Characterization of A/H7 influenza virus global antigenic diversity and key determinants in the hemagglutinin globular head mediating A/H7N9 antigenic evolution

IMPORTANCE

A/H7 avian influenza viruses cause outbreaks in poultry globally, resulting in outbreaks with significant socio-economical impact and zoonotic risks. Occasionally, poultry vaccination programs have been implemented to reduce the burden of these viruses, which might result in an increased immune pressure accelerating antigenic evolution. In fact, evidence for antigenic diversification of A/H7 influenza viruses exists, posing challenges to pandemic preparedness and the design of vaccination strategies efficacious against drifted variants. Here, we performed a comprehensive analysis of the global antigenic diversity of A/H7 influenza viruses and identified the main substitutions in the hemagglutinin responsible for antigenic evolution in A/H7N9 viruses isolated between 2013 and 2019. The A/H7 antigenic map and knowledge of the molecular determinants of their antigenic evolution add value to A/H7 influenza virus surveillance programs, the design of vaccines and vaccination strategies, and pandemic preparedness.

Impact of the anaerobic feeding mode on substrate distribution in aerobic granular sludge

There is a growing interest to implement aerobic granular sludge (AGS) in existing conventional activated sludge (CAS) systems with a continuous flow-through configuration. The mode of anaerobic contact of raw sewage with the sludge is an important aspect in the adaptation of CAS systems to accommodate AGS. It remains unclear how the distribution of substrate over the sludge by a conventional anaerobic selector compares to the distribution via bottom-feeding applied in sequencing batch reactors (SBRs). This study investigated the effect of the anaerobic contact mode on the substrate (and storage) distribution by operating two lab-scale SBRs; one with the traditional bottom-feeding through a settled sludge bed similar to full-scale AGS systems, and one where the synthetic wastewater was fed as a pulse at the start of the anaerobic phase while the reactor was mixed through sparging of nitrogen gas (mimicking a plug-flow anaerobic selector in continuous flow-through systems). The distribution of the substrate over the sludge particle population was quantified via PHA analysis, combined with the obtained granule size distribution. Bottom-feeding was found to primarily direct substrate towards the large granular size classes (i.e. large volume and close to the bottom), while completely mixed pulse-feeding gives a more equal distribution of substrate over all granule sizes (i.e. surface area dependant). The anaerobic contact mode directly controls the substrate distribution over the different granule sizes, irrespective of the solids retention time of a granule as an entity. Preferential feeding of the larger granules will enhance and stabilise the granulation compared to pulse-feeding, certainly under less advantageous conditions imposed by real sewage.

Impact of aerobic availability of readily biodegradable COD on morphological stability of aerobic granular sludge

Operational disturbances in aerobic granular sludge (AGS) systems can result in aerobic availability of readily biodegradable COD (rbCOD). Different from activated sludge, morphological consequences on the short and long term are not well described in literature. This study investigated the effect of incomplete anaerobic uptake of acetate on the morphological and process stability of AGS using a lab-scale reactor. A fraction of the total acetate load was dosed aerobically, which was increased stepwise while monitoring granular morphology. A good granular morphology and an SVI of 40 ml/g were obtained during initial enrichment and maintained for ≤20% aerobic acetate load dosed at 4 mg COD/g VSS/h. Biological phosphorus removal efficiency was initially unaffected, but the aerobic acetate dosage rate did decrease the aerobic phosphate uptake rate. This led to loss of phosphorus removal for >20% aerobic acetate load dosed at 8 mg COD/g VSS/h over the course of 12 days. Subsequently, significant outgrowth formed on the granular surfaces and developed over time into finger-like structures. Under these high aerobic acetate loads the SVI increased to 80 ml/g and resulted in significant biomass washout due to deteriorating settling properties of the sludge. The sludge settleability and biological phosphorus removal recovered 10 days after aerobic feeding of acetate was stopped. Aerobic presence of rbCOD can be tolerated if mostly anaerobic acetate uptake is maintained, thereby ensuring stable granular morphology and good settleability. The high enrichment of phosphate accumulating organisms in the granular sludge through bottom-feeding and selective wasting of flocs makes aerobic granular sludge resilient to morphological deterioration in aerobic presence of rbCOD.

Author Correction: Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China¹. The causative agent was identified as the species Severe acute respiratory syndrome-related coronavirus and was named SARS-CoV-2 (ref. ²). By 16 April the virus had spread to 185 different countries, infected over 2,000,000 people and resulted in over 130,000 deaths³. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands.

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

Background

10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers.

Methods

We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients.

Findings

Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community.

Interpretation

Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers.

Funding

EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.

The acid soluble extracellular polymeric substance of aerobic granular sludge dominated by Defluviicoccus sp

A new acid soluble extracellular polymeric substance (acid soluble EPS) was extracted from an acetate fed aerobic granular sludge reactor operated at 35 °C. Acid soluble EPS dominated granules exhibited a remarkable and distinctive tangled tubular morphology. These granules are dominated by Defluviicoccus Cluster II organisms. Acetic acid instead of the usually required alkaline extraction medium was needed to dissolve the granules and solubilise the polymeric matrix. The extracted acid soluble EPS was analysed and identified using various instrumental analysis including ¹H and ¹³C Nuclear Magnetic Resonance, Fourier Transform Infrared Spectroscopy and Raman spectroscopy. In addition, the glycoconjugates were characterized by fluorescence lectin-binding analysis. The acid soluble EPS is α-(1 → 4) linked polysaccharide, containing both glucose and galactose as monomers. There are OCH₃ groups connected to the glucose monomer. Transmission and scanning electron microscopy (TEM, SEM) as well as confocal laser scanning microscopy (CLSM) showed that the acid soluble EPS was present as a tightly bound capsular EPS around bacterial cells ordered into a sarcinae-like growth pattern. The special granule morphology is decided by the acid soluble EPS produced by Defluviicoccus Cluster II organisms. This work shows that no single one method can be used to extract all possible extracellular polymeric substances. Results obtained here can support the elucidation of biofilm formation and structure in future research.

Influenza virus-specific antibody dependent cellular cytoxicity induced by vaccination or natural infection

Influenza viruses are responsible for substantial morbidity and mortality during seasonal epidemics. Vaccination is the most effective method to prevent infection, however due to antigenic drift of the viral surface protein hemagglutinin (HA), annual influenza virus vaccination is required. In addition to seasonal viruses, certain (avian) influenza A viruses of other subtypes, like H5N1 or H7N9, cause sporadic zoonotic infections. Therefore, the availability of game-changing novel vaccines that induce "universal" immune responses to a wide variety of influenza A virus subtypes is highly desirable. The quest for universal influenza vaccines has fueled the interest in broadly-reactive antibodies specific for the stalk of hemagglutinin (HA) and biological activities of antibodies other than direct virus neutralization, like antibody-dependent cellular cytotoxicity (ADCC). In the present study, we investigated the ADCC response upon influenza virus vaccination and infection in humans using a robust ADCC assay that is based on the use of recombinant HA and a continuous NK cell line that expresses FcγRIII (CD16). This assay offers advantages over existing methods, like ease to perform and possibilities to standardize. We showed that HA-specific ADCC mediating antibodies are induced by vaccination with adjuvanted trivalent seasonal and monovalent H1N1pdm09 inactivated vaccines, and by infection with H1N1pdm09 virus. In addition, the use of chimeric influenza HA with a H1 stem but antigenically irrelevant head domain derived from an avian virus allowed detection of H1-stalk-specific ADCC mediating antibodies. This assay will facilitate the assessment of ADCC mediating serum antibodies after (universal) influenza vaccination or infection and may define ADCC activity as a correlate of (cross-) protection in the future.

Full scale performance of the aerobic granular sludge process for sewage treatment

Recently, aerobic granular sludge technology has been scaled-up and implemented for industrial and municipal wastewater treatment under the trade name Nereda(®). With full-scale references for industrial treatment application since 2006 and domestic sewage since 2009 only limited operating data have been presented in scientific literature so far. In this study performance, granulation and design considerations of an aerobic granular sludge plant on domestic wastewater at the WWTP Garmerwolde, the Netherlands were analysed. After a start-up period of approximately 5 months, a robust and stable granule bed (>8 g L(-1)) was formed and could be maintained thereafter, with a sludge volume index after 5 min settling of 45 mL g(-1). The granular sludge consisted for more than 80% of granules larger than 0.2 mm and more than 60% larger than 1 mm. Effluent requirements (7 mg N L(-1) and 1 mg P L(-1)) were easily met during summer and winter. Maximum volumetric conversion rates for nitrogen and phosphorus were respectively 0.17 and 0.24 kg (m(3) d)(-1). The energy usage was 13.9 kWh (PE150·year)(-1) which is 58-63 % lower than the average conventional activated sludge treatment plant in the Netherlands. Finally, this study demonstrated that aerobic granular sludge technology can effectively be implemented for the treatment of domestic wastewater.

Effect of sludge age on methanogenic and glycogen accumulating organisms in an aerobic granular sludge process fed with methanol and acetate

The influence of sludge age on granular sludge formation and microbial population dynamics in a methanol- and acetate-fed aerobic granular sludge system operated at 35°C was investigated. During anaerobic feeding of the reactor, methanol was initially converted to methane by methylotrophic methanogens. These methanogens were able to withstand the relatively long aeration periods. Lowering the anaerobic solid retention time (SRT) from 17 to 8 days enabled selective removal of the methanogens and prevented unwanted methane formation. In absence of methanogens, methanol was converted aerobically, while granule formation remained stable. At high SRT values (51 days), γ-Proteobacteria were responsible for acetate removal through anaerobic uptake and subsequent aerobic growth on storage polymers formed [so called metabolism of glycogen-accumulating organisms (GAO)]. When lowering the SRT (24 days), Defluviicoccus-related organisms (cluster II) belonging to the α-Proteobacteria outcompeted acetate consuming γ-Proteobacteria at 35°C. DNA from the Defluviicoccus-related organisms in cluster II was not extracted by the standard DNA extraction method but with liquid nitrogen, which showed to be more effective. Remarkably, the two GAO types of organisms grew separately in two clearly different types of granules. This work further highlights the potential of aerobic granular sludge systems to effectively influence the microbial communities through sludge age control in order to optimize the wastewater treatment processes.

Efficacy of tenofovir and efavirenz in combination with lamivudine or emtricitabine in antiretroviral-naive patients in Europe

BACKGROUND

The combination of tenofovir and efavirenz with either lamivudine or emtricitabine (TELE) has proved to be highly effective in clinical trials for first-line treatment of HIV-1 infection. However, limited data are available on its efficacy in routine clinical practice.

METHODS

A multicentre cohort study was performed in therapy-naive patients initiating ART with TELE before July 2009. Efficacy was studied using ITT (missing or switch = failure) and on-treatment (OT) analyses. Genotypic susceptibility scores (GSSs) were determined using the Stanford HIVdb algorithm.

RESULTS

Efficacy analysis of 1608 patients showed virological suppression to <50 copies/mL at 48 weeks in 91.5% (OT) and 70.6% (ITT). Almost a quarter of all patients (22.9%) had discontinued TELE at week 48, mainly due to CNS toxicity. Virological failure within 48 weeks was rarely observed (3.3%, n = 53). In multilevel, multivariate analysis, infection with subtype B (P = 0.011), baseline CD4 count <200 cells/mm³ (P < 0.001), GSS <3 (P = 0.002) and use of lamivudine (P < 0.001) were associated with a higher risk of virological failure. After exclusion of patients using co-formulated compounds, virological failure was still more often observed with lamivudine. Following virological failure, three-quarters of patients switched to a PI-based regimen with GSS <3. After 1 year of second-line therapy, viral load was suppressed to <50 copies/mL in 73.5% (OT).

CONCLUSIONS

In clinical practice, treatment failure on TELE regimens is relatively frequent due to toxicity. Virological failure is rare and more often observed with lamivudine than with emtricitabine. Following virological failure on TELE, PI-based second-line therapy was often successful despite GSS <3.

Adult hearing screening: follow-up and outcomes1

PURPOSE

To screen hearing and evaluate outcomes in community-dwelling older adults.

METHOD

Three thousand and twenty-five adults responded to an invitation to be screened by questionnaire, otoscopy, and pure-tone audiometry. Pure-tone average (PTA) >35 dB HL in the worse ear, unilateral hearing loss, or otoscopic findings were the criteria for referral for services. A questionnaire related to compliance with referral recommendations was completed by telephone interview for 160 randomly selected participants after 1-2 years from referral.

RESULTS

The referral rate for audiologic/hearing aid evaluation was 46%, and referral for cerumen removal/medical evaluation was 17%. Of the people referred for audiologic/hearing aid evaluation, 18% tried a hearing aid; 2 years later, 11% were using a hearing aid. Screening recommendations affected participants' decision to seek help. Study participants stated that the screening was helpful, it should be offered to everybody, and they would participate in future screenings.

CONCLUSION

Although adult hearing screening offered timely identification of hearing loss for adults seeking help, follow-up with hearing aid treatment was low.

Diagnostic performance of selected commercial HEV IgM and IgG ELISAs for immunocompromised and immunocompetent patients

BACKGROUND

Hepatitis E virus (HEV) genotype 3 is recognised as an emerging pathogen in industrialised countries. The currently commercially available HEV-specific enzyme linked immunosorbent assays (ELISAs) are primarily designed for the detection of antibodies against genotypes 1 (Burma) and 2 (Mexico) and may not sensitively detect HEV genotypes 3 or 4.

OBJECTIVES

This study aimed to evaluate the analytical and clinical performances of eight commercially available HEV serum antibody immunoglobulin M (IgM)- and immunoglobulin G (IgG)-specific ELISAs for genotype 1 and 3 HEV infections in a clinical setting and to study the antibody responses against HEV of immunocompromised versus immunocompetent patient groups.

STUDY DESIGN

Analytical performance and diagnostic sensitivity and specificity were assessed using well-defined reference samples and samples from patients with polymerase chain reaction (PCR)-confirmed HEV infection (n=88) and a specificity panel (n=98).

RESULTS

Limiting dilutions indicated that the highest analytical sensitivity in head-to-head comparison was measured for the Mikrogen_new IgG assay. Taking the serum working dilutions of each assay into account, the Wantai IgG assay was the most sensitive assay. Receiver operator curve (ROC) analysis showed area under the curve (AUC) values of 0.943, 0.964, 0.969, 0.971, 0.974 and 0.994 for the DSI, Mikrogen_old, MP Diagnostics, Mikrogen_new, Wantai and DiaPro anti-HEV IgM assays, respectively. The highest specificity of currently available assays was found for the IgM Wantai assay (>99%). If anti-HEV IgM and IgG results from each supplier were combined, DSI and Wantai assays were able to detect the highest number of (passed) HEV infections.

CONCLUSIONS

Our study showed that current commercial HEV ELISAs could be used to diagnose HEV genotype 3 infection adequately in a clinical setting.

Effect of elevated salt concentrations on the aerobic granular sludge process: linking microbial activity with microbial community structure

The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), "Candidatus Accumulibacter phosphatis" bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal ("Candidatus Accumulibacter").

Ammonium adsorption in aerobic granular sludge, activated sludge and anammox granules

The ammonium adsorption properties of aerobic granular sludge, activated sludge and anammox granules have been investigated. During operation of a pilot-scale aerobic granular sludge reactor, a positive relation between the influent ammonium concentration and the ammonium adsorbed was observed. Aerobic granular sludge exhibited much higher adsorption capacity compared to activated sludge and anammox granules. At an equilibrium ammonium concentration of 30 mg N/L, adsorption obtained with activated sludge and anammox granules was around 0.2 mg NH4-N/g VSS, while aerobic granular sludge from lab- and pilot-scale exhibited an adsorption of 1.7 and 0.9 mg NH4-N/g VSS, respectively. No difference in the ammonium adsorption was observed in lab-scale reactors operated at different temperatures (20 and 30 °C). In a lab-scale reactor fed with saline wastewater, we observed that the amount of ammonium adsorbed considerably decreased when the salt concentration increased. The results indicate that adsorption or better ion exchange of ammonium should be incorporated into models for nitrification/denitrification, certainly when aerobic granular sludge is used.

Formation of aerobic granules and conversion processes in an aerobic granular sludge reactor at moderate and low temperatures

Temperature changes can influence biological processes considerably. To investigate the effect of temperature changes on the conversion processes and the stability of aerobic granular sludge, an aerobic granular sludge sequencing batch reactor (GSBR) was exposed to short-term and long-term temperature changes. Start-up at 8 degrees C resulted in irregular granules that aggregated as soon as aeration was stopped, which caused severe biomass washout and instable operation. The presence of COD during the aerobic phase is considered to be the major reason for this granule instability. Start-up at 20 degrees C and lowering the temperature to 15 degrees C and 8 degrees C did not have any effect on granule stability and biomass could be easily retained in the system. The temperature dependency of nitrification was lower for aerobic granules than usually found for activated sludge. Due to decreased activity in the outer layers of granules at lower temperatures, the oxygen penetration depth could increase, which resulted in a larger aerobic biomass volume, compensating the decreased activity of individual organisms. Consequently the denitrifying capacity of the granules decreased at reduced temperatures, resulting in an overall poorer nitrogen removal capacity. The overall conclusion that can be drawn from the experiments at low temperatures is that start-up in practice should take place preferentially during warm summer periods, while decreased temperatures during winter periods should not be a problem for granule stability and COD and phosphate removal in a granular sludge system. Nitrogen removal efficiencies should be optimized by changes in reactor operation or cycle time during this season.