Cytomegalovirus High-risk Kidney Transplant Recipients Show No Difference in Long-term Outcomes Following Preemptive Versus Prophylactic Management.

BACKGROUND: Following kidney transplantation (KT), cytomegalovirus (CMV) infection remains an important challenge. Both prophylactic and preemptive antiviral protocols are used for CMV high-risk kidney recipients (donor seropositive/recipient seronegative; D+/R-). We performed a nationwide comparison of the 2 strategies in de novo D+/R- KT recipients accessing long-term outcomes. METHODS: A nationwide retrospective study was conducted from 2007 to 2018, with follow-up until February 1, 2022. All adult D+/R- and R+ KT recipients were included. During the first 4 y, D+/R- recipients were managed preemptively, changing to 6 mo of valganciclovir prophylaxis from 2011. To adjust for the 2 time eras, de novo intermediate-risk (R+) recipients, who received preemptive CMV therapy throughout the study period, served as longitudinal controls for possible confounders. RESULTS: A total of 2198 KT recipients (D+/R-, n = 428; R+, n = 1770) were included with a median follow-up of 9.4 (range, 3.1-15.1) y. As expected, a greater proportion experienced a CMV infection in the preemptive era compared with the prophylactic era and with a shorter time from KT to CMV infection ( P < 0.001). However, there were no differences in long-term outcomes such as patient death (47/146 [32%] versus 57/282 [20%]; P = 0.3), graft loss (64/146 [44%] versus 71/282 [25%]; P = 0.5), or death censored graft loss (26/146 [18%] versus 26/282 [9%]; P = 0.9) in the preemptive versus prophylactic era. Long-term outcomes in R+ recipients showed no signs of sequential era-related bias. CONCLUSIONS: There were no significant differences in relevant long-term outcomes between preemptive and prophylactic CMV-preventive strategies in D+/R- kidney transplant recipients.

The Burden of Human Bocavirus 1 in Hospitalized Children With Respiratory Tract Infections.

BACKGROUND: Human bocavirus 1 (HBoV1) is frequently codetected with other viruses, and detected in asymptomatic children. Thus, the burden of HBoV1 respiratory tract infections (RTI) has been unknown. Using HBoV1-mRNA to indicate true HBoV1 RTI, we assessed the burden of HBoV1 in hospitalized children and the impact of viral codetections, compared with respiratory syncytial virus (RSV). METHODS: Over 11 years, we enrolled 4879 children <16 years old admitted with RTI. Nasopharyngeal aspirates were analyzed with polymerase chain reaction for HBoV1-DNA, HBoV1-mRNA, and 19 other pathogens. RESULTS: HBoV1-mRNA was detected in 2.7% (130/4850) samples, modestly peaking in autumn and winter. Forty-three percent with HBoV1 mRNA were 12-17 months old, and only 5% were <6 months old. A total of 73.8% had viral codetections. It was more likely to detect HBoV1-mRNA if HBoV1-DNA was detected alone (odds ratio [OR]: 3.9, 95% confidence interval [CI]: 1.7-8.9) or with 1 viral codetection (OR: 1.9, 95% CI: 1.1-3.3), compared to ≥2 codetections. Codetection of severe viruses like RSV had lower odds for HBoV1-mRNA (OR: 0.34, 95% CI: 0.19-0.61). The yearly lower RTI hospitalization rate per 1000 children <5 years was 0.7 for HBoV1-mRNA and 8.7 for RSV. CONCLUSIONS: True HBoV1 RTI is most likely when HBoV1-DNA is detected alone, or with 1 codetected virus. Hospitalization due to HBoV1 LRTI is 10-12 times less common than RSV.

The Contribution of Viruses and Bacteria to Childhood Community-acquired Pneumonia: 11-Year Observational Study From Norway.

BACKGROUND: Viruses are associated with pediatric community-acquired pneumonia (CAP) but are also common in the upper airways of healthy children. We have determined the contribution of respiratory viruses and bacteria by comparing children with CAP and hospital controls. METHODS: Children less than 16 years old with radiologically confirmed CAP (n = 715) were enrolled over an 11-year period. Children admitted for elective surgery during the same period served as controls (n = 673). Nasopharyngeal aspirates were tested for 20 respiratory pathogens by semiquantitative polymerase chain reaction tests and cultivated for bacteria and viruses. We used logistic regression to calculate adjusted odds ratios [aOR; 95% confidence intervals (CIs)], and estimated population-attributable fractions (95% CI). RESULTS: At least 1 virus was detected in 85% of cases and 76% of controls, and greater than or equal to 1 bacterium was detected in 70% of cases and controls. The presence of respiratory syncytial virus (RSV) (aOR, 16.6; 95% CI: 9.81-28.2), human metapneumovirus (HMPV) (13.0; 6.17-27.5) and Mycoplasma pneumoniae (27.7; 8.37-91.6) were most strongly associated with CAP. For RSV and HMPV, there were significant trends between lower cycle-threshold values indicating higher viral genomic loads, and higher aORs for CAP. The population-attributable fraction estimates of RSV, HMPV, human parainfluenza virus, influenza virus and M. pneumoniae were 33.3% (32.2-34.5), 11.2% (10.5-11.9), 3.7% (1.0-6.3), 2.3% (1.0-3.6) and 4.2% (4.1-4.4), respectively. CONCLUSIONS: RSV, HMPV and M. pneumoniae were most strongly related to pediatric CAP and accounted for half of all cases. There were positive trends between increasing viral genomic loads of RSV and HMPV, and higher odds for CAP.

Detection of subgenomic mRNA from endemic human coronavirus OC43 and NL63 compared to viral genomic loads, single virus detection and clinical manifestations in children with respiratory tract infections.

BACKGROUND: The importance of endemic human coronavirus (HCoV) in children has been insufficiently elucidated upon. Our aims were to develop subgenomic (sg) mRNA tests for HCoV species OC43 and NL63, and to evaluate the relationships to HCoV genomic loads, single HCoV detections and clinical manifestations. METHODS: We have used an 11-yearlong cohort study of children admitted with respiratory tract infection (RTI) and hospital controls. Nasopharyngeal aspirates were analyzed for HCoV subtypes OC43 and NL63 with in-house diagnostic PCR. Positive samples were tested with newly developed real-time PCRs targeting sg mRNA coding for the nucleocapsid protein. RESULTS: OC43 sg mRNA was detected in 86% (105/122) of available OC43-positive samples in the RTI group, and in 63% (12/19) of control samples. NL63 sg mRNA was detected in 72% (71/98) and 71% (12/17) of available NL63-positive patient and control samples, respectively. In RTI samples, sg mRNA detection was strongly associated with a Ct value <32 in both diagnostic PCR tests (OC43: OR = 54, 95% CI [6.8-428]; NL63: OR = 42, 95% CI [9.0-198]) and single NL63 detections (OR = 6.9, 95% CI [1.5-32]). Comparing RTI and controls, only OC43 was associated with RTI when adjusted for age (aOR = 3.2, 95% CI [1.1-9.4]). CONCLUSION: We found strong associations between OC43 and NL63 sg mRNA and high viral genomic loads. sg mRNA for OC43 was associated with RTI. The association between sg mRNA and clinical manifestations needs further evaluation.

Diagnostic stewardship aiming at expectorated or induced sputum promotes microbial diagnosis in community-acquired pneumonia.

PURPOSE: Studies on aetiology of community-acquired pneumonia (CAP) vary in terms of microbial sampling methods, anatomical locations, and laboratory analyses, since no gold standard exists. In this large, multicentre, retrospective, regional study from Norway, our primary objective was to report the results of a strategic diagnostic stewardship intervention, targeting diagnostic yield from lower respiratory tract sampling. The secondary objective was to report hospitalized CAP aetiology and the diagnostic yield of various anatomical sampling locations. METHODS: Medical records from cases diagnosed with hospitalized CAP were collected retrospectively from March throughout May for three consecutive years at six hospitals. Between year one and two, we launched a diagnostic stewardship intervention at the emergency room level for the university teaching hospital only. The intervention was multifaceted aiming at upscaling specimen collection and enhancing collection techniques. Year one at the interventional hospital and every year at the five other emergency hospitals were used for comparison. RESULTS: Of the 1280 included cases of hospitalized CAP, a microbiological diagnosis was established for 29.1% among 1128 blood cultures and 1444 respiratory tract specimens. Blood cultures were positive for a pathogenic respiratory tract microbe in 4.9% of samples, whereas upper and lower respiratory tract samples overall provided a probable microbiological diagnosis in 21.3% and 47.5%, respectively. Expectorated or induced sputum overall provided aetiology in 51.7% of the samples. At the interventional hospital, the number of expectorated or induced sputum samples were significantly increased, and diagnostic yield from expectorated or induced sputum was significantly enhanced from 41.2 to 62.0% after the intervention (p = 0.049). There was an over-representation of samples from the interventional hospital during the study period. Non-typeable Haemophilus influenza and Streptococcus pneumoniae accounted for 25.3% and 24.7% of microbiologically confirmed cases, respectively. CONCLUSION: Expectorated or induced sputum outperformed other sampling methods in providing a reliable microbiological diagnosis for hospitalized CAP. A diagnostic stewardship intervention significantly improved diagnostic yield of lower respiratory tract sampling.

Hospitalized Children With Common Human Coronavirus Clinical Impact of Codetected Respiratory Syncytial Virus and Rhinovirus.

BACKGROUND: The clinical impact of common human coronavirus (cHCoV) remains unclear. We studied the clinical manifestations of pediatric cHCoV infections and the possible modifying effects of codetected human rhinovirus (RV) and respiratory syncytial virus (RSV). METHODS: We used data from an 11-year-long prospective study of hospitalized children with community-acquired respiratory tract infections. Nasopharyngeal aspirates were analyzed with real-time polymerase chain reaction assay for cHCoV OC43, NL63, HKU1 and 229E, and 15 other respiratory viruses. We assessed disease severity based on the clinical factors hospitalization length, oxygen requirement, other respiratory support and supplementary fluids. RESULTS: cHCoV was detected in 341 (8%) of 4312 children. Among 104 children with single cHCoV detections, 58 (56%) had lower respiratory tract infection (LRTI) and 20 (19%) developed severe disease. The proportion with severe disease was lower among single cHCoV detections compared with single RSV detections (338 of 870; 39%), but similar to single RV detections (136 of 987; 14%). Compared with single cHCoV, codetected cHCoV-RSV was more often associated with LRTI (86 of 89; 97%) and severe disease (adjusted odds ratio, 3.3; 95% confidence interval: 1.6-6.7). LRTI was more frequent in codetected cHCoV-RV (52 of 68; 76%) than single cHCoV, but the risk of severe disease was lower (adjusted odds ratios, 0.3; 95% confidence interval: 0.1-1.0). CONCLUSIONS: cHCoV was associated with severe LRTI in hospitalized children. Viral codetections were present in two-thirds. Codetections of cHCoV-RV were associated with lower proportions of severe disease, suggesting a modifying effect of RV on HCoV.

Introducing a flat ontology into landscape research: a case study of water governance experiments in South Africa.

CONTEXT: Contemporary resource management paradigms within the developed world build on an understanding of human agency as ontologically distinct from the mode of existence of plants and animals. Because of this perspective, which gives priority to human agency, policies typically take their point of departure with human societies and associated ecosystems deemed of particular value. OBJECTIVES: As an alternative to this worldview, social theorists have introduced what is known as "flat ontology", where all beings are bestowed equal rights to negotiate their existence. To explore the implications of introducing such an understanding into landscape management, a participatory planning process for water allocation was developed and tested in a case study in the Eerste River Catchment in South Africa. METHODS: The planning process was mediated using the approach "politics of nature" (PoN), which aims to operationalize flat ontology to renegotiate water allocation based on the needs of all beings instead of the desire of a subset of humans. PoN allowed participants to playfully co-develop a common ontology and value-set. Data documenting these processes were collected digitally and analysed. RESULTS: Results indicate that the approach engendered a rethinking of key relationships between human agency and ecosystem functionality, illustrating a potential for PoN-approaches to be deployed for governance of complex landscapes. CONCLUSIONS: On the basis of experiments using PoN-methodology in the context of watershed management, it is discussed how the introduction of a flat ontology in landscape research, could inspire new ways of designing and intervening with collaborative resource management processes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10980-021-01374-9.

Viral and Atypical Bacterial Detection in Young Nepalese Children Hospitalized with Severe Pneumonia.

Respiratory viruses cause a substantial proportion of respiratory tract infections in children but are underrecognized as a cause of severe pneumonia hospitalization in low-income settings. We employed 22 real-time PCR assays and retrospectively reanalyzed 610 nasopharyngeal aspirate specimens from children aged 2 to 35 months with severe pneumonia (WHO definition) admitted to Kanti Childrens' Hospital in Kathmandu, Nepal, from January 2006 through June 2008. Previously, ≥1 of 7 viruses had been detected by multiplex reverse transcription-PCR in 30% (188/627) of cases. Reanalyzing the stored specimens, we detected ≥1 pathogens, including 18 respiratory viruses and 3 atypical bacteria, in 98.7% (602/610) of cases. Rhinovirus (RV) and respiratory syncytial virus (RSV) were the most common, detected in 318 (52.1%) and 299 (49%) cases, respectively, followed by adenovirus (AdV) (10.6%), human metapneumovirus (hMPV) (9.7%), parainfluenza virus type 3 (8.4%), and enterovirus (7.7%). The remaining pathogens were each detected in less than 5%. Mycoplasma pneumoniae was most common among the atypical bacteria (3.7%). Codetections were observed in 53.3% of cases. Single-virus detection was more common for hMPV (46%) and RSV (41%) than for RV (22%) and AdV (6%). The mean cycle threshold value for detection of each pathogen tended to be lower in single-pathogen detections than in codetections. This finding was significant for RSV, RV, and AdV. RSV outbreaks occurred at the end of the monsoon or during winter. An expanded diagnostic PCR panel substantially increased the detection of respiratory viruses in young Nepalese children hospitalized with severe pneumonia. IMPORTANCE Respiratory viruses are an important cause of respiratory tract infections in children but are underrecognized as a cause of pneumonia hospitalization in low-income settings. Previously, we detected at least one of seven respiratory viruses by PCR in 30% of young Nepalese children hospitalized with severe pneumonia over a period of 36 months. Using updated PCR assays detecting 21 different viruses and atypical bacteria, we reanalyzed 610 stored upper-respiratory specimens from these children. Respiratory viruses were detected in nearly all children hospitalized for pneumonia. RSV and rhinovirus were the predominant pathogens detected. Detection of two or more pathogens was observed in more than 50% of the pneumonia cases. Single-virus detection was more common for human metapneumovirus and RSV than for rhinovirus and adenovirus. The concentration of virus was higher (low cycle threshold [CT] value) for single detected pathogens, hinting at a high viral load as a marker of clinical significance.

Parechovirus A in Hospitalized Children With Respiratory Tract Infections: A 10-Year-Long Study From Norway.

BACKGROUND: The role of Parechovirus A (PeV-A) in hospitalized children with respiratory tract infections (RTIs) is unclear. We studied the occurrence and impact of PeV-A over 10 years. METHODS: Children from Sør-Trøndelag County, Norway, hospitalized with RTI and a comparison group of asymptomatic children admitted to elective surgery, were prospectively enrolled from 2006 to 2016. Nasopharyngeal aspirates were cultured and analyzed with polymerase chain reaction tests for PeV-A and 19 other pathogens. The cycle threshold levels of PeV-A were reported as measures of viral genomic loads. Parechovirus A-positive samples were genotyped by amplification and sequencing of the VP3/VP1 junction. RESULTS: Parechovirus A was detected in 8.8% (323/3689) patients with RTI and in 10.1% (45/444) of the children in the comparison group (P = .34). Parechovirus A genotyping (n = 188) revealed PeV-A1 (n = 121), PeV-A3 (n = 15), PeV-A5 (n = 6), and PeV-A6 (n = 46). Viral codetections occurred in 95% of patients and in 84% of the children in the comparison group (P = .016). In multivariable logistic regression analysis, RTI was unrelated to PeV-A genomic loads, adjusted for other viruses and covariates. Similar results were found for PeV-A1 and PeV-A6. CONCLUSIONS: Parechovirus A and viral codetections were common in hospitalized children with RTI and asymptomatic children in a comparison group. Our findings suggest that PeV-A has a limited role in hospitalized children with RTI.

Diagnostic performance of a SARS-CoV-2 rapid antigen test in a large, Norwegian cohort.

BACKGROUND: Rapid antigen tests (RATs) may be included in national strategies for handling the SARS-CoV-2 pandemic, as they provide test results rapidly, are easily performed outside laboratories, and enable immediate contract tracing. However, before implementation further clinical evaluation of test sensitivity is warranted. OBJECTIVES: To examine the performance of Abbott's Panbio™ COVID-19 Ag Rapid Test Device for SARS-CoV-2 testing in a low to medium prevalence setting in Norway. STUDY DESIGN: A prospective study comparing the results of the Panbio RAT with PCR in 4857 parallel samples collected at a SARS-CoV-2 test station in Oslo, and from COVID-19 outbreaks in six Norwegian municipalities. RESULTS: A total of 4857 cases were included in the study; 3991 and 866 cases from the test station and the outbreak municipalities, respectively. The prevalence at the test station in Oslo was 6.3 %, and the overall sensitivity of the RAT was 74 %. Increased sensitivity was observed in patients who experienced symptoms (79 %) and when considering samples with viral loads above estimated level of infectivity (84 %), while it was lower in asymptomatic persons (55 %). In the outbreak municipalities, the overall prevalence was 6.9 %, and the total sensitivity of the RAT was 70 %. CONCLUSIONS: Our results indicate that the test correctly identified most infectious individuals. Nevertheless, the sensitivity is considerably lower than for PCR, and it is important that the limitations of the test are kept in mind in the follow-up of tested individuals.

Comparison of phenotypic and genotypic diagnosis of acute human bocavirus 1 infection in children.

BACKGROUND: Diagnosis of human bocavirus 1 (HBoV1) has been based on qualitative PCRs detecting HBoV1 DNA or detection of HBoV1 mRNA. OBJECTIVE: This study aims to assess whether a rapid and automated HBoV1 antigen test is suitable for diagnosis of acute HBoV1 infection. STUDY DESIGN: HBoV1 antigen detection has been compared with quantitative HBoV1 DNA PCR and HBoV1 mRNA RT-PCR. RESULTS AND CONCLUSION: We conclude that HBoV1 antigen detection has higher clinical specificity and positive predictive value than HBoV1 DNA qualitative PCRs, yet a lower sensitivity than HBoV1 mRNA detection. Additionally, HBoV1 antigen detection is beneficial in its rapidity and availability as a point-of-care test.

Pursuing implementation solutions for targeted nitrogen management in agriculture- a novel approach to synthesize knowledge and facilitate sustainable decision making based on collaborative landscape modelling.

Regulation of nitrate emission from agriculture to aquatic environments in Denmark currently depend on general rules for nutrient application and associated farm-level reporting schemes. Similar or comparable centralized regulation instruments dedicated to controlling and limiting rather than focusing and improving N application practices exist in large parts of the OECD. Recent policy debates have exposed an array of problems relating to this type of regulation. Problems include issues of appropriate scale, transparency and failures to adapt intervention and regulation to relevant geo-ecological variations in contexts where general rules are being imposed on varied agro-ecosystems. Therefore it has been proposed to rescale regulation to better fit relevant socio-political and agro-environmental processes including the scale of farmers' decision making, the scale of relevant hydrological systems and the scale of key agro-ecological conditions such as soil characteristics and drainage. However, the challenge of shifting the regulation to a more local scale raises a number of questions. These include (1) How information produced locally can be integrated with national scale data? (2) In what way integrated datasets can used to model environmental effects of current and possible land use patterns? (3) In what way data and estimates of consequences of land use changes are best made available in decision making processes? To address these questions this article reports on ongoing work in Denmark to develop a decision support tool for N-management at the scale of agricultural landscapes, which are areas where a similar pattern of land use is repeated across the land surface, reflecting a specific mode of adapting agriculture to natural conditions. The aim of the article is to evaluate the design of a decision support tool aiming at enabling strategic N-management at landscape scales by linking decision support at the scale of individual farms with decision support targeted at groups of farms where a coordinated effort to solve common problems may be more efficient. Design targets for the tool were established empirically based on evidence from exploratory workshops with farmers and other stakeholders in 6 case areas across Denmark. On this basis a prototype GIS-tool for capturing, storing, editing, displaying and modelling landscape scale farming practices and associated emission consequences was developed. The tool was designed to integrate locally held knowledge with national scale datasets in live scenario situations through the implementation of a flexible, uniform and editable data model for land use data - the dNmark landscape model. Based on input data that is corrected and co-authored by workshop participants, the tool estimates the effect of potential land use scenarios on nutrient emissions. The tool was tested in 5 scenario workshops in case areas in Denmark in 2016, on the basis of which its design is evaluated and discussed in this article.

Human bocaviruses and paediatric infections.

Human bocavirus 1 (HBoV1), belonging to the Parvoviridae family, was discovered in 2005, in nasopharyngeal samples from children with respiratory tract infections. Three additional bocaviruses, HBoV2-4, were discovered in 2009-10. These viruses have mainly been found in faecal samples and their role in human diseases is still uncertain. HBoV1 causes a wide spectrum of respiratory diseases in children, including common cold, acute otitis media, pneumonia, bronchiolitis, and asthma exacerbations. HBoV1 DNA can persist in airway secretions for months after an acute infection. Consequently, acute HBoV1 infection cannot be diagnosed with standard DNA PCR; quantitative PCR and serology are better diagnostic approaches. Because of their high clinical specificity, diagnostic developments such as HBoV1 mRNA and antigen detection have shown promising results. This Review summarises the knowledge on human bocaviruses, with a special focus on HBoV1.

No Correlation Between Nasopharyngeal Human Bocavirus 1 Genome Load and mRNA Detection or Serology in Adeno-/Tonsillectomy Patients.

Human bocavirus 1 (HBoV1) can persist in nasopharynx and tonsils. Using HBoV1 serology, reverse-transcription polymerase chain reaction (PCR) for detecting messenger RNA (mRNA) and quantitative PCR for HBoV1 genome load count, we studied to what extent the HBoV1 DNA loads in nasopharynx correlate with acute infection markers. Tonsillar tissue, nasopharyngeal aspirate, and serum were obtained from 188 elective adeno-/tonsillectomy patients. Relatively high loads of HBoV1 DNA were detected in the nasopharynx of 14 (7%) primarily asymptomatic subjects with negative mRNA and/or serodiagnostic results. Quantitative HBoV1 DNA PCR may have lower specificity than HBoV1 mRNA detection for diagnosing symptomatic infection.

Comparison of procalcitonin, C-reactive protein, white blood cell count and clinical status in diagnosing pneumonia in patients hospitalized with acute exacerbations of COPD: A prospective observational study.

Lower respiratory tract infection is the most common cause of acute exacerbations of chronic obstructive pulmonary disease (AECOPD). The aim of the present study was to compare the accuracy of procalcitonin (PCT), C-reactive protein (CRP) and white blood cell count (WBC) as single diagnostic tests and in combination with clinical signs and symptoms to diagnose pneumonia in patients hospitalized with AECOPD. This was a prospective, single centre observational study. Patients with spirometry-confirmed COPD who were hospitalized due to AECOPD were consecutively recruited at the hospital's Emergency Unit. Pneumonia was defined as a new pulmonary infiltrate on chest X-ray. The values of PCT, CRP and WBC were determined at admission. Receiver operating characteristic (ROC) curve analysis was used to study the accuracy of various diagnostic tests. Of the 113 included patients, 35 (31%) had pneumonia at admission. Area under the ROC curve (AUC) for PCT, CRP and WBC as a single test to distinguish between patients with and without pneumonia was 0.67 (95% CI 0.55-0.79), 0.73 (95% CI 0.63-0.84) and 0.67 (95% CI 0.55-0.79), respectively ( p = 0.42 for the test of difference). The AUC for a model of clinical signs and symptoms was 0.84 (95% CI 0.76-0.92). When biomarkers were added to the clinical model, the AUCs of the combined models were not significantly different from that of the clinical model alone ( p = 0.54). PCT had about the same accuracy as CRP and WBC in predicting pneumonia in patients hospitalized with AECOPD both as a single test and in combination with clinical signs and symptoms.

Human Coronavirus in Hospitalized Children With Respiratory Tract Infections: A 9-Year Population-Based Study From Norway.

BACKGROUND: The burden of human coronavirus (HCoV)-associated respiratory tract infections (RTIs) in hospitalized children is poorly defined. We studied the occurrence and hospitalization rates of HCoV over 9 years. METHODS: Children from Sør-Trøndelag County, Norway, hospitalized with RTIs and asymptomatic controls, were prospectively enrolled from 2006 to 2015. Nasopharyngeal aspirates were analyzed with semiquantitative polymerase chain reaction (PCR) tests for HCoV subtypes OC43, 229E, NL63, and HKU1, and 13 other respiratory pathogens. RESULTS: HCoV was present in 9.1% (313/3458) of all RTI episodes: 46.6% OC43, 32.3% NL63, 16.0% HKU1, and 5.8% 229E. Hospitalization rates for HCoV-positive children with lower RTIs were 1.5 and 2.8 per 1000 <5 and <1 years of age, respectively. The detection rate among controls was 10.2% (38/373). Codetections occurred in 68.1% of the patients and 68.4% of the controls. In a logistic regression analysis, high HCoV genomic loads (cycle threshold <28 in PCR analysis) were associated with RTIs (odds ratio = 3.12, P = .016) adjusted for relevant factors. CONCLUSIONS: HCoVs occurred in 1 of 10 hospitalized children with RTIs and asymptomatic controls. A high HCoV genomic load was associated with RTI. HCoVs are associated with a substantial burden of RTIs in need of hospitalization.

Human adenovirus in nasopharyngeal and blood samples from children with and without respiratory tract infections.

BACKGROUND: Human adenovirus (HAdV) is a double-stranded DNA virus associated with respiratory tract infections (RTI) in children. Using polymerase chain reaction (PCR) tests, HAdV often is detected together with other virus species, even in healthy controls. OBJECTIVES: The aim of this study was to compare molecular detection of HAdV with culture, and to examine the associations of various methods to RTI. STUDY DESIGN: Nasopharyngeal aspirates (NPA) were collected from 4319 children admitted with RTI and from 361 controls. The NPAs were examined for 23 viral and bacterial pathogens, using inhouse real-time PCR-assays based on TaqMan probes, in addition to bacterial and viral culture. HAdV concentration was evaluated semi-quantitatively from the Ct-value and quantitatively by use of ADENOVIRUS R-gene®. RESULTS: HAdV-DNA was detected in 6.1% patient samples and in 10.5% controls (p< 0.001). Compared to controls, patients had an OR of 3.8 (95% CI 1.4-10.3) for mono-detection of HAdV DNA, and an OR of 5.1 (95% CI 2.0-13.4) for HAdV-positive samples grew adenovirus by culture. HAdV DNA loads from children with RTI consisted of two clusters: one cluster with high viral loads (Ct < 30 and >106 copies/ml) and one cluster with low viral loads, whereas among the controls, nearly all had low viral loads (OR 7.8, 95% CI 2.2-27.1). In 61 available plasma samples, 16.4% were positive for HAdV DNA, all were from patients. CONCLUSION: The detection of HAdV DNA per se by qualitative PCR is not useful as a diagnostic test. Detection of HAdV by use of viral culture and a high viral HAdV DNA load are the two methods most strongly associated with RTI in children.

A global view of shifting cultivation: Recent, current, and future extent.

Mosaic landscapes under shifting cultivation, with their dynamic mix of managed and natural land covers, often fall through the cracks in remote sensing-based land cover and land use classifications, as these are unable to adequately capture such landscapes' dynamic nature and complex spectral and spatial signatures. But information about such landscapes is urgently needed to improve the outcomes of global earth system modelling and large-scale carbon and greenhouse gas accounting. This study combines existing global Landsat-based deforestation data covering the years 2000 to 2014 with very high-resolution satellite imagery to visually detect the specific spatio-temporal pattern of shifting cultivation at a one-degree cell resolution worldwide. The accuracy levels of our classification were high with an overall accuracy above 87%. We estimate the current global extent of shifting cultivation and compare it to other current global mapping endeavors as well as results of literature searches. Based on an expert survey, we make a first attempt at estimating past trends as well as possible future trends in the global distribution of shifting cultivation until the end of the 21st century. With 62% of the investigated one-degree cells in the humid and sub-humid tropics currently showing signs of shifting cultivation-the majority in the Americas (41%) and Africa (37%)-this form of cultivation remains widespread, and it would be wrong to speak of its general global demise in the last decades. We estimate that shifting cultivation landscapes currently cover roughly 280 million hectares worldwide, including both cultivated fields and fallows. While only an approximation, this estimate is clearly smaller than the areas mentioned in the literature which range up to 1,000 million hectares. Based on our expert survey and historical trends we estimate a possible strong decrease in shifting cultivation over the next decades, raising issues of livelihood security and resilience among people currently depending on shifting cultivation.

The Burden of Human Metapneumovirus and Respiratory Syncytial Virus Infections in Hospitalized Norwegian Children.

Background: The burden of severe human metapneumovirus (HMPV) respiratory tract infections (RTIs) in European children has not been clarified. We assessed HMPV in Norwegian children and compared hospitalization rates for HMPV and respiratory syncytial virus (RSV). Methods: We prospectively enrolled children (<16 years old) hospitalized with RTI and asymptomatic controls (2006-2015). Nasopharyngeal aspirate samples were analyzed with polymerase chain reaction (PCR) tests for HMPV, RSV, and 17 other pathogens. We genotyped HMPV-positive samples and assessed shedding time in 32 HMPV-infected children. Results: In children with RTI, HMPV was detected in 7.3% (267 of 3650) and RSV in 28.7% (1048 of 3650). Among controls, 2.1% (7 of 339) had low HMPV levels detected by PCR, but all were culture negative. HMPV primarily occurred from January to April and in regular epidemics. At least 2 HMPV subtypes occurred each season. The average annual hospitalization rates in children <5 years old with lower RTI were 1.9/1000 (HMPV) and 10.4/1000 (RSV). Among children with RTI, the median HMPV shedding time by PCR was 13 days (range, 6-28 days), but all were culture negative (noninfectious) after 13 days. Conclusions: HMPV appears in epidemics in Norwegian children, with a hospitalization rate 5 times lower than RSV. Low levels of HMPV are rarely detected in healthy children.