higher when someone exhibits the expanded allele. For a carrier of the risk allele G the chance is 16.5 times higher.DISCUSSION:An expanded TGC allele with more than 50 TGC repeats in intron 2 and the described risk allele G of the polymorphism rs613872 in intron 3 of the TCF4 gene appear as an association to FECD. The chance to be affected by FECD is up to 30 times higher. With molecular genetics also donors with clinically unknown FECD may be detected.

Hintergrund: Als molekulargenetische Ursache der Fuchs-Hornhautendotheldystrophie (FECD), eine der häufigsten Indikationen für eine Keratoplastik, wurde sowohl eine TGC-Trinukleotid-Repeat-Expansion im Intron 2 des TCF4-Gens als auch das Allel G des Polymorphismus rs613872 im Intron 3 desselben Gens in verschiedenen Arbeiten beschrieben. Unser Ziel war es, die molekulargenetische Ursache in der deutschen Bevölkerung zu untersuchen und das Odds Ratio als Indikator für die Chance zu erkranken zu berechnen. Material und Methoden: Wir untersuchten 42 nicht verwandte Patienten mit FECD, 93 nicht verwandte Kontrollprobanden und 17 Mitglieder einer Familie mit 4 betroffenen Patienten auf beide beschriebene Veränderungen im TCF4-Gen. Die TGC-Repeats wurden mit spezifischer PCR amplifiziert, die gewonnenen Produkte elektrophoretisch aufgetrennt und mit einer Triplet-primed PCR untersucht. Die Untersuchung des Polymorphismus rs613872 erfolgte durch Sanger-Sequenzierung. Alle codierenden Exons der benachbarten Gene TCF4 und LOXHD1 wurden bei 6 Patienten nach Sanger sequenziert, um eventuelle Mutationen in diesen Genen als Krankheitsursache auszuschließen. Ergebnisse: Von den 42 untersuchten nicht verwandten Patienten hatten 33 (79 %) eine TGC-Repeat-Expansion (> 50 TGC-Repeats) im Intron 2 des TCF4-Gens. Bei 93 Kontrollprobanden waren dies nur 10 (10,8 %). Für den Polymorphismus rs613872 im Intron 3 des TCF4-Gens zeigten sich 33 der 42 nicht verwandten Patienten (78,6 %) heterozygot TG und 4 homozygot GG (9,5 %). Von der Kontrollgruppe zeigten sich 65 der untersuchten 93 Probanden homozygot TT (69,9 %) und nur 21 heterozygot TG (22,6 %). Bei der Sequenzierung der codierenden Exons von TCF4 und LOXHD1 konnte keine mit der Erkrankung beschriebene Variante gezeigt werden. Das Odds Ratio als Maßzahl, von der Erkrankung betroffen zu sein, ist in unseren Daten bei expandiertem TGC-Repeat-Allel 30. Die Chance, von der FECD betroffen zu sein, ist so 30-fach erhöht. Für Träger des Risikoallels G besteht eine 16,5-fach erhöhte Chance. Diskussion: Auch bei Patienten aus unserem geografischen Gebiet stellt ein expandiertes Allel mit mehr als 50 TGC-Repeats im Intron 2 und das beschriebene Risikoallel G des Polymorphismus rs613872 im Intron 3 des TCF4-Gens eine Assoziation mit einer bis zu 30-fach höheren Chance dar, an der FECD zu erkranken. Durch die Molekulargenetik können somit auch Spender mit noch nicht klinisch erfasster FECD detektiert werden.

Mit der Etablierung der lamellierenden Techniken in der Hornhautchirurgie bei Erkrankungen des Hornhautendothels nimmt die Diagnostik bei Hornhautdystrophien einen immer höheren Stellenwert ein.

Zusammenfassung Es werden wichtige Probleme in der Diagnostik bei Patienten mit Arthrogryposis dargestellt und Definitionen eingeführt. Danach werden praktische Ansätze für die Diagnostik und humangenetische Betreuung vorgeschlagen.

Zusammenfassung Schwere kongenitale Lipodystrophie, progeroide Fazies und variable Symptome eines Marfan-Syndroms stellen eine eigene Entität dar, nämlich eine Sonderform des Marfan-Syndroms mit einer trunkierenden Mutation am 3’-Ende des Fibrillin-1-Gens im vorletzten und letzten kodierenden Exon. Das mutierte Protein entgeht hochwahrscheinlich dem „nonsense mediated decay“ (NMD) und ruft dadurch offenbar diesen speziellen Phänotyp hervor. Es sind bislang erst 5 Fälle mit diesem Krankheitsbild publiziert worden; bei 3 dieser Patienten wurde das Krankheitsbild bisher molekulargenetisch bestätigt. Bei folgenden klinischen Zeichen sollte diese Diagnose berücksichtigt und abgeklärt werden: intrauterine Wachstumsretardierung, progeroide Fazies schon bei Geburt, vermindertes subkutanes Fettgewebe und variable Zeichen eines Marfan-Syndroms.

The cerebellum is the primary motor coordination centre of the central nervous system. Lesions or congenital defects of the cerebellum cause incoordination of the muscles resulting in irregular gait and falling. Recently, we reported a large family with cerebellum hypoplasia and quadrupedal locomotion as a recessive trait, which we mapped to chromosome 17p13. We identified one additional family with the same condition and mapped the underlying gene to a 14-cM interval on chromosome 9ptel using a genome-wide linkage approach. Sequencing of candidate genes identified a homozygous frameshift mutation in the very low-density lipoprotein receptor (VLDLR) gene in all affected individuals. The association of cerebellar hypoplasia with mutations in VLDLR has been reported previously in the Hutterite population and in a family from Iran. However, quadrupedal locomotion was never observed indicating that environmental factors play a major role in the pathogenesis of this form of locomotion.

Excessive skin wrinkling and cutis laxa are seen in many genetic conditions and overlapping features can make a clinical diagnosis difficult. Here we report on 22 Omani patients from 11 consanguineous families with the diagnosis of wrinkly skin syndrome (WSS, OMIM 278250) or geroderma osteodysplasticum hereditaria (GO, OMIM 231070). The WSS phenotype evolves during early childhood and includes a generalized and excessive skin wrinkling, dental problems, herniae, foot deformities, hip dislocations, growth retardation, and a large anterior fontanelle. The facial gestalt is characterized by a broad nasal bridge, hypertelorism, and downslanting palpebral fissures. We were unable to differentiate between WSS and cutis laxa with growth and developmental delay (CLGDD, OMIM 219200) suggesting that both can be considered as one entity. Distinct hallmarks of GO were skin wrinkling limited to the dorsum of hands and feet and to the abdomen, normal fontanelles, maxillary hypoplasia, bowed long bones, and osteopenia with frequent fractures. In contrast to the attenuation of the skin phenotype with age in WSS, adult patients with GO appeared prematurely aged. A serum sialotransferrin type 2 pattern was found in all four WSS patients tested. Apolipoprotein CIII (a marker for O ‐glycosylation) was normal suggesting that WSS is frequently associated with a N ‐protein glycosylation defect, probably at the level of processing (CDG‐II). All four investigated GO patients showed normal sialotransferrin patterns. The known loci for cutis laxa and WSS on 2q31, 5q23‐q31, 7q11, 11q13, and 14q32 were excluded. We suggest that WSS and GO are distinct entities with overlapping features. © 2008 Wiley‐Liss, Inc.