Interlaboratory comparison using inactivated SARS-CoV-2 variants as a feasible tool for quality control in COVID-19 wastewater monitoring

Wastewater-based SARS-CoV-2 epidemiology (WBE) has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies. WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants. However, for a timely transmission of results, sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required. Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis, comparative quality control of the analytical procedures is essential to report reliable and comparable results. In this study, we performed an interlaboratory comparison at laboratories specialized for PCR and high-throughput-sequencing (HTS)-based WBE analysis. Frozen reserve samples from low COVID-19 incidence periods were spiked with different inactivated authentic SARS-CoV-2 variants in graduated concentrations and ratios. Samples were sent to the participating laboratories for analysis using laboratory specific methods and the reported viral genome copy numbers and the detection of viral variants were compared with the expected values. All PCR-laboratories reported SARS-CoV-2 genome copy equivalents (GCE) for all spiked samples with a mean intra- and inter-laboratory variability of 19 % and 104 %, respectively, largely reproducing the spike-in scheme. PCR-based genotyping was, in dependence of the underlying PCR-assay performance, able to predict the relative amount of variant specific substitutions even in samples with low spike-in amount. The identification of variants by HTS, however, required >100 copies/ml wastewater and had limited predictive value when analyzing at a genome coverage below 60 %. This interlaboratory test demonstrates that despite highly heterogeneous isolation and analysis procedures, overall SARS-CoV-2 GCE and mutations were determined accurately. Hence, decentralized SARS-CoV-2 wastewater monitoring is feasible to generate comparable analysis results. However, since not all assays detected the correct variant, prior evaluation of PCR and sequencing workflows as well as sustained quality control such as interlaboratory comparisons are mandatory for correct variant detection.

Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance

Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.

Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance

Despite high vaccination rates in the Netherlands, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate. Longitudinal sewage surveillance was implemented along with the notification of cases as two parts of the surveillance pyramid to validate the use of sewage for surveillance, as an early warning tool, and to measure the effect of interventions. Sewage samples were collected from nine neighborhoods between September 2020 and November 2021. Comparative analysis and modeling were performed to understand the correlation between wastewater and case trends. Using high resolution sampling, normalization of wastewater SARS-CoV-2 concentrations, and 'normalization' of reported positive tests for testing delay and intensity, the incidence of reported positive tests could be modeled based on sewage data, and trends in both surveillance systems coincided. The high collinearity implied that high levels of viral shedding around the onset of disease largely determined SARS-CoV-2 levels in wastewater, and that the observed relationship was independent of variants of concern and vaccination levels. Sewage surveillance alongside a large-scale testing effort where 58 % of a municipality was tested, indicated a five-fold difference in the number of SARS-CoV-2-positive individuals and reported cases through standard testing. Where trends in reported positive cases were biased due to testing delay and testing behavior, wastewater surveillance can objectively display SARS-CoV-2 dynamics for both small and large locations and is sensitive enough to measure small variations in the number of infected individuals within or between neighborhoods. With the transition to a post-acute phase of the pandemic, sewage surveillance can help to keep track of re-emergence, but continued validation studies are needed to assess the predictive value of sewage surveillance with new variants. Our findings and model aid in interpreting SARS-CoV-2 surveillance data for public health decision-making and show its potential as one of the pillars of future surveillance of (re)emerging viruses.

Normalisation of SARS-CoV-2 concentrations in wastewater: The use of flow, electrical conductivity and crAssphage

Over the course of the Corona Virus Disease-19 (COVID-19) pandemic in 2020-2022, monitoring of the severe acute respiratory syndrome coronavirus 2 ribonucleic acid (SARS-CoV-2 RNA) in wastewater has rapidly evolved into a supplementary surveillance instrument for public health. Short term trends (2 weeks) are used as a basis for policy and decision making on measures for dealing with the pandemic. Normalisation is required to account for the dilution rate of the domestic wastewater that can strongly vary due to time- and location-dependent sewer inflow of runoff, industrial discharges and extraneous waters. The standard approach in sewage surveillance is normalisation using flow measurements, although flow based normalisation is not effective in case the wastewater volume sampled does not match the wastewater volume produced. In this paper, two alternative normalisation methods, using electrical conductivity and crAssphage have been studied and compared with the standard approach using flow measurements. For this, a total of 1116 24-h flow-proportional samples have been collected between September 2020 and August 2021 at nine monitoring locations. In addition, 221 stool samples have been analysed to determine the daily crAssphage load per person. Results show that, although crAssphage shedding rates per person vary greatly, on a population-level crAssphage loads per person per day were constant over time and similar for all catchments. Consequently, crAssphage can be used as a quantitative biomarker for populations above 5595 persons. Electrical conductivity is particularly suitable to determine dilution rates relative to dry weather flow concentrations. The overall conclusion is that flow normalisation is necessary to reliably determine short-term trends in virus circulation, and can be enhanced using crAssphage and/or electrical conductivity measurement as a quality check.

Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities

For community-level monitoring, the European Commission under the EU Sewage Sentinel System recommends wastewater-based SARS-CoV-2 surveillance. Tracking SARS-CoV-2 variants in a community is pivotal for appropriate public health response. Genome sequencing of SARS-CoV-2 in wastewater samples for tracking variants is challenging, often resulting in low coverage genome sequences, thereby impeding the detection of the SARS-CoV-2 mutations. Therefore, we aimed at high-coverage SARS-CoV-2 genome sequences from sewage samples which we successfully accomplished. This first pan-European surveillance compared the mutation profiles associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2 across 20 European countries, including 54 municipalities. The results highlight that SARS-CoV-2 variants detected in the wastewater samples mirror the variants profiles reported in clinical data. This study demonstrated that >98% coverage of SARS-CoV-2 genomic sequences is possible and can be used to track SARS-CoV-2 mutations in wastewater to support identifying variants circulating in a city at the community level.

Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater

Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.

Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater

Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of lineage B.1.351 (containing the 501Y mutation) and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. Monitoring these mutations can be used to obtain insight in the introduction and spread of VOC and support public health decision-making regarding measures to limit viral spread or allocation of testing or vaccination.

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.

Spatial and Temporal Dynamics in Attached and Suspended Bacterial Communities in Three Drinking Water Distribution Systems with Variable Biological Stability

Microbial presence and regrowth in drinking water distribution systems (DWDSs) is routinely monitored to assess the biological stability of drinking water without a residual disinfectant, but the conventional microbiological culture methods currently used target only a very small fraction of the complete DWDS microbiome. Here, we sequenced 16S rRNA gene amplicons to elucidate the attached and suspended prokaryotic community dynamics within three nonchlorinated DWDSs with variable regrowth conditions distributing similarly treated surface water from the same source. One rural location, with less regrowth related issues, differed most strikingly from the other two urban locations by the exclusive presence of Pseudonocardia (Actinobacteria) in the biofilm and the absence of Limnobacter (Betaproteobacteriales) in the water and loose deposits during summer. There was a dominant seasonal effect on the drinking water microbiomes at all three locations. For one urban location, it was established that the most significant changes in the microbial community composition on a spatial scale occurred shortly after freshly treated water entered the DWDS. However, summerly regrowth of Limnobacter, one of the dominant genera in the distributed drinking water, already occurred in the clean water reservoir at the treatment plant before further distribution. The highlighted bacterial lineages within these highly diverse DWDS communities might be important new indicators for undesirable regrowth conditions affecting the final drinking water quality.

Implementation of environmental surveillance for SARS-CoV-2 virus to support public health decisions: Opportunities and challenges

Analysing wastewater can be used to track infectious disease agents that are shed via stool and urine. Sewage surveillance of SARS-CoV-2 has been suggested as a tool to determine the extent of COVID-19 in cities and serve as an early warning for (re-)emergence of SARS-CoV-2 circulation in communities. The focus of this review is on the strength of evidence, opportunities and challenges for the application of sewage surveillance to inform public health decision making. Considerations for undertaking sampling programs are reviewed including sampling sites, strategies, sample transport, storage and quantification methods; together with the approach and evidence base for quantifying prevalence of infection from measured wastewater concentration. Published SARS-CoV-2 sewage surveillance studies (11 peer reviewed and 10 preprints) were reviewed to demonstrate the current status of implementation to support public health decisions. Although being very promising, a number of areas were identified requiring additional research to further strengthen this approach and take full advantage of its potential. In particular, design of adequate sampling strategies, spatial and temporal resolution of sampling, sample storage, replicate sampling and analysis, controls for the molecular methods used for the quantification of SARS-CoV-2 RNA in wastewater. The use of appropriate prevalence data and methods to correlate or even translate SARS-CoV-2 concentrations in wastewater to prevalence of virus shedders in the population is discussed.

Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands

In the current COVID-19 pandemic, a significant proportion of cases shed SARS-Coronavirus-2 (SARS-CoV-2) with their faeces. To determine if SARS-CoV-2 RNA was present in sewage during the emergence of COVID-19 in The Netherlands, sewage samples of six cities and the airport were tested using four qRT-PCR assays, three targeting the nucleocapsid gene (N1-N3) and one the envelope gene (E). No SARS-CoV-2 RNA was detected on February 6, 3 weeks before the first Dutch case was reported. On March 4/5, one or more gene fragments were detected in sewage of three sites, in concentrations of 2.6-30 gene copies per mL. In Amersfoort, N3 was detected in sewage 6 days before the first cases were reported. As the prevalence of COVID-19 in these cities increased in March, the RNA signal detected by each qRT-PCR assay increased, for N1-N3 up to 790-2200 gene copies per mL. This increase correlated significantly with the increase in reported COVID-19 prevalence. The detection of the virus RNA in sewage, even when the COVID-19 prevalence is low, and the correlation between concentration in sewage and reported prevalence of COVID-19, indicate that sewage surveillance could be a sensitive tool to monitor the circulation of the virus in the population.

Mobility and redox transformation of arsenic during treatment of artificially recharged groundwater for drinking water production

In this study we investigate opportunities for reducing arsenic (As) to low levels, below 1 μg/L in produced drinking water from artificially infiltrated groundwater. We observe that rapid sand filtration is the most important treatment step for the oxidation and removal of As at water treatment plants which use artificially recharged groundwater as source. Removal of As is mainly due to As co-precipitation with Fe(III)(oxyhydr)oxides, which shows higher efficiency in rapid sand filter beds compared to aeration and supernatant storage. This is due to an accelerated oxidation of As(III) to As(V) in the filter bed which may be caused by the manganese oxides and/or As(III) oxidizing bacteria, as both are found in the coating of rapid sand filter media grains by chemical analysis and taxonomic profiling of the bacterial communities. Arsenic removal does not take place in treatment steps such as granular activated carbon filtration, ultrafiltration or slow sand filtration, due to a lack of hydrolyzing iron in their influent and a lack of adsorption affinity between As and the filtration surfaces. Further, we found that As reduction to below 1 μg/L can be effectively achieved at water treatment plants either by treating the influent of rapid sand filters by dosing potassium permanganate in combination with ferric chloride or by treating the effluent of rapid sand filters with ferric chloride dosing only. Finally, we observe that reducing the pH is an effective measure for increasing As co-precipitation with Fe(III)(oxyhydr)oxides, but only when the oxidized arsenic, As(V), is the predominant species in water.

Multiple Sources of the Outbreak of Legionnaires' Disease in Genesee County, Michigan, in 2014 and 2015

BACKGROUND

A community-wide outbreak of Legionnaires' disease (LD) occurred in Genesee County, Michigan, in 2014 and 2015. Previous reports about the outbreak are conflicting and have associated the outbreak with a change of water source in the city of Flint and, alternatively, to a Flint hospital.

OBJECTIVE

The objective of this investigation was to independently identify relevant sources of Legionella pneumophila that likely resulted in the outbreak.

METHODS

An independent, retrospective investigation of the outbreak was conducted, making use of public health, health care, and environmental data and whole-genome multilocus sequence typing (wgMLST) of clinical and environmental isolates.

RESULTS

Strong evidence was found for a hospital-associated outbreak in both 2014 and 2015: a) 49% of cases had prior exposure to Flint hospital A, significantly higher than expected from Medicare admissions; b) hospital plumbing contained high levels of L. pneumophila; c) Legionella control measures in hospital plumbing aligned with subsidence of hospital A-associated cases; and d) wgMLST showed Legionella isolates from cases exposed to hospital A and from hospital plumbing to be highly similar. Multivariate analysis showed an increased risk of LD in 2014 for people residing in a home that received Flint water or was located in proximity to several Flint cooling towers.

DISCUSSION

This is the first LD outbreak in the United States with evidence for three sources (in 2014): a) exposure to hospital A, b) receiving Flint water at home, and c) residential proximity to cooling towers; however, for 2015, evidence points to hospital A only. Each source could be associated with only a proportion of cases. A focus on a single source may have delayed recognition and remediation of other significant sources of L. pneumophila. https://doi.org/10.1289/EHP5663.

Diagnosis and treatment of depression following acquired brain injury: a comparison of practice in the UK and the Netherlands

Objective: To describe and compare current practice in diagnosis and treatment of depression following acquired brain injury in two countries (UK and the Netherlands) which have different sets of guidelines.

Setting and design: A cross-sectional survey of reported practice among rehabilitation physician members of the British and Dutch specialist societies.

Methods: A 12-item postal questionnaire was sent to 496 rehabilitation physicians with two reminders: N = 353 (71%) responded, 146 of whom did not manage people with acquired brain injury, leaving 207 questionnaires for analysis (Netherlands N = 121, UK N = 86). Descriptive summary statistics were compiled. Categorical and dichotomous data were compared between the groups using chi-squared tests.

Results: Sixty-seven (78%) of British respondents served a predominantly younger adult (65 years) population, compared with only 27 (22%) of the Dutch, who mainly treated patients of all ages. In line with their respective guidelines, more British respondents reported that they screened all acquired brain injury patients for depression (68/86 (79%) British versus 71/121 (59%) Dutch, P < 0.01), and used formal measures (37/68 (54%) versus 14/69 (20%), P < 0.001). They also took a more active role in treatment of depression: only 1 (1%) never used antidepressants, compared with 22 (18%) of Dutch respondents (P < 0.001). On the other hand, where antidepressants were prescribed, the Dutch respondents were more likely than the British to follow-up their patients (93/98 (95%) versus 67/84 (80%), P < 0.01).

Conclusions: The survey demonstrates a broadly similar approach, but highlights some significant variance in practice between the two countries which may stem from differences in population and service provision as well as their respective guidelines.

Surveillance of influenza A and the pandemic influenza A (H1N1) 2009 in sewage and surface water in the Netherlands

The role of the water cycle in spreading human pathogenic influenza viruses is poorly studied and is not considered to be significant. However, gastrointestinal symptoms developed in a large proportion of influenza A (H1N1) 2009 virus infected people during the pandemic in 2009 and fecal shedding was reported. This fecal route could potentially play a role in the entry of human pathogenic influenza viruses in to the water cycle. Monitoring of influenza viruses in sewage and surface water during the pandemic in 2009 showed that influenza A viruses were detected in sewage and surface water. However, the pandemic influenza A (H1N1) 2009 virus was not detected. These findings imply that the water cycle did not play a relevant role in spreading the pandemic influenza virus during the epidemic in the Netherlands in 2009. Analyses of deliberately contaminated water samples confirmed the ability of quantitative RT-PCR to detect influenza viruses in sewage samples whereas the analysis of large volumes of surface water was strongly hampered by the presence of PCR-inhibiting substances.

Method for rapid detection of viable Escherichia coli in water using real-time NASBA

A rapid real-time NASBA method was developed for detection of Escherichia coli in water samples. In this method, a fragment of the clpB-mRNA is amplified and a specific molecular beacon probe is used to detect the amplified mRNA fragment during the NASBA reaction. The method was shown to be specific and sensitive (1 viable E. coli in 100ml) and can be performed within 3-4h. Different inactivation processes (starvation, heat, UV-irradiation and chlorine) were employed to study the relationship between culturability and the ability to detect E. coli using NASBA. Detection of clpB-mRNA correlated with culturability after starvation or chlorine treatment. After UV-irradiation or heat-inactivation, detection of the increase in production of clpB-mRNA in viable E. coli cells after heat-shock induction correlated with culturability. Application of the NASBA method on tap water, treated sewage and surface water samples showed that culture and NASBA yielded comparable results in these different matrices. This study demonstrates that the NASBA method has high potential as a rapid test for microbiological water quality monitoring.

Quantitative detection of E. coli, E. coli O157 and other shiga toxin producing E. coli in water samples using a culture method combined with real-time PCR

Recent water related outbreaks of shiga toxin producing E. coli O157 have resulted in increased attention of the water industry to this potentially deadly pathogen. Current methods to detect E. coli O157 and its virulence genes are laborious and time-consuming. Specificity, sensitivity and simple use of a real-time PCR method makes it an attractive alternative for the detection of STEC E. coli O157. This study describes the development and application of real-time PCR methods for the detection of E. coli O157, shiga toxin genes (Stx1 and Stx2) and E. coli. The specificity of the methods was confirmed by performing colony-PCR assays on characterized bacterial isolates, demonstrating the applicability of these assays as rapid tests to confirm the presence of E. coli or E. coli O157 colonies on culture plates. Sensitive culture-PCR methods were developed by combining culture enrichment with real-time PCR detection. This rapid method allowed detection of low concentrations of E. coli O157 in the presence of high concentrations of non-O157-E. coli (1:104). Culture-PCR methods were applied to 27 surface water and 4 wastewater samples. E. coli O157 and both Stx genes were detected in two wastewater samples, whereas only E. coli O157 was detected in two surface water samples. Culture-PCR methods were not influenced by matrix effects and also enabled quantitative (MPN) detection of E. coli in these samples.

The use of a disability model in haemophilia research

Most haemophilia research is medically orientated. However, assessment of the impact of disease on the individual is different when viewed from a rehabilitation perspective. Several models are available to explore functioning and health from this perspective. The disablement process (DP) is such a model, and the aim of this study was to introduce this process in haemophilia research to see whether this type of research could lead to meaningful data. Forty-three adult patients with severe haemophilia participated in this study in which the three 'main pathway' domains of the DP (impairments, functional limitations and disability) and two additional factors (intra-individual and risk factors) were addressed. Three questionnaires (HAL, Dutch-AIMS2 and IPA) were incorporated, and Pettersson scores for 21 patients were retrieved. Step-wise and hierarchical regression analysis was used to assess relationship between the various domains. Arthropathy explained 48% of the variance in functional limitations and nearly 25% of the variance in disability. Functional limitations explained 54% of the variance in disability. Patients identified pain as an important aspect of health which addressed 22% and 13% of the variance in functional limitations and disability respectively. Age was correlated with arthropathy (r = 0.85; P < 0.001), whereas psychological health correlated with pain (r = 0.67; P < 0.001). Both variables were also correlated with functional limitations and disability. Analyses adjusting for the effects of age and psychological health were subsequently performed resulting in more insight in the associations within the DP. The use of the DP in haemophilia research proved to be useful.

Measuring patients' perceptions on their functional abilities: validation of the Haemophilia Activities List

Recently, the Haemophilia Activities List (HAL), a haemophilia-specific self-assessment questionnaire to assess a patient's self-perceived functional ability, was introduced and a limited pilot study warranted its further development. The present study finalizes the HAL and assesses the convergent and construct validity, as well as the internal consistency of its definitive version. Three questionnaires (HAL, Dutch-Arthritis Impact Measurement Scales 2 and the Impact on Participation and Autonomy questionnaire) were completed by 127 patients with severe haemophilia (<1% clotting activity), as well as four performance tests (button test, 50 metre walking test, timed-up-and-go test and figure-8 walking test). After removal of 15 non-informative items from the provisional HAL, three components within the questionnaire were identified (upper extremity activities, basic lower extremity activities and complex lower extremity activities). The internal consistency of these components was high (Cronbach's alpha = 0.93-0.95), as was internal consistency for the seven domains of the HAL (alpha = 0.61-0.96). The convergent validity of the HAL when compared to the other two questionnaires was good (r = 0.47-0.84). The construct validity of the HAL when compared to the four performance tests was generally lower (r = 0.23-0.77). The final version of the HAL has good internal consistency and convergent validity and gives the clinician insight into a patient's self-perceived ability to perform activities of daily life. It is likely that self-assessment instruments (questionnaires) and performance tests consider different concepts of functional health status and it is therefore recommended that both types are included when clinicians assess a patient's functional abilities.

Mortality and causes of death in patients with hemophilia, 1992-2001: a prospective cohort study

BACKGROUND

Clotting factor products have been safe for HIV since 1985, and for hepatitis C since 1992. Few studies have reported on mortality in the total population of hemophilia patients after the period of risk of viral infection transmission.

OBJECTIVES

We studied the mortality, causes of death, and life expectancy of hemophilia patients between 1992 and 2001. We compared these findings with those of previous cohorts, together spanning the periods before, during, and after the use of potentially contaminated clotting products.

PATIENTS AND METHODS

We performed a prospective cohort study among 967 patients with hemophilia A and B. Death rates, overall and cause-specific, were compared with national mortality figures for males adjusted for age and calendar period as standardized mortality ratio (SMRs).

RESULTS

Between 1992 and 2001, 94 (9.7%) patients had died and two patients were lost to follow-up (0.2%). Mortality was 2.3-times higher in hemophilia patients than in the general male population (SMR 2.3 95% confidence interval 1.9-2.8). In patients with severe hemophilia, life expectancy decreased from 63 (1972-1985) to 59 years (1992-2001). Exclusion of virus-related deaths resulted in a life expectancy at birth of 72 years.

CONCLUSIONS

AIDS was the main cause of death (26%) and 22% of deaths were because of hepatitis C. In patients not affected by viral infections, there still appeared to be a trend toward a moderately increased mortality compared with the Dutch male population. Thus, mortality of patients with hemophilia is still increased; this is largely because of the consequences of viral infections.

Pain and functional limitations in patients with severe haemophilia

Patients with severe haemophilia often experience pain caused by haemophilic arthropathy, and it is known that pain acts as a predictor of disability. The role of pain in functional limitations in these patients, however, has not been systematically investigated. The aim of this study was to describe pain as experienced by patients with haemophilia and to address the role of pain in subsequent functional limitations. Seventy-eight adult patients (18-70 years) with severe haemophilia completed one questionnaire on pain and one on self-perceived functional abilities. Two-thirds of the patients suffered from more than one painful joint, the ankle being mentioned most frequently (n=43). Analgesics were used by 36% of the patients indicating having pain. Six of 10 most frequently mentioned pain descriptors were of evaluative nature. Evaluative qualities of pain were associated with pain intensity, which in turn was associated with the impact of pain on daily life. Pain outcomes, after adjusting for age and treatment modality, explained 3-22% of the variance in self-perceived functional abilities. Data on radiological joint damage (Pettersson scores) were retrieved for a subgroup of 28 younger patients on prophylaxis and no significant correlations with pain parameters were found. Over two-thirds of the patients with severe haemophilia had one or more painful joints. Pain plays a small, but significant role in functional limitations. In the identified subgroup, arthropathy, as measured by the Pettersson score, seemed to have no role in pain experience. Promoting analgesic use might decrease the impact of pain on functional limitations.

Escherichia coli O157:H7 in drinking water from private water supplies in the Netherlands

The microbiological quality of drinking water from 144 private water supplies in the Netherlands was tested and additionally the occurrence of Escherichia coli O157 was examined. Faecal indicators were enumerated by using standard membrane filtration methods. The presence of E. coli O157 was determined using a specific enrichment method. Eleven percent of the samples contained faecal indicators whereas E. coli O157:H7 was isolated from 2.7% of the samples that otherwise met the drinking water standards. The E. coli O157 positive water supplies were located on camp-sites in agricultural areas with large grazer densities. Pulsed field gel electrophoresis (PFGE) analysis suggested that cattle might have been the cause of contamination. Our results indicate that compliance with microbiological quality standards obtained in routine monitoring does not always guarantee the absence of pathogens. The presence of pathogens such as E. coli O157 may suggest possible health consequences; however, a risk assessment process should be performed as the monitoring of both faecal indicator parameters and pathogens do not predict the effect of microbial contamination of drinking water on a population.

Direct comparison of selected methods for genetic categorisation of Cryptosporidium parvum and Cryptosporidium hominis species

A study was undertaken to compare the performance of five different molecular methods (available in four different laboratories) for the identification of Cryptosporidium parvum and Cryptosporidium hominis and the detection of genetic variation within each of these species. The same panel of oocyst DNA samples derived from faeces (n=54; coded blindly) was sent for analysis by: (i) DNA sequence analysis of a fragment of the HSP70 gene; (ii) DNA sequence analysis and the ssrRNA gene in laboratory 1; (iii) single-strand conformation polymorphism analysis of part of the ssrRNA; (iv) SSCP analysis of the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA region in laboratory 2; (v) 60 kDa glycoprotein (gp60) gene sequencing with prior species determination using PCR with restriction fragment length polymorphism analysis of the ssrRNA gene in laboratory 3; and (vi) multilocus genotyping at three microsatellite markers in laboratory 4. For detecting variation within C. parvum and C. hominis, SSCP analysis of ITS-2 was considered to have superior utility and determined 'subgenotypes' in samples containing DNA from both species. SSCP was also most cost effective in terms of time, cost and consumables. Sequence analysis of gp60 and microsatellite markers ML1, ML2 and 'gp15' provided good comparators for the SSCP of ITS-2. However, applicability of these methods to other Cryptosporidium species or genotypes and to environmental samples needs to be evaluated. This trial provided, for the first time, a direct comparison of multiple methods for the genetic characterisation of C. parvum and C. hominis samples. A protocol has been established for the international distribution of samples for the characterisation of Cryptosporidium. This can be applied in further evaluation of molecular methods by investigation of a larger number of unrelated samples to establish sensitivity, typability, reproducibility and discriminatory power based on internationally accepted methods for evaluation of microbial typing schemes.

Functional consequences of haemophilia in adults: the development of the Haemophilia Activities List

Several instruments can be used to evaluate the functional status of patients with haemophilia, but none of these instruments is specific for haemophilia. We developed a haemophilia-specific self-assessment questionnaire to evaluate and monitor a patient's perceived functional health status: the Haemophilia Activities List (HAL). In three separate but interlinked substudies, the questionnaire was constructed and tested for face, expert, and convergent validity, as well as internal consistency and patient-evaluated relevance. Items for the questionnaire were collected by interviewing 162 patients, using the McMaster-Toronto Arthritis Patient Preference Disability Questionnaire (MACTAR). The items were combined to generate the first version of the questionnaire [HAL(1)]. This version was evaluated and commented on by two focus groups (patients and caregivers), and then the questionnaire was adapted on the basis of these comments, forming the final version, HAL(2). This version was then validated in a pilot study with 50 consecutive patients using the Dutch Arthritis Impact Measurements Scales 2 (Dutch-AIMS2) and the Impact on Participation and Autonomy (IPA) questionnaires. The HAL(2) showed good convergent validity (Pearson correlation 0.80-0.91; P < 0.01), and the internal consistency was good for six of the eight domains (Cronbach's alpha 0.83-0.95). Patients considered the content of the HAL to be more relevant to their situation than the content of the other questionnaires (P < 0.01). Three major factors (upper extremity function, lower extremity function, key activities/major problem activities) were identified by factor analysis. The questionnaire seems to be a useful tool to identify problematic activities as part of the functional health status of patients with haemophilia. The construct validity, test-retest reliability, and responsiveness of the HAL will be established in the future.

Clinimetric instruments to assess functional health status in patients with haemophilia: a literature review

The World Federation of Hemophilia scoring system (WFH-1) evaluates primarily body functions and structures, whereas assessment of the whole area of functional health status is considered nowadays to be a better measure. In addition, the WFH-1 lacks psychometric properties (reliability, validity and sensitivity to change). This study aimed to gain insight into the clinimetric assessment of functional health status in patients with haemophilia by way of a systematic literature search. A standardized literature search and selection was performed on the databases of CINAHL (1982-2001), Medline (1966-2001), and PubMed (January-July 2001). Clinimetric instruments applied in the selected articles were classified based on the international classification of functioning, disability, and health (ICF) and analysed for their psychometric properties. In 19 articles published between 1979 and 2001, 34 clinimetric instruments were used to assess functional health status. Instruments were classified as measuring the ICF components body structure and function (n = 17), activities (12) and participation (4). Reliability was measured in four articles on three different instruments, the validity (construct) of the instruments for patients with haemophilia was reported in six articles on five instruments, and sensitivity to change in three articles on three instruments. The populations under study varied in number (7-9 35), mean age (21.6-50.8 years), and in the distribution of haemophilia severity. Reports on the evaluation of functional health status in patients with haemophilia are increasing. Further research on the psychometric properties of the instruments is warranted in more groups of patients with haemophilia. Development of the new core set of clinimetric instruments, the WFH-2, might benefit from this strategy.

Participation in sports by Dutch persons with haemophilia

Patients with haemophilia are now widely advised to participate in sports. However, no extensive data are available about their actual participation. A self-administered questionnaire was used to investigate sports participation by persons with haemophilia in the Netherlands. All 293 questionnaires that were distributed have been returned; 217 were from people with severe haemophilia A or B (this is 40% of the severely affected Dutch population with haemophilia). Of this group, 155 (71%) participate in one or more sports: 66 swim, 36 cycle, 21 play tennis, 18 do fitness exercises, 16 ice skate, 10 ski and 10 play table tennis; in total 44 different sports are mentioned. Of a group of 16 persons with haemophilia who are unable to run, 10 (63%) participate in sport and of a group of 91 who can only run sometimes, 64 (70%) engage in sports. This shows that there are ample opportunities for persons with haemophilia to participate in sports, even if they are unable to run. Severely affected persons with haemophilia are as active as the general Dutch population; in fact, a higher proportion swims and/or cycles. In conclusion, sports participation in the Netherlands by persons with haemophilia is in accordance with World Federation of Hemophilia directives.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Physiotherapy for the treatment of articular contractures in haemophilia

Articular contractures in haemophilia are impairments that can not be cured by means of physiotherapy because of the pathophysiology of the joint. Rehabilitation, however, tries to diminish the disabilities and prevent handicaps caused by the impairments. Physiotherapy aims at pain reduction by means of manual traction. Next to manual traction the intensive physiotherapy programme includes mobilization techniques, muscle strengthening exercises and stretching, joint stability training, postural and gait, training, and functional training. In all 50 haemophilia patients have undergone this intensive 4-week clinical rehabilitation programme. Data of 20 of these severe haemophilia patients show that the mean range of motion at the start of the rehabilitation period, after 4 weeks and after 5 years do not differ. In spite of progressing arthropathy after 5 years the activities of daily living (ADL), walking range and pain are equal or better according to 13 of 15 patients.

Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4

As part of the European Scientists Sequencing Arabidopsis program, a contiguous region (396607 bp) located on chromosome 4 around the APETALA2 gene was sequenced. Analysis of the sequence and comparison to public databases predicts 103 genes in this area, which represents a gene density of one gene per 3.85 kb. Almost half of the genes show no significant homology to known database entries. In addition, the first 45 kb of the contig, which covers 11 genes, is similar to a region on chromosome 2, as far as coding sequences are concerned. This observation indicates that ancient duplications of large pieces of DNA have occurred in Arabidopsis.

Functional kinesiology in haemophilia, an area yet to be explored

In haemophilic arthropathy there is a progressive limitation of the range of motion (ROM) which may lead to disabilities in the activities of daily living (ADL). In the literature the pathology of haemophilic arthropathy is described extensively, but only one paper describing functional limitations caused by limited range of motion (LOM) in haemophilia was found. The aim of the pilot study was to estimate on theoretical grounds, how many patients with haemophilia might suffer from functional disabilities.

MATERIAL

ROM of elbows, knees and ankles of 155 Haemophilia A and B patients.

METHODS

Flexion and extension were measured with an ordinary goniometer. The ROM of joints of patients with haemophilia was compared with normal values.

RESULTS

39 of 155 patients had a normal ROM in both elbows; 22 in one elbow; 34 patients had disabilities in ADL with both arms; 14 with one arm; 18 were able to compensate; 89 had no problems; 79 of 155 patients had a near normal ROM of both knees; 38 patients could not ride an ordinary bicycle.

CONCLUSION

Only limited data are available concerning the normal ROM needed for individual ADL. Until additional data are available, it is not possible to predict which patients will be disabled in their activities of daily living and individual counselling should be done during the yearly outpatient comprehensive care clinics. Conservative and surgical measures should be taken to ensure elbow flexion of at least 120 degrees and knee flexion of 100 degrees for Western societies. In Asian countries patients with haemophilia need maximum knee flexion and ankle dorsi flexion.

Synovium in haemophilic arthropathy

Synovium is an essential component of the joint and plays a critical role in maintaining a balance between physiological processes and pathological changes in the joint. Recurrent intra-articular bleeding as occur in haemophilia induce pathological synovial changes in the joint. From a certain point on, synovitis inevitably plays a major role in joint destruction, although in the early phase of haemophilic arthropathy its role may be secondary to cartilage damage as a result of the direct effects of blood on cartilage. The changed haemosiderotic, synovial tissue produces catabolic cytokines and enzymes harmful for cartilage.

Orthotics and rehabilitation for chronic hemophilic synovitis of the ankle. An overview

The ankle is the second most affected joint in hemophilia. Recurrent bleeding leads to chronic synovitis. Prevention of chronic synovitis should start with prophylactic replacement therapy or on demand treatment of recurrent hemarthrosis. Attention must be given to the function of the ankle joint. When instability is present, an extensive range of exercises is important. An orthotic or shoe adaption may be useful during the rehabilitation process. Viscoheels worn in shoes seem to reduce the bleeding frequency and pain.

Lower limb prosthetic considerations in persons with coagulopathies

Most able-bodied amputees use artificial limbs for ambulation. Special considerations are required for persons with coagulopathies because excess pressure or friction may result in soft-tissue haemorrhages. Persons with haemophilia have multi-articular pathologies, hence the necessity to consider carefully the use of accessory walking aids. The use of walking aids results in biomechanical forces being applied through the upper limb joints and this may cause haemarthroses.

Mutational analysis of the murine coronavirus spike protein: effect on cell-to-cell fusion

The spike (S) protein of murine coronavirus strain A59 (MHV-A59) is a type I membrane protein that induces membrane fusion. In this study we have analyzed the role of two domains in the S protein on fusion. The 180-kDa mature S protein is partially cleaved into two 90-kDa subunits during transport to the plasma membrane. We have identified several amino acids that are important for cleavage of S, and we show that cleavage is not strictly required for fusion. However, the level of cleavage seems to influence the fusion kinetics. After introduction of an arginine at position P2 to mimick the MHV-JHM cleavage site, full cleavage of the spike protein was obtained. Further, we analyzed the effect of mutations in the transmembrane (TM) domain of the S protein. Maturation and cell surface expression of the mutant proteins were not affected, and all proteins became acylated. The mutant in which the predicted transmembrane domain was shortened did not induce syncytia. From a group of mutants in which several conserved cysteines in the TM domain had been replaced by serines, one was unable to induce syncytia, another showed delayed syncytia formation, and the third mutant induced syncytia as did the wild-type protein. The potential role of the transmembrane domain in fusion is discussed.

Site directed mutagenesis of the murine coronavirus spike protein. Effects on fusion

Mutations were introduced in the transmembrane region of the spike protein of the murine coronavirus A59. The maturation of these mutant S proteins was not affected, they were all expressed at the cell surface, and became acylated, however some mutant S proteins did not induce cell-to-cell fusion. An I-->K change in the middle of the predicted transmembrane (TM) anchor and mutation of the first three cysteine residues of the TM domain resulted in a fusion-negative phenotype. We propose a model by which these data can be explained.

Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs

We describe a novel strategy to site-specifically mutagenize the genome of an RNA virus by exploiting homologous RNA recombination between synthetic defective interfering (DI) RNA and the viral RNA. Marker mutations introduced in the DI RNA were replaced by the wild-type residues during replication. More importantly, however, these genetic markers were introduced into the viral genome: even in the absence of positive selection MHV recombinants could be isolated. This finding provides new prospects for the study of coronavirus replication using recombinant DNA techniques. As a first application, we describe the rescue of the temperature sensitive mutant MHV Albany-4 using DI-directed mutagenesis. Possibilities and limitations of this strategy are discussed.

A novel glycoprotein of feline infectious peritonitis coronavirus contains a KDEL-like endoplasmic reticulum retention signal

A new protein of the feline infectious peritonitis virus (FIPV) was discovered in lysates of infected cells. Expression of the gene encoding open reading frame (ORF) 6b of FIPV in recombinant vaccinia virus infected cells was used to identify it as the 6b protein. It is a novel type of viral glycoprotein whose function is not clear. It is a soluble protein contained in microsomes; its slow export from the cell is caused by the presence of an ER-retention signal at the C-terminus. This amino acid sequence, KTEL, closely resembles the consensus KDEL-signal of soluble resident ER proteins. A mutant 6b protein with the C-terminal sequence KTEV became resistant to digestion by endo-beta-N-acetylglucosaminidase H with a half-time that was reduced threefold. In contrast, a mutant with the sequence KDEL was completely retained in the ER. The FIPV 6b protein is the first example of a viral protein with a functional KDEL-like ER-retention signal.

Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs

We describe a novel strategy to site-specifically mutagenize the genome of an RNA virus by exploiting homologous RNA recombination between synthetic defective interfering (DI) RNA and viral RNA. Marker mutations introduced in the DI RNA were replaced by the wild-type residues during replication. More importantly, however, these genetic markers were introduced into the viral genome; even in the absence of positive selection, MHV recombinants were isolated. This finding provides new prospects for the study of coronavirus replication using recombinant DNA techniques. As a first application, we describe the rescue of the temperature sensitive mutant MHV Albany-4 using DI-directed mutagenesis. Possibilities and limitations of this strategy are discussed.

A novel glycoprotein of feline infectious peritonitis coronavirus contains a KDEL-like endoplasmic reticulum retention signal

A new protein of feline infectious peritonitis coronavirus (FIPV) was discovered in lysates of [35S]cysteine-labeled infected cells. Expression of open reading frame (ORF) 6b of FIPV in recombinant vaccinia virus-infected cells was used to identify it as the 6b protein. Further characterization revealed that it is a novel type of viral glycoprotein whose function is not clear. It is a soluble protein contained in microsomes; its slow export from the cell is caused by the presence of an endoplasmic reticulum (ER) retention signal at the C terminus. This amino acid sequence, KTEL, closely resembles the consensus KDEL signal of soluble resident ER proteins. A mutant 6b protein with the C-terminal sequence KTEV became resistant to digestion by endo-beta-N-acetylglucosaminidase H with a half-time that was reduced threefold. In contrast, a mutant with the sequence KDEL was completely retained in the ER. The FIPV 6b protein is the first example of a viral protein with a functional KDEL-like ER retention signal.