Background SARS-CoV-2 emerged in China as the cause of CoVID-19 in December 2019 reaching Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the WHO-recommended SARS-CoV-2-assay and analyzed the epidemiology of SARS-CoV-2 and CARVs. Methods Naso-oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by Basel-S-gene and WHO-based E-gene-assay (Roche) in parallel using Basel-N-gene-assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex-NAT, including 1816 (75%) simultaneously for SARS-CoV-2. Results Basel-S-gene and Roche-E-gene-assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2-positives. In 188 (2.5%) discordant cases, SARS-CoV-2-loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2-positive, while children tested more frequently CARV-positive. CARV co-infections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks reaching 48% of all detected respiratory viruses followed by rhino/enterovirus (13%), influenzavirus (12%), coronavirus (9%), respiratory syncytial (6%) and metapneumovirus (6%). Conclusions Winter CARVs were dominant during the early SARS-CoV-2 pandemic impacting infection control and treatment decisions, but were rapidly replaced suggesting competitive infection. We hypothesize that pre-existing immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.

Sequence variability, amplicon length, and non-encapsidated genomes obstruct standardization and commutability of CMV loads needed to develop thresholds for clinical research and management. Besides regular sequence surveys, matrix and extraction standardization, we propose developing reference calibrators using 100 bp amplicons.

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BK polyomavirus has been linked to urothelial carcinoma in immunosuppressed patients. Here, we performed comprehensive genomic analysis of a BK polyomavirus-associated, metachronous, multifocal and metastatic micropapillary urothelial cancer in a kidney transplant recipient. Dissecting cancer heterogeneity by sorting technologies prior to array-comparative genomic hybridization followed by short tandem repeat analysis revealed that the metastatic urothelial cancer was of donor origin (4-year-old male). The top 50 cancer-associated genes showed no key driver mutations as assessed by next-generation sequencing. Whole genome sequencing and BK polyomavirus-specific amplification provided evidence for episomal and subgenomic chromosomally integrated BK polyomavirus genomes, which carried the same unique 17-bp deletion signature in the viral non-coding control region (NCCR). Whereas no role in oncogenesis could be attributed to the host gene integration in chromosome 1, the 17-bp deletion in the NCCR increased early viral gene expression, but decreased viral replication capacity. Consequently, urothelial cells were exposed to high levels of the transforming BK polyomavirus early proteins large tumour antigen and small tumour antigen from episomal and integrated gene expression. Surgery combined with discontinuation of immunosuppression resulted in complete remission, but sacrificed the renal transplant. Thus, this report links, for the first time, BK polyomavirus NCCR rearrangements with oncogenic transformation in urothelial cancer in immunosuppressed patients. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Objectives Detecting severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is key to the clinical and epidemiological assessment of CoVID‐19. We cross‐validated manual and automated high‐throughput testing for SARS‐CoV‐2‐RNA, evaluated SARS‐CoV‐2 loads in nasopharyngeal–oropharyngeal swabs (NOPS), lower respiratory fluids, and plasma, and analyzed detection rates after lockdown and relaxation measures. Methods Basel‐S‐gene, Roche‐E‐gene, and Roche‐cobas®6800‐Target1 and Target2 were prospectively validated in 1344 NOPS submitted during the first pandemic peak (Week 13). Follow‐up cohort (FUP) 1, 2, and 3 comprised 10,999, 10,147, and 19,389 NOPS submitted during a 10‐week period until Weeks 23, 33, and 43, respectively. Results Concordant results were obtained in 1308 cases (97%), including 97 (9%) SARS‐CoV‐2‐positives showing high quantitative correlations (Spearman's r > .95; p < .001) for all assays and high precision by Bland–Altman analysis. Discordant samples (N = 36, 3%) had significantly lower SARS‐CoV‐2 loads (p < .001). Following lockdown, detection rates declined to <1% in FUP‐1, reducing single‐test positive predictive values from 99.3% to 85.1%. Following relaxation, rates flared up to 4% and 12% in FUP‐2 and ‐3, but infected patients were younger than during lockdown (34 vs. 52 years, p < .001). In 261 patients providing 936 NOPS, SARS‐CoV‐2 loads declined by three orders of magnitude within 10 days postdiagnosis (p < .001). SARS‐CoV‐2 loads in NOPS correlated with those in time‐matched lower respiratory fluids or in plasma but remained detectable in some cases with negative follow‐up NOPS, respectively. Conclusion Manual and automated assays significantly correlated qualitatively and quantitatively. Following a successful lockdown, declining positive predictive values require independent dual‐target confirmation for reliable assessment. Confirmatory and quantitative follow‐up testing should be obtained within <5 days and consider lower respiratory fluids in symptomatic patients with SARS‐CoV‐2‐negative NOPS.

Background. SARS-CoV-2 emerged in China in December 2019 as new cause of severe viral pneumonia (CoVID-19) reaching Europe by late January 2020. We validated the WHO-recommended assay and describe the epidemiology of SARS-CoV-2 and community-acquired respiratory viruses (CARVs). Methods. Naso-oropharyngeal swabs (NOPS) from 7663 individuals were prospectively tested by the Basel-S-gene and the WHO-based E-gene-assay (Roche) using Basel-N-gene-assay for confirmation. CARVs were tested in 2394 NOPS by multiplex-NAT, including 1816 together with SARS-CoV-2. Results. Basel-S-gene and Roche-E-gene-assays were concordant in 7475 cases (97.5%) including 825 (11%) positive samples. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 NOPS. Adults were more likely to test positive for SARS-CoV-2, while children were more likely to test CARV-positive. CARV co-infections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced other CARVs within 3 weeks reaching 48% of all detected respiratory viruses followed by rhino/enterovirus (13%), influenzavirus (12%), coronavirus (9%), respiratory syncytial (6%) and metapneumovirus (6%). Conclusions. The differential diagnosis for respiratory infections was broad during the early pandemic, affecting infection control and treatment decisions. We discuss the role of pre-existing immunity and competitive CARV replication for the epidemiology of SARS-CoV-2 infection among adults and children.

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Background Cytomegalovirus (CMV) serostatus and CMV replication are considered as risk factors for inferior graft and patient survival after renal transplantation, but long-term outcome data are limited. The aim of this retrospective single-centre study was to investigate the impact of CMV serostatus and CMV replication/disease on long-term outcomes in a well-defined cohort managed by a standardized CMV prevention/treatment protocol. Methods We investigated 599 consecutive kidney transplantations having a CMV prevention protocol consisting of either prophylaxis (D+/R− and R+ with ATG induction) or screening/deferred therapy (R+ without ATG induction). Patients were grouped according to CMV serostatus [high risk (D+/R−): n = 122; intermediate risk (R+): n = 306; low risk (D−/R−): n = 171] and occurrence of CMV replication/disease (no CMV replication: n = 419; asymptomatic CMV replication: n = 110; CMV syndrome: n = 39; tissue-invasive CMV disease: n = 31). The median follow-up time was 6.5 years. Results Graft and patient survival were not different among the three CMV serostatus groups as well as the four CMV replication/disease groups (P ≥ 0.44). Eighty-seven patients died, 17 due to infections (21%), but none was attributable to CMV. The overall hospitalization incidence for CMV-related infection was 3% (17/599 patients). The incidence of clinical and (sub)clinical rejection was similar among the groups (P ≥ 0.17). In a multivariate Cox proportional hazard model, neither CMV serostatus, nor CMV replication, nor CMV disease were independent predictors for patient death or graft failure, respectively. Conclusions This retrospective single-centre study suggests that the negative impact of CMV infection on long-term patient and allograft survival as well as on allograft rejection can be largely eliminated with current diagnostic/therapeutic management.