Tackling late HIV diagnosis: Lessons from the UK in the COVID-19 era

INTRODUCTION

Late diagnosis of HIV is associated with increased morbidity and mortality, and an increased risk of non-infectious comorbidities. On a societal level, late diagnosis leads to higher treatment and healthcare costs and is a major driver of HIV transmission. Despite improvements in other areas of the HIV care pathway, late diagnosis remains an individual and public health concern globally.

OBJECTIVE

To examine the barriers to HIV testing and highlight successful strategies to improve prompt diagnosis. This review describes the prevalence of late diagnosis in the UK and discusses key factors that contribute to late diagnosis, including the effect of the COVID-19 pandemic. Late HIV diagnosis is lower in the UK than in most other European countries. In this review, pilot projects and ongoing initiatives that have reduced late diagnosis in the UK are highlighted; moreover, further strategies for improving prompt diagnosis are suggested.

CONCLUSIONS

Insufficient testing is the fundamental reason for late HIV diagnosis, with societal, systemic, and individual factors all contributing to inadequate testing. Improving access to testing, removing barriers to health-seeking behaviour, and ensuring all people with HIV indicator conditions are promptly tested are key to reducing the rates of late diagnosis globally.

The predictive role of symptoms in COVID-19 diagnostic models: A longitudinal insight

To investigate the symptoms of SARS-CoV-2 infection, their dynamics and their discriminatory power for the disease using longitudinally, prospectively collected information reported at the time of their occurrence. We have analysed data from a large phase 3 clinical UK COVID-19 vaccine trial. The alpha variant was the predominant strain. Participants were assessed for SARS-CoV-2 infection via nasal/throat PCR at recruitment, vaccination appointments, and when symptomatic. Statistical techniques were implemented to infer estimates representative of the UK population, accounting for multiple symptomatic episodes associated with one individual. An optimal diagnostic model for SARS-CoV-2 infection was derived. The 4-month prevalence of SARS-CoV-2 was 2.1%; increasing to 19.4% (16.0%-22.7%) in participants reporting loss of appetite and 31.9% (27.1%-36.8%) in those with anosmia/ageusia. The model identified anosmia and/or ageusia, fever, congestion, and cough to be significantly associated with SARS-CoV-2 infection. Symptoms' dynamics were vastly different in the two groups; after a slow start peaking later and lasting longer in PCR+ participants, whilst exhibiting a consistent decline in PCR- participants, with, on average, fewer than 3 days of symptoms reported. Anosmia/ageusia peaked late in confirmed SARS-CoV-2 infection (day 12), indicating a low discrimination power for early disease diagnosis.

Effects of field-aging on the impact of biochar on herbicide fate and microbial community structure in the soil environment

Biochar can enhance organic carbon storage and mitigate the adverse effects of pesticides in the soil. However, the mechanisms by which field-aging affects the impacts of biochar on herbicide behavior and the composition of microbial communities in the soil remain unclear. This study aimed to investigate the influences of aged and fresh biochar on herbicide behavior and microbial community structure in the soil. Herein, with 14C-labeled technology, aged treatment (soil amended with field-aged biochar), fresh treatment (soil amended with fresh biochar), and control (soil without biochar) were installed to evaluate their treatment capacities. The results showed that the average leaching out and mineralization of simazine in the aged treatment were significantly higher by 4.8% and 1.66% (P < 0.05) compared with the fresh treatment. Relative to the control, the pesticide was significantly adsorbed (P < 0.05) in the aged treatment. The abundance of arbuscular mycorrhizal fungi (AMF) significantly increased by 1.03 and 1.16-fold, whereas fungi increased dramatically by 1.02-fold and decreased by 1.21-fold in the aged and fresh treatments, respectively (P < 0.05). In addition, eukaryotes were effectively reduced by 1.02 and 1.14-fold in these treatments, respectively (P < 0.05). This study suggests that field aging can undermine the impacts of biochar on pesticides and modify the microbial community structure in the soil environment.

COVID-19 infection in people living with HIV

BACKGROUND

Coronavirus disease 2019 (COVID-19) and human immunodeficiency virus (HIV) are intersecting pandemics, with implications for care at an individual and global scale.

SOURCES OF DATA

PubMed search with relevant articles and their references reviewed.

AREAS OF AGREEMENT

COVID-19 has changed the delivery of care to people living with HIV (PLWH). Vaccines are efficacious and safe for PLWH; patient care for symptomatic COVID-19 is similar to that of people without HIV.

AREAS OF CONTROVERSY

It remains unclear whether PLWH experience increased COVID-19-specific mortality. Treatments to reduce severity in early COVID-19 infection lack evidence in PLWH.

GROWING POINTS

The effects of the COVID-19 pandemic on HIV-related morbidity and mortality are yet to be seen. COVID-19 epidemiology among PLWH is complicated by changes to the severe acute respiratory syndrome coronavirus 2, population behaviours and vaccine availability.

AREAS TIMELY FOR DEVELOPING RESEARCH

Global trends in HIV-related morbidity and mortality should be monitored to appreciate the effects of the COVID-19 pandemic. The benefits of early antiviral and/or neutralizing monoclonal antibody (nMAb) treatment for PLWH and nMAb prophylaxis require investigation.

Increasing concentration of pure micro- and macro-LDPE and PP plastic negatively affect crop biomass, nutrient cycling, and microbial biomass

Over the last 50 years, the intense use of agricultural plastic in the form of mulch films has led to an accumulation of plastic in soil, creating a legacy of plastic in agricultural fields. Plastic often contains additives, however it is still largely unknown how these compounds affect soil properties, potentially influencing or masking effects of the plastic itself. Therefore, the aim of this study was to investigate the effects of pure plastics of varying sizes and concentrations, to improve our understanding of plastic-only interactions within soil-plant mesocosms. Maize (Zea mays L.) was grown over eight weeks following the addition of micro and macro low-density polyethylene and polypropylene at increasing concentrations (equivalent to 1, 10, 25, and 50 years mulch film use) and the effects of plastic on key soil and plant properties were measured. We found the effect of both macro and microplastic on soil and plant health is negligible in the short-term (1 to <10 years). However, ≥ 10 years of plastic application for both plastic types and sizes resulted in a clear negative effect on plant growth and microbial biomass. This study provides vital insight into the effect of both macro and microplastics on soil and plant properties.

Differential cellular and humoral immune responses in immunocompromised individuals following multiple SARS-CoV-2 vaccinations

Introduction

The heterogeneity of the immunocompromised population means some individuals may exhibit variable, weak or reduced vaccine-induced immune responses, leaving them poorly protected from COVID-19 disease despite receiving multiple SARS-CoV-2 vaccinations. There is conflicting data on the immunogenicity elicited by multiple vaccinations in immunocompromised groups. The aim of this study was to measure both humoral and cellular vaccine-induced immunity in several immunocompromised cohorts and to compare them to immunocompetent controls.

Methods

Cytokine release in peptide-stimulated whole blood, and neutralising antibody and baseline SARS-CoV-2 spike-specific IgG levels in plasma were measured in rheumatology patients (n=29), renal transplant recipients (n=46), people living with HIV (PLWH) (n=27) and immunocompetent participants (n=64) post third or fourth vaccination from just one blood sample. Cytokines were measured by ELISA and multiplex array. Neutralising antibody levels in plasma were determined by a 50% neutralising antibody titre assay and SARS-CoV-2 spike specific IgG levels were quantified by ELISA.

Results

In infection negative donors, IFN-γ, IL-2 and neutralising antibody levels were significantly reduced in rheumatology patients (p=0.0014, p=0.0415, p=0.0319, respectively) and renal transplant recipients (p<0.0001, p=0.0005, p<0.0001, respectively) compared to immunocompetent controls, with IgG antibody responses similarly affected. Conversely, cellular and humoral immune responses were not impaired in PLWH, or between individuals from all groups with previous SARS-CoV-2 infections.

Discussion

These results suggest that specific subgroups within immunocompromised cohorts could benefit from distinct, personalised immunisation or treatment strategies. Identification of vaccine non-responders could be critical to protect those most at risk.

Atmospheric deposition of microplastics in a rural region of North China Plain

Microplastics (MPs) pollution is becoming one of the most pressing environmental issues globally. MPs in the marine, freshwater and terrestrial environments have been fairly well investigated. However, knowledge of the atmospheric-mediated deposition of MPs within rural environments is limited. Here, we present the results of bulk (dry and wet) atmospheric MPs deposition in a rural region of Quzhou County in the North China Plain (NCP). Samples of MPs in the atmospheric bulk deposition were collected for individual rainfall events over a 12-month period from August 2020 to August 2021. The number and size of MPs from 35 rainfall samples were measured by fluorescence microscopy, while the chemical composition of MPs was identified using micro-Fourier transform infrared spectroscopy (μ-FTIR). The results showed that the atmospheric MPs deposition rate in summer (892-75,421 particles/m²/day) was highest compared to 735-9428, 280-4244 and 86-1347 particles/m²/day in spring, autumn, and winter, respectively. Furthermore, the MPs deposition rates in our study were 1-2 orders of magnitude higher than those in other regions, indicating a higher rate of MPs deposition in the rural region of the NCP. MPs with a diameter of 3-50 μm accounted for 75.6 %, 78.4 %, 73.4 % and 66.1 % of total MPs deposition in spring, summer, autumn, and winter, respectively, showing that the majority of MPs in the current study were small in size. Rayon fibers accounted for the largest proportion (32 %) of all MPs, followed by polyethylene terephthalate (12 %) and polyethylene (8 %). This study also found that a significant positive correlation between rainfall volume and MPs deposition rate. In addition, HYSPLIT back-trajectory modelling showed that the farthest source of deposition MPs may have come from Russia.

Biochar application to temperate grasslands: challenges and opportunities for delivering multiple ecosystem services

Grasslands (natural, semi-natural and improved) occupy approximately one-third of the terrestrial biosphere and are key for global ecosystem service provision, storing up to 30% of soil organic carbon (SOC). To date, most research on soil carbon (C) sequestration has focused on croplands where the levels of native soil organic matter (SOM) are typically low and significant potential exists to replenish SOM stocks. However, with the renewed push to achieve "net zero" C emissions by 2050, grasslands may offer an additional C store, utilising tools such as biochar. Here, we critically evaluate the potential for biochar as a technology for increasing grassland C stocks, identifying a number of practical, economic, social and legislative challenges that need to be addressed before the widescale adoption of biochar may be achieved. We critically assess the current knowledge within the field of grassland biochar research in the context of ecosystem service provision and provide opinions on the applicability of biochar as an amendment to different types of grassland (improved, semi-improved and unimproved) and the potential effect on ecosystem provision using a range of application techniques in the topsoil and subsoil. We concluded that the key question remains, is it possible for managed grasslands to store more C, without causing a loss in additional ecosystem services? To address this question future research must take a more multidisciplinary and holistic approach when evaluating the potential role of biochar at sequestering C in grasslands to mitigate climate change.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s42773-023-00232-y.

Separating N2O production and consumption in intact agricultural soil cores at different moisture contents and depths

Agricultural soils are a major source of the potent greenhouse gas and ozone depleting substance, N2O. To implement management practices that minimize microbial N2O production and maximize its consumption (i.e., complete denitrification), we must understand the interplay between simultaneously occurring biological and physical processes, especially how this changes with soil depth. Meaningfully disentangling of these processes is challenging and typical N2O flux measurement techniques provide little insight into subsurface mechanisms. In addition, denitrification studies are often conducted on sieved soil in altered O2 environments which relate poorly to in situ field conditions. Here, we developed a novel incubation system with headspaces both above and below the soil cores and field-relevant O2 concentrations to better represent in situ conditions. We incubated intact sandy clay loam textured agricultural topsoil (0-10 cm) and subsoil (50-60 cm) cores for 3-4 days at 50% and 70% water-filled pore space, respectively. 15N-N2O pool dilution and an SF6 tracer were injected below the cores to determine the relative diffusivity and the net N2O emission and gross N2O emission and consumption fluxes. The relationship between calculated fluxes from the below and above soil core headspaces confirmed that the system performed well. Relative diffusivity did not vary with depth, likely due to the preservation of preferential flow pathways in the intact cores. Gross N2O emission and uptake also did not differ with depth but were higher in the drier cores, contrary to expectation. We speculate this was due to aerobic denitrification being the primary N2O consuming process and simultaneously occurring denitrification and nitrification both producing N2O in the drier cores. We provide further evidence of substantial N2O consumption in drier soil but without net negative N2O emissions. The results from this study are important for the future application of the 15N-N2O pool dilution method and N budgeting and modelling, as required for improving management to minimize N2O losses.

Recommendations for defining preventable HIV-related mortality for public health monitoring in the era of Getting to Zero: an expert consensus

Getting to Zero is a commonly cited strategic aim to reduce mortality due to both HIV and avoidable deaths among people with HIV. However, no clear definitions are attached to these aims with regard to what constitutes HIV-related or preventable mortality, and their ambition is limited. This Position Paper presents consensus recommendations to define preventable HIV-related mortality for a pragmatic approach to public health monitoring by use of national HIV surveillance data. These recommendations were informed by a comprehensive literature review and agreed by 42 international experts, including clinicians, public health professionals, researchers, commissioners, and community representatives. By applying the recommendations to 2019 national HIV surveillance data from the UK, we show that 30% of deaths among people with HIV were HIV-related or possibly HIV-related, and at least 63% of these deaths were preventable or potentially preventable. The application of these recommendations by health authorities will ensure consistent monitoring of HIV elimination targets and allow for the identification of inequalities and areas for intervention.

Resilience of ecosystem service delivery in grasslands in response to single and compound extreme weather events

Extreme weather events are increasing in frequency and magnitude with profound effects on ecosystem functioning. Further, there is now a greater likelihood that multiple extreme events are occurring within a single year. Here we investigated the effect of a single drought, flood or compound (flood + drought) extreme event on temperate grassland ecosystem processes in a field experiment. To assess system resistance and resilience, we studied changes in a wide range of above- and below-ground indicators (plant diversity and productivity, greenhouse gas emissions, soil chemical, physical and biological metrics) during the 8 week stress events and then for 2 years post-stress. We hypothesized that agricultural grasslands would have different degrees of resistance and resilience to flood and drought stress. We also investigated two alternative hypotheses that the combined flood + drought treatment would either, (A) promote ecosystem resilience through more rapid recovery of soil moisture conditions or (B) exacerbate the impact of the single flood or drought event. Our results showed that flooding had a much greater effect than drought on ecosystem processes and that the grassland was more resistant and resilient to drought than to flood. The immediate impact of flooding on all indicators was negative, especially for those related to production, and climate and water regulation. Flooding stress caused pronounced and persistent shifts in soil microbial and plant communities with large implications for nutrient cycling and long-term ecosystem function. The compound flood + drought treatment failed to show a more severe impact than the single extreme events. Rather, there was an indication of quicker recovery of soil and microbial parameters suggesting greater resilience in line with hypothesis (A). This study clearly reveals that contrasting extreme weather events differentially affect grassland ecosystem function but that concurrent events of a contrasting nature may promote ecosystem resilience to future stress.

Safety and Efficacy of the NVX-CoV2373 Coronavirus Disease 2019 Vaccine at Completion of the Placebo-Controlled Phase of a Randomized Controlled Trial

BACKGROUND

The recombinant protein-based vaccine, NVX-CoV2373, demonstrated 89.7% efficacy against coronavirus disease 2019 (COVID-19) in a phase 3, randomized, observer-blinded, placebo-controlled trial in the United Kingdom. The protocol was amended to include a blinded crossover. Data to the end of the placebo-controlled phase are reported.

METHODS

Adults aged 18-84 years received 2 doses of NVX-CoV2373 or placebo (1:1) and were monitored for virologically confirmed mild, moderate, or severe COVID-19 (onset from 7 days after second vaccination). Participants who developed immunoglobulin G (IgG) against nucleocapsid protein but did not show symptomatic COVID-19 were considered asymptomatic. Secondary outcomes included anti-spike (S) IgG responses, wild-type virus neutralization, and T-cell responses.

RESULTS

Of 15 185 participants, 13 989 remained in the per-protocol efficacy population (6989 NVX-CoV2373, 7000 placebo). At a maximum of 7.5 months (median, 4.5) postvaccination, there were 24 cases of COVID-19 among NVX-CoV2373 recipients and 134 cases among placebo recipients, a vaccine efficacy of 82.7% (95% confidence interval [CI], 73.3%-88.8%). Vaccine efficacy was 100% (95% CI, 17.9%-100.0%) against severe disease and 76.3% (95% CI, 57.4%-86.8%) against asymptomatic disease. High anti-S and neutralization responses to vaccination were evident, together with S-protein-specific induction of interferon-γ secretion in peripheral blood T cells. Incidence of serious adverse events and adverse events of special interest were similar between groups.

CONCLUSIONS

A 2-dose regimen of NVX-CoV2373 conferred a high level of ongoing protection against asymptomatic, symptomatic, and severe COVID-19 through >6 months postvaccination. A gradual decrease of protection suggests that a booster may be indicated.

CLINICAL TRIALS REGISTRATION

EudraCT, 2020-004123-16.

Leaching of phthalate acid esters from plastic mulch films and their degradation in response to UV irradiation and contrasting soil conditions

Phthalate acid esters (PAEs) are commonly used plastic additives, not chemically bound to the plastic that migrate into surrounding environments, posing a threat to environmental and human health. Dibutyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) are two common PAEs found in agricultural soils, where degradation is attributed to microbial decomposition. Yet the impact of the plastic matrix on PAE degradation rates is poorly understood. Using ¹⁴C-labelled DBP and DEHP we show that migration from the plastic matrix into soil represents a key rate limiting step in their bioavailability and subsequent degradation. Incorporating PAEs into plastic film decreased their degradation in soil, DBP (DEHP) from 79% to 21% (9% to <1%), over four months when compared to direct application of PAEs. Mimicking surface soil conditions, we demonstrated that exposure to ultraviolet radiation accelerated PAE mineralisation twofold. Turnover of PAE was promoted by the addition of biosolids, while the presence of plants and other organic residues failed to promote degradation. We conclude that PAEs persist in soil for longer than previously thought due to physical trapping within the plastic matrix, suggesting PAEs released from plastics over very long time periods lead to increasing levels of contamination.

Increased adverse events following third dose of BNT162b2/Pfizer vaccine in those with previous COVID-19, but not with concurrent influenza vaccine

Prior studies suggest that adverse events (AEs) following doses one and two of BNT162b2/Pfizer vaccine are worse in those with a prior history of COVID-19. To establish whether this outcome applies to a third/booster dose, we conducted a survey with 534 healthcare workers (HCW) in Northeast England, who reported AEs following all three doses of BNT162b2/Pfizer vaccine. We also explored AEs associated with concurrent seasonal influenza immunisation, in a subset of 492 HCWs. For all doses of BNT162b2/Pfizer vaccine there was a cluster of systemic AEs that were consistently worse in HCWs with a prior history of COVID-19. AEs were no worse in HCWs who received their third/booster dose within 7 days of the influenza jab, rather than further apart. Gender and the presence of ongoing COVID-19 symptoms (OCS) had no effect on AEs associated with COVID-19 or influenza vaccination, though younger HCWs experienced more AEs overall. Our findings have implications for vaccine hesitancy and immunisation protocols.

Low N2O emissions associated with sheep excreta deposition in temperate managed lowland grassland and extensively grazed hill pasture

Nitrous oxide (N₂O) is a potent greenhouse gas (GHG) whose emission from soil can be enhanced by ruminant excretal returns in grasslands. The default (Tier 1) emission factors (EF_3PRP; i.e. proportion of deposited nitrogen emitted as N₂O) for ruminant excreta deposition are associated with a wide range of uncertainties and the development of country-specific (Tier 2) EF_3PRP is encouraged. In Ireland, a Tier 2 EF_3PRP has been developed for cattle excreta but no data are available for sheep. The aim of this study was to generate data to contribute to the derivation of a Tier 2 EF_3PRP for sheep excreta, while assessing the effect of excreta type, grassland type and season of deposition on N₂O emissions. An experiment was carried out on two sites in the west of Ireland: a managed lowland grassland (LOW) and an extensively grazed hill pasture (HILL), characterised by mineral and acid peat soils, respectively. For each season, four treatments were applied to the soil in a fully randomized block design: control (C), sheep urine (U), sheep dung (D), and artificial urine (AU). Nitrous oxide fluxes were assessed over a full year following each application of treatments, using a static chambers methodology. Results showed a brief initial peak following each application of U/AU in LOW but not in HILL. Cumulative N₂O emissions were significantly higher from the lowland site. Average EF_3PRP for combined excreta was negligible on both sites, thus lower than the IPCC Tier 1 EF_3PRP. Causes of low emissions are likely to depend on site characteristics (e.g. soil acidity in HILL) and season of application (i.e. ammonia volatilisation in summer). This study showed very low N₂O emissions from sheep excretal returns in Irish grasslands and highlighted the importance of developing Tier 2, animal-specific EF_3PRP. More experimental grasslands should be assessed to confirm these results.

Development of a LoRaWAN IoT Node with Ion-Selective Electrode Soil Nitrate Sensors for Precision Agriculture

Crop productivity is highly dependent on the availability of soluble nitrogen (N), e.g. nitrate, in soil. When N levels are low, fertilisers are applied to replenish the soil's reserves. Typically the timing of these applications is based on paper-based guidance and sensor-based measurements of canopy greenness, which provides an indirect measure of soil N status. However this approach often means that N fertiliser is applied inappropriately or too late, resulting in excess N being lost to the environment, or too little N to meet crop demand. To promote greater N use efficiency and improve agricultural sustainability, we developed an Internet of Things (IoT) approach for the real-time measurement of soil nitrate levels using ion-selective membrane sensors in combination with digital soil moisture probes. The node incorporates state-of-the-art IoT connectivity using a LoRaWAN transceiver. The sensing platform can transfer real-time data via a cloud-connected gateway for processing and storage. In summary, we present a validated soil sensor system for real-time monitoring of soil nitrate concentrations, which can support fertiliser management decisions, improve N use efficiency and reduce N losses to the environment.

Changes in microbial community composition drive the response of ecosystem multifunctionality to elevated ozone

Increasing tropospheric ozone poses a potential threat to both above- and belowground components of the terrestrial biosphere. Microorganisms are the main drivers of soil ecological processes, however, the link between soil microbial communities and ecological functions under elevated ozone remains poorly understood. In this study, we assessed the responses of three crop seedlings (i.e., soybean, maize, and wheat) growth and soil microbial communities to elevated ozone (40 ppb O₃ above ambient air) in a pot experiment in the solardomes. Results showed that elevated ozone adversely affected ecosystem multifunctionality by reducing crop biomass, inhibiting soil extracellular enzyme activities, and altering nutrient availability. Elevated ozone increased bacterial and fungal co-occurrence network complexity, negatively correlated with ecosystem multifunctionality. Changes in the relative abundance of some specific bacteria and fungi were associated with multiple ecosystem functioning. In addition, elevated ozone significantly affected fungal community composition but not bacterial community composition and microbial alpha-diversity. Crop type played a key role in determining bacterial alpha-diversity and microbial community composition. In conclusion, our findings suggest that short-term elevated ozone could lead to a decrease in ecosystem multifunctionality associated with changes in the complexity of microbial networks in soils.

A national audit of the management of HIV-2 in adults in the UK

BACKGROUND

HIV-2 is rare in the UK. Many UK centres therefore only treat small numbers of people and there are few clinical trials to guide treatment. The British HIV Association (BHIVA) 2010 guidelines for management of HIV-2 formed the basis for this national audit, which aims to describe current practice and adherence to guidelines.

METHODS

All UK centres providing HIV care were contacted via the BHIVA "Members Matters" newsletter, and asked to submit anonymised, retrospective data for individuals living with HIV-2 accessing care at their service.

RESULTS

Thirty-five sites responded and data were analysed for 167 individuals. Nearly half of individuals accessed care at one of four large London centres (77/167, 46%).Most people living with HIV-2 have taken antiretroviral therapy (ART) (132/167, 79%). The most common reasons for initiating treatment were clinical disease (34/89, 38%) and pregnancy (11/89, 12%). Most treatment-naïve individuals were initiated on a protease inhibitor based regimen (70/89, 79%). The use of integrase strand transfer inhibitor based regimens has increased over time.A significant minority of patients did not have baseline drug resistance testing performed, despite having a detectable viral load (15/52, 29%). Virological failure occurred in a minority of individuals (21/132, 16%); the most common drug regimen change in this context was the addition of an integrase strand transfer inhibitor (12/26 regimen changes, 46%).

CONCLUSIONS

Most individuals living with HIV-2 were managed according to national guidance, with key areas for improvement including the choice of ART, drug resistance testing and the management of virological failure. It is hoped that this national audit, performed in conjunction with the updated 2021 BHIVA guidelines will improve the care of individuals living with HIV-2 in the UK.

Effects of plastic residues and microplastics on soil ecosystems: A global meta-analysis

Plastic pollution is one of the global pressing environmental problems, threatening the health of aquatic and terrestrial ecosystems. However, the influence of plastic residues and microplastics (MPs) in soil ecosystems remains unclear. We conducted a global meta-analysis to quantify the effect of plastic residues and MPs on indicators of global soil ecosystem functioning (i.e. soil physicochemical properties, plant and soil animal health, abundance and diversity of soil microorganisms). Concentrations of plastic residues and MPs were 1-2700 kg ha^-1 and 0.01-600,000 mg kg^-1, respectively, based on 6223 observations. Results show that plastic residues and MPs can decrease soil wetting front vertical and horizontal movement, dissolved organic carbon, and total nitrogen content of soil by 14%, 10%, 9%, and 7%, respectively. Plant height and root biomass were decreased by 13% and 14% in the presence of plastic residues and MPs, while the body mass and reproduction rate of soil animals decreased by 5% and 11%, respectively. However, soil enzyme activity increased by 7%441% in the presence of plastic residues and MPs. For soil microorganisms, plastic residues and MPs can change the abundance of several bacteria phyla and families, but the effects vary between different bacteria.

Iron-Modified Biochar Strengthens Simazine Adsorption and Decreases Simazine Decomposition in the Soil

Currently, modified biochar has been successfully used in the remediation of soil polluted with heavy metals. However, the effects of the modified biochar on pesticides (such as simazine) are still unclear. Herein, the environmental fate of simazine, such as decomposition, leaching, and adsorption in unamended soil, in the soil amended with unmodified and modified biochar (biochar + FeCl₃, biochar + FeOS, biochar + Fe) were evaluated. In addition, an incubation experiment was also performed to observe the influence of modified biochar on the microbial community and diversity in the soil. The results showed that modified biochar significantly decreased the decomposition of simazine in the soil compared to its counterpart. Modified biochar also reduced the concentration of simazine in the leachate. Compared with the control, soil microbial biomass in the soil amended with unmodified biochar, biochar + FeCl₃, biochar + Fe, and biochar + FeOS was decreased by 5.3%, 18.8%, 8.7%, and 18.1%, respectively. Furthermore, modified biochar changed the structure of the microbial community. This shows that modified biochar could increase the soil adsorption capacity for simazine and change the amount and microbial community that regulates the fate of simazine in the soil. This study concludes that iron-modified biochar has positive and negative effects on the soil. Therefore, its advantages and side effects should be considered before applying it to the soil.

Microplastics shape microbial communities affecting soil organic matter decomposition in paddy soil

Microplastics (MPs) can alter microbial communities and carbon (C) cycling in agricultural soils. However, the mechanism by which MPs affect the decomposition of microbe-driven soil organic matter remains unknown. We investigated the bacterial community succession and temporal turnover during soil organic matter decomposition in MP-amended paddy soils (none, low [0.01% w/w], or high [1% w/w]). We observed that MPs reduced the CO₂ efflux rate on day 3 and subsequently promoted it on day 15 of incubation. This increased CO₂ emission in MP-amended soil may be related to (i) enhanced hydrolase enzyme activities or; (ii) shifts in the Shannon diversity, positive group interactions, and temporal turnover rates (from 0.018 to 0.040). CO₂ efflux was positively correlated (r > 0.8, p < 0.01) with Ruminiclostridium_1, Mobilitalea, Eubacterium xylanophilum, Sporomusa, Anaerobacteriu, Papillibacter, Syntrophomonadaceae, and Ruminococcaceae_UCG_013 abundance in soil with high MPs, indicating that these genera play important roles in soil organic C mineralization. These results demonstrate how microorganisms adapt to MPs and thus influence the C cycle in MP-polluted paddy ecosystems.

Renal mitochondrial toxicity: effects of thymidine analogues and tenofovir disoproxil fumarate in African people with HIV

We investigated the contributions of thymidine analogue and tenofovir disoproxil fumarate (TDF) antiretroviral therapy on renal mitochondrial toxicity in Ghanaian people with HIV (PWH). Similar levels of renal biochemical and mitochondrial dysfunction were seen, and there was no increased risk in PWH who had sequenced from thymidine analogue to TDF. However, mild renal impairment was associated with mitochondrial DNA damage in TDF but not thymidine analogue-treated PWH. These data support the continued use of TDF in resource-limited settings.

Responsible agriculture must adapt to the wetland character of mid-latitude peatlands

Drained, lowland agricultural peatlands are greenhouse gas (GHG) emission hotspots and a large but vulnerable store of irrecoverable carbon. They exhibit soil loss rates of ~2.0 cm yr^-1 and are estimated to account for 32% of global cropland emissions while producing only 1.1% of crop kilocalories. Carbon dioxide emissions account for >80% of their terrestrial GHG emissions and are largely controlled by water table depth. Reducing drainage depths is, therefore, essential for responsible peatland management. Peatland restoration can substantially reduce emissions. However, this may conflict with societal needs to maintain productive use, to protect food security and livelihoods. Wetland agriculture strategies will, therefore, be required to adapt agriculture to the wetland character of peatlands, and balance GHG mitigation against productivity, where halting emissions is not immediately possible. Paludiculture may substantially reduce GHG emissions but will not always be viable in the current economic landscape. Reduced drainage intensity systems may deliver partial reductions in the rate of emissions, with smaller modifications to existing systems. These compromise systems may face fewer hurdles to adoption and minimize environmental harm until societal conditions favour strategies that can halt emissions. Wetland agriculture will face agronomic, socio-economic and water management challenges, and careful implementation will be required. Diversity of values and priorities among stakeholders creates the potential for conflict. Successful implementation will require participatory research approaches and co-creation of workable solutions. Policymakers, private sector funders and researchers have key roles to play but adoption risks would fall predominantly on land managers. Development of a robust wetland agriculture paradigm is essential to deliver resilient production systems and wider environmental benefits. The challenge of responsible use presents an opportunity to rethink peatland management and create thriving, innovative and green wetland landscapes for everyone's future benefit, while making a vital contribution to global climate change mitigation.

Nitrogen availability mediates the priming effect of soil organic matter by preferentially altering the straw carbon-assimilating microbial community

Straw incorporation into soil increases carbon (C) sequestration but can induce priming effects (PE), the enhanced breakdown of soil organic matter. The direction and magnitude of PE and the consequences for the C balance induced by straw addition depend on nitrogen (N) availability and soil management history. Using ¹³C-labeled maize straw, we conducted a 56-day incubation to determine the dynamics of PE and the underlying microbial mechanisms after straw and/or mineral N addition to three soils with contrasting cultivation and fertilization histories, i) unfertilized soil (Unfertilized), ii) 8 years farmyard manure amended soil (Manured), and iii) abandoned cropland soil (Abandoned). ¹³C-PLFAs (phospholipid fatty acids) were analyzed to identify microbial groups utilizing straw and to explore their contribution to the PE. Straw addition increased microbial biomass (MBC), activities of enzymes related to the C and N cycles, and changed microbial community composition. SOC decomposition was enhanced by microbes activated by straw addition, leading to a positive cumulative PE ranging from 494 to 789 μg C g^-1 soil. The magnitude of positive PE and straw decomposition in the manured soil was higher than that in the unfertilized and abandoned soils due to larger MBC and higher enzyme activities, resulting in a lower net SOC gain. Compared with straw only, the combination of straw addition with N fertilizer did not influence MBC, but increased positive PE (average increase of 18.1%) and straw decomposition (17.1%), further limiting SOC gain. ¹³C-labeled fungi: bacteria ratios and Gram-positive (G+): negative (G-) bacteria ratios increased with the increasing PE after N fertilization, but soil-derived (un-labeled) PLFAs remained stable. Random forest analysis further showed that straw C-assimilating microbial attributes are important predictors in driving the greater PE after N addition. Our study highlights the importance of straw C-assimilating fungi and G+ bacteria in mediating N-induced PE in arable soils.

Comparison of nitrogen losses from different manure treatment and application management systems in China

There is a worldwide focus on reducing the environmental impacts of livestock manure management. In China, there are different manure treatment and application modes, including complete treatment to remove nitrogen (N) for direct discharge into watercourses. But we lack a systematic quantitative comparison of the environmental losses that occur from different management modes. We used an example farm of 10,000 finisher pigs to quantitatively analyze the annual N losses from land application (LA) and treatment to remove N from manure to the level of discharge consent (DS) under 24 sub-modes. This is an important study to unravel the effect of choice of different manure management systems on subsequent N losses. The results showed that the N losses from the LA mode (52.6% of total N excretion) were significantly lower than that from the DS mode (75.9%). Compared with other sub-modes, N emission from whole slurry injection was the smallest, accounting for 43.2% of total N excretion. NH₃-N was the main source of N loss which accounted for 72.9% and 50.2% in LA and DS mode, respectively. The lowest N emission of LA mode with mitigation options, including slurry store covers, composting with bio-filter deodorization and injection application, was 28.8% of total N excretion, which is only 42.2% of N emission from DS mode with mitigation options. Insights from this systematic study of different manure management modes in China show the imperative of control ammonia emission for China, and provide guidance to the sustainable manure management in rapidly developing countries.

Uncertainties in direct N2O emissions from grazing ruminant excreta (EF3PRP) in national greenhouse gas inventories

Excreta deposition onto pasture, range and paddocks (PRP) by grazing ruminant constitute a source of nitrous oxide (N₂O), a potent greenhouse gas (GHG). These emissions must be reported in national GHG inventories, and their estimation is based on the application of an emission factor, EF_3PRP (proportion of nitrogen (N) deposited to the soil through ruminant excreta, which is emitted as N₂O)_. Depending on local data available, countries use various EF_3PRPs and approaches to estimate N₂O emissions from grazing ruminant excreta. Based on ten case study countries, this review aims to highlight the uncertainties around the methods used to account for these emissions in their national GHG inventories, and to discuss the efforts undertaken for considering factors of variation in the calculation of emissions. Without any local experimental data, 2006 the IPCC default (Tier 1) EF_3PRPs are still widely applied although the default values were revised in 2019. Some countries have developed country-specific (Tier 2) EF_3PRP based on local field studies. The accuracy of estimation can be improved through the disaggregation of EF_3PRP or the application of models; two approaches including factors of variation. While a disaggregation of EF_3PRP by excreta type is already well adopted, a disaggregation by other factors such as season of excreta deposition is more difficult to implement. Empirical models are a potential method of considering factors of variation in the establishment of EF_3PRP. Disaggregation and modelling requires availability of sufficient experimental and activity data, hence why only few countries have currently adopted such approaches. Replication of field studies under various conditions, combined with meta-analysis of experimental data, can help in the exploration of influencing factors, as long as appropriate metadata is recorded. Overall, despite standard IPCC methodologies for calculating GHG emissions, large uncertainties and differences between individual countries' accounting remain to be addressed.

Implied consent for HIV testing in the UK: time for a new approach?

Despite HIV infection being a treatable chronic illness and with many advances in testing for HIV, late diagnosis is still common with associated avoidable morbidity and mortality. Requirements for explicit consent for HIV testing are different to other blood tests and are major barriers to testing. We argue that the disparity is illogical and outdated. We propose a model for normalising HIV testing which allows routine testing in various healthcare settings via implied consent, where other blood tests are being performed. Inclusion of testing for hepatitis B and C might also be incorporated into this model. The ethical argument for this is principally beneficence towards those with undiagnosed infection and those they may infect. Patient autonomy would be maintained using systems allowing individuals to opt-out of implied consent.

Prior COVID-19 infection is associated with increased Adverse Events (AEs) after the first, but not the second, dose of the BNT162b2/Pfizer vaccine

The BNT162b2/Pfizer SARS-CoV-2 vaccine has been widely used in the UK, particularly amongst healthcare workers (HCWs). To establish whether previous COVID-19 influenced vaccine-associated Adverse Events (AEs), we conducted a survey-based study of HCWs in Northeast England. Out of 1238 HCWs, 32% self-reported prior positive PCR and/or antibody test for SARS-CoV-2. Post-dose AEs were worse in those with prior COVID-19 after the first, but not the second dose of vaccine. Second dose AEs were greater in frequency/severity, regardless of COVID-19 history, and they were more systemic in nature. Women and younger HCW were more likely to report AEs after both doses, while dosing interval had no effect on AEs. Ongoing Symptomatic COVID-19 was associated with greater frequency/severity of AEs after dose 2, but not dose one. Overall, AEs were self-limiting and short-lived (i.e.,<48 h) in nature. These findings have implications for vaccine hesitancy and informing guidelines for recommended dosing protocols.

Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine

BACKGROUND

Early clinical data from studies of the NVX-CoV2373 vaccine (Novavax), a recombinant nanoparticle vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that contains the full-length spike glycoprotein of the prototype strain plus Matrix-M adjuvant, showed that the vaccine was safe and associated with a robust immune response in healthy adult participants. Additional data were needed regarding the efficacy, immunogenicity, and safety of this vaccine in a larger population.

METHODS

In this phase 3, randomized, observer-blinded, placebo-controlled trial conducted at 33 sites in the United Kingdom, we assigned adults between the ages of 18 and 84 years in a 1:1 ratio to receive two intramuscular 5-μg doses of NVX-CoV2373 or placebo administered 21 days apart. The primary efficacy end point was virologically confirmed mild, moderate, or severe SARS-CoV-2 infection with an onset at least 7 days after the second injection in participants who were serologically negative at baseline.

RESULTS

A total of 15,187 participants underwent randomization, and 14,039 were included in the per-protocol efficacy population. Of the participants, 27.9% were 65 years of age or older, and 44.6% had coexisting illnesses. Infections were reported in 10 participants in the vaccine group and in 96 in the placebo group, with a symptom onset of at least 7 days after the second injection, for a vaccine efficacy of 89.7% (95% confidence interval [CI], 80.2 to 94.6). No hospitalizations or deaths were reported among the 10 cases in the vaccine group. Five cases of severe infection were reported, all of which were in the placebo group. A post hoc analysis showed an efficacy of 86.3% (95% CI, 71.3 to 93.5) against the B.1.1.7 (or alpha) variant and 96.4% (95% CI, 73.8 to 99.5) against non-B.1.1.7 variants. Reactogenicity was generally mild and transient. The incidence of serious adverse events was low and similar in the two groups.

CONCLUSIONS

A two-dose regimen of the NVX-CoV2373 vaccine administered to adult participants conferred 89.7% protection against SARS-CoV-2 infection and showed high efficacy against the B.1.1.7 variant. (Funded by Novavax; EudraCT number, 2020-004123-16.).

Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine

BACKGROUND

Early clinical data from studies of the NVX-CoV2373 vaccine (Novavax), a recombinant nanoparticle vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that contains the full-length spike glycoprotein of the prototype strain plus Matrix-M adjuvant, showed that the vaccine was safe and associated with a robust immune response in healthy adult participants. Additional data were needed regarding the efficacy, immunogenicity, and safety of this vaccine in a larger population.

METHODS

In this phase 3, randomized, observer-blinded, placebo-controlled trial conducted at 33 sites in the United Kingdom, we assigned adults between the ages of 18 and 84 years in a 1:1 ratio to receive two intramuscular 5-μg doses of NVX-CoV2373 or placebo administered 21 days apart. The primary efficacy end point was virologically confirmed mild, moderate, or severe SARS-CoV-2 infection with an onset at least 7 days after the second injection in participants who were serologically negative at baseline.

RESULTS

A total of 15,187 participants underwent randomization, and 14,039 were included in the per-protocol efficacy population. Of the participants, 27.9% were 65 years of age or older, and 44.6% had coexisting illnesses. Infections were reported in 10 participants in the vaccine group and in 96 in the placebo group, with a symptom onset of at least 7 days after the second injection, for a vaccine efficacy of 89.7% (95% confidence interval [CI], 80.2 to 94.6). No hospitalizations or deaths were reported among the 10 cases in the vaccine group. Five cases of severe infection were reported, all of which were in the placebo group. A post hoc analysis showed an efficacy of 86.3% (95% CI, 71.3 to 93.5) against the B.1.1.7 (or alpha) variant and 96.4% (95% CI, 73.8 to 99.5) against non-B.1.1.7 variants. Reactogenicity was generally mild and transient. The incidence of serious adverse events was low and similar in the two groups.

CONCLUSIONS

A two-dose regimen of the NVX-CoV2373 vaccine administered to adult participants conferred 89.7% protection against SARS-CoV-2 infection and showed high efficacy against the B.1.1.7 variant. (Funded by Novavax; EudraCT number, 2020-004123-16.).

COVID-19 mortality among people with diagnosed HIV compared to those without during the first wave of the COVID-19 pandemic in England

Objectives

We describe COVID‐19 mortality among people with and without HIV during the first wave of the pandemic in England.

Methods

National surveillance data on adults (aged ≥ 15 years) with diagnosed HIV resident in England were linked to national COVID‐19 mortality surveillance data (2 March 2020–16 June 2020); HIV clinicians verified linked cases and provided information on the circumstances of death. We present COVID‐19 mortality rates by HIV status, using negative binomial regression to assess the association between HIV and mortality, adjusting for gender, age and ethnicity.

Results

Overall, 99 people with HIV, including 61 of black ethnicity, died of/with COVID‐19 (107/100 000) compared with 49 483 people without HIV (109/100 000). Compared to people without HIV, higher COVID‐19 mortality rates were observed in people with HIV of black (188 vs. 122/100 000) and Asian (131 vs. 77.0/100 000) ethnicity, and in both younger (15–59 years: 58.3 vs. 10.2/100 000) and older (≥ 60 years: 434 vs. 355/100 000) people. After adjustment for demographic factors, people with HIV had a higher COVID‐19 mortality risk than those without (2.18; 95% CI: 1.76–2.70). Most people with HIV who died of/with COVID‐19 had suppressed HIV viraemia (91%) and at least one comorbidity reported to be associated with poor COVID‐19 outcomes (87%).

Conclusions

In the first wave of the pandemic in England, COVID‐19 mortality among people with HIV was low, but was higher than in those without HIV, after controlling for demographic factors. This supports the strategy of prioritizing COVID‐19 vaccination for people with HIV and strongly encouraging its uptake, especially in those of black and Asian ethnicity.

Optimising storage conditions and processing of sheep urine for nitrogen cycle and gaseous emission measurements from urine patches

In grazing systems, urine patches deposited by livestock are hotspots of nutrient cycling and the most important source of nitrous oxide (N2O) emissions. Studies of the effects of urine deposition, including, for example, the determination of country-specific N2O emission factors, require natural urine for use in experiments and face challenges obtaining urine of the same composition, but of differing concentrations. Yet, few studies have explored the importance of storage conditions and processing of ruminant urine for use in subsequent gaseous emission experiments. We conducted three experiments with sheep urine to determine optimal storage conditions and whether partial freeze-drying could be used to concentrate the urine, while maintaining the constituent profile and the subsequent urine-derived gaseous emission response once applied to soil. We concluded that filtering of urine prior to storage, and storage at - 20 °C best maintains the nitrogen-containing constituent profile of sheep urine samples. In addition, based on the 14 urine chemical components determined in this study, partial lyophilisation of sheep urine to a concentrate represents a suitable approach to maintain the constituent profile at a higher overall concentration and does not alter sheep urine-derived soil gaseous emissions.

Microbial diversity dynamics during the self-acidification of dairy slurry

Slurry acidification has been shown to be effective in reducing environmentally damaging gases. However, this involved the use of concentrated acids on farms. Therefore, due to the health and safety concerns, there is an interest in self-acidification of slurry technique. This study was designed to determine the microbial dynamics leading to self-acidification of slurry. A fresh cattle slurry was amended 10% brewing sugar and stored over 30 days. This fermentable carbon source promoted self-acidification of the slurry from pH 7.0 to 4.7 within four days, and was associated with the accumulation of lactic acid and a reduction in methane and relative ammonia emissions. A metagenomics approach through next generation sequencing (NGS) using an Illumina MiSeq platform was used to determine the microbial diversity and dynamics (bacteria and archaea) in the stored amended slurry. 16S ribosomal ribonucleic acid (rRNA) sequence data revealed the presence of the Order of Lactobacillales was associated with the lactic acid production. The operational taxonomic units (OTUs) abundance indicates that the methanogenic community was dominated by hydrogenotrophic methanogens from the member Order of Methanobacteriales, Methanomicrobiales, and Methanosarcinales. The decrease in tolerance by the methanogens in the self-acidified slurry was probably the main reason for the reduced methane emission. These results confirm, at the microbial level, the mechanism of inhibiting methane production via self-acidification during storage period.

Evaluating a pilot process for reviewing late HIV diagnoses in England and Wales

Late HIV diagnosis is associated with significant mortality in people living with HIV (PLWH) and high numbers of missed opportunities (MO) for earlier testing have been identified. A pilot of a national late diagnosis review process (LDRP) was undertaken in 15 HIV services evaluating the feasibility of LDRP implementation, as a patient safety initiative. All newly diagnosed PLWH with CD4 counts <200 cells/mm³ were included, and healthcare episodes within 5 years of presentation reviewed. Of 127 patients identified, 40 (31.5%) had MO and were more often white, UK-born and suffered more serious harm around diagnosis. Of these, four were designated serious incidents (undergoing root cause analysis) and eight were serious learning events. Engagement with services where MO occurred was challenging, however 75% of services found the LDRP sustainable. Widespread implementation of the LDRP should enable progress with training and policy changes within external services, enabling earlier HIV diagnosis and preventing deaths.

Precipitation-optimised targeting of nitrogen fertilisers in a model maize cropping system

Typically, half of the nitrogen (N) fertiliser applied to agricultural fields is lost to the wider environment. This inefficiency is driven by soil processes such as denitrification, volatilisation, surface run-off and leaching. Rainfall plays an important role in regulating these processes, ultimately governing when and where N fertiliser moves in soil and its susceptibility to gaseous loss. The interaction between rainfall, plant N uptake and N losses, however, remains poorly understood. In this study we use numerical modelling to predict the optimal N fertilisation strategy with respect to rainfall patterns and offer mechanistic explanations to the resultant differences in optimal times of fertiliser application. We developed a modelling framework that describes water and N transport in soil over a growing season and assesses nitrogen use efficiency (NUE) of split fertilisations within the context of different rainfall patterns. We used ninety rainfall patterns to determine their impact on optimal N fertilisation times. We considered the effects of root growth, root N uptake, microbial transformation of N and the effect of soil water saturation and flow on N movement in the soil profile. On average, we show that weather-optimised fertilisation strategies could improve crop N uptake by 20% compared to the mean uptake. In drier years, weather-optimising N applications improved the efficiency of crop N recovery by 35%. Further analysis shows that maximum plant N uptake is greatest under drier conditions due to reduced leaching, but it is harder to find the maximum due to low N mobility. The model could capture contrasting trends in NUE seen in previous arable cropping field trials. Furthermore, the model predicted that the variability in NUE seen in the field could be associated with precipitation-driven differences in N leaching and mobility. In conclusion, our results show that NUE in cropping systems could be significantly enhanced by synchronising fertiliser timings with both crop N demand and local weather patterns.

A national audit of the management pathways for new HIV diagnoses

The British HIV Association recommends that new diagnoses be reviewed by an HIV specialist within two weeks. NHS England outcome measures include the proportion of new diagnoses commencing antiretroviral therapy (ART) within 91 days. We aimed to review the extent to which these recommendations were followed, to explore the topics discussed with new diagnoses, and to identify reasons behind delayed ART initiation. UK specialist HIV services were invited to retrospectively review the notes of their last 40 new diagnoses over a 15-month period. One-hundred and thirty-two services provided data for 2281 eligible individuals. Most new diagnoses were reviewed by a specialist within two weeks (67.7%) and were commenced on ART within 91 days (83%), however, there were some concerning delays in those tested at home and in general practice. Partner notification and treatment benefits were discussed with most individuals, unlike the availability of community support and U = U ("undetectable equals untransmittable"). Lengthy delays in ART initiation were mostly due to individuals initially declining ART or missing appointments. Our findings suggest a need for more streamlined pathways into HIV care, review of new diagnoses who have not commenced ART within 8 weeks, and protocol development to ensure discussion of relevant topics.

Presentation and outcome of COVID-19 in HIV patients with high viral loads and opportunistic infections: a case series

Coronavirus disease 2019 (COVID-19) is especially severe in patients with underlying chronic conditions, with increased risk of mortality. There is concern that people living with HIV (PLWH), especially those with severe immunosuppression, and COVID-19 may have severe disease and a negative clinical outcome. Most studies on COVID-19 in PLWH are from Asia, Europe and America where population dynamics, antiretroviral treatment coverage and coexisting opportunistic infections may differ from that in sub-Saharan Africa. We report on the clinical profile and outcome of three cases of PLWH co-infected with SARS-CoV-2. They all presented with fever, cough and breathlessness and also had advanced HIV infection as evidenced by opportunistic infections, high HIV viral loads and low CD4 counts. The patients responded favourably to the standard of care and were discharged home. Our findings suggest that PLWH with advanced immunosuppression may not necessarily have an unfavourable disease course and outcome. However, case-controlled studies with a larger population size are needed to better understand the impact of COVID-19 in this patient population.

FUNDING

Not declared.

Spatial co-localisation of extreme weather events: a clear and present danger

Extreme weather events have become a dominant feature of the narrative surrounding changes in global climate with large impacts on ecosystem stability, functioning and resilience; however, understanding of their risk of co-occurrence at the regional scale is lacking. Based on the UK Met Office's long-term temperature and rainfall records, we present the first evidence demonstrating significant increases in the magnitude, direction of change and spatial co-localisation of extreme weather events since 1961. Combining this new understanding with land-use data sets allowed us to assess the likely consequences on future agricultural production and conservation priority areas. All land-uses are impacted by the increasing risk of at least one extreme event and conservation areas were identified as the hotspots of risk for the co-occurrence of multiple event types. Our findings provide a basis to regionally guide land-use optimisation, land management practices and regulatory actions preserving ecosystem services against multiple climate threats.

Global Research Alliance N2 O chamber methodology guidelines: Introduction, with health and safety considerations

Non-steady-state (NSS) chamber techniques have been used for decades to measure nitrous oxide (N₂ O) fluxes from agricultural soils. These techniques are widely used because they are relatively inexpensive, easy to adopt, versatile, and adaptable to varying conditions. Much of our current understanding of the drivers of N₂ O emissions is based on studies using NSS chambers. These chamber techniques require decisions regarding multiple methodological aspects (e.g., chamber materials and geometry, deployment, sample analysis, and data and statistical analysis), each of which may significantly affect the results. Variation in methodological details can lead to challenges in comparing results between studies and assessment of reliability and uncertainty. Therefore, the New Zealand Government, in support of the objectives of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases (GRA), funded two international projects to, first, develop standardized guidelines on the use of NSS chamber techniques and, second, refine them based on the most up to date knowledge and methods. This introductory paper summarizes a collection of papers that represent the revised guidelines. Each article summarizes existing knowledge and provides guidance and minimum requirements on chamber design, deployment, sample collection, storage and analysis, automated chambers, flux calculations, statistical analysis, emission factor estimation and data reporting, modeling, and "gap-filling" approaches. The minimum requirements are not meant to be highly prescriptive but instead provide researchers with clear direction on best practices and factors that need to be considered. Health and safety considerations of NSS chamber techniques are also provided with this introductory paper.

Global Research Alliance N2 O chamber methodology guidelines: Recommendations for deployment and accounting for sources of variability

Adequately estimating soil nitrous oxide (N₂ O) emissions using static chambers is challenging due to the high spatial variability and episodic nature of these fluxes. We discuss how to design experiments using static chambers to better account for this variability and reduce the uncertainty of N₂ O emission estimates. This paper is part of a series, each discussing different facets of N₂ O chamber methodology. Aspects of experimental design and sampling affected by spatial variability include site selection and chamber layout, size, and areal coverage. Where used, treatment application adds a further level of spatial variability. Time of day, frequency, and duration of sampling (both individual chamber closure and overall experiment duration) affect the temporal variability captured. We also present best practice recommendations for chamber installation and sampling protocols to reduce further uncertainty. To obtain the best N₂ O emission estimates, resources should be allocated to minimize the overall uncertainty in line with experiment objectives. Sometimes this will mean prioritizing individual flux measurements and increasing their accuracy and precision by, for example, collecting four or more headspace samples during each chamber closure. However, where N₂ O fluxes are exceptionally spatially variable (e.g., in heterogeneous agricultural landscapes, such as uneven and woody grazed pastures), using available resources to deploy more chambers with fewer headspace samples per chamber may be beneficial. Similarly, for particularly episodic N₂ O fluxes, generated for example by irrigation or freeze-thaw cycles, increasing chamber sampling frequency will improve the accuracy and reduce the uncertainty of temporally interpolated N₂ O fluxes.

Image-based quantification of soil microbial dead zones induced by nitrogen fertilization

Microbial communities in agricultural soils underpin many ecosystem services including the maintenance of soil structure, food production, water purification and carbon storage. However, the impact of fertilization on the health of microbial communities is not well understood. This study investigates the spatial and temporal dynamics of nitrogen (N) transport away from a fertilizer granule with pore scale resolution. Specifically, we examined how soil structure and moisture content influence fertilizer derived N movement through the soil pore network and the subsequent impact of on soil microbial communities. We develop a mathematical model to describe N transport and reactions in soil at the pore-scale. Using X-ray Computed Tomography scans, we reconstructed a microscale description of a soil-pore geometry as a computational mesh. Solving two-phase water/air model produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The N-speciation model considered ammonium (NH₄⁺), nitrate (NO₃^-) and dissolved organic N (DON), and included N immobilization, ammonification and nitrification processes, as well as diffusion in soil solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at three different water saturations. To aid interpretation of the model results, microbial activity at a range of N concentrations was measured. The model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predict that the maximum NH₄⁺ and NO₃^- concentrations in soil solution around the pellet under dry conditions are in the order of 1 × 10³ and 1 × 10⁴ mol m^-3 respectively, and under wet conditions 2 × 10² and 1 × 10³ mol m^-3, respectively. Supporting experimental evidence suggests that these concentrations would be sufficient to reduce microbial activity in the short-term in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm), causing a major loss of soil biological functioning. This model demonstrates the importance of pore-scale processes in regulating N movement and their interactions with the soil microbiome.

Impact of water table levels and winter cover crops on greenhouse gas emissions from cultivated peat soils

Drainage and cultivation have turned peatlands from carbon (C) sinks into hotspots for greenhouse gas (GHG) emissions. Raising the water table and planting of winter cover crops are potential strategies to help reduce peat oxidation and re-initiate net C accumulation during the non-cropping period. However, the effects of these practices as well as their interactions on GHG emissions remain unclear. Here, we carried out an outdoor mesocosm experiment to elucidate the effect of water table levels (-30 cm and -50 cm) and winter cover crop cultivation (vetch, rye, no plant) on carbon dioxide (CO₂), nitrous oxide (N₂O) and methane (CH₄) fluxes during the winter period (November-April). Soil-atmosphere GHG exchange, GHG concentrations within the peat profile and soil water solute concentrations were monitored. Our results showed that high water table significantly reduced ecosystem respiration, while it had no net effect on N₂O and CH₄ fluxes. Uptake of available N by the cover crop significantly reduced nitrate in soil solution, thereby lowering the potential for leaching and both direct and indirect N₂O emissions. No interactive effects between water table levels and cover crops were detected for any of the measured GHG fluxes. Seasonal variations of GHG fluxes were positively correlated with soil air concentrations at -15 cm and -40 cm depths, which were further regulated by dissolved organic C, nitrate concentration, and anaerobic conditions in the soil. This study suggests that there is great potential to raise water table levels and introduce green cover crops to reduce GHG emissions. Further studies are needed to achieve a complete evaluation of these strategies outside of the growing season, which may provide a significant mitigation benefit in C-rich cultivated peatlands.

Adherence to guidelines across different specialties to prevent infections in patients undergoing immunosuppressive therapies

BACKGROUND

Substantial numbers of patients are now receiving either immunosuppressive therapies or chemotherapy. There are significant risks in such patients of developing opportunistic infections or re-activation of latent infections, with higher associated morbidity and mortality. The aim of this quality improvement project was to determine how effective 5 different specialties were in assessing and mitigating risks of developing opportunistic infections or re-activation of latent infections in patients undergoing immunosuppressive therapies.

METHODS

This was a single centre audit where records of patients attending clinics providing immunosuppressive therapies were reviewed for the following: evidence of screening for blood-borne virus [BBV] infections, varicella and measles immunity, latent/active TB or hypogammaglobulinaemia, and whether appropriate vaccines had been advised or various infection risks discussed. These assessments were audited against both national and international guidelines, or a cross-specialty consensus guideline where specific recommendations were lacking. Two sub-populations were also analysed separately: patients receiving more potent immunosuppression and black and minority ethnic [BME] patients,.

RESULTS

For the 204 patients fulfilling the inclusion criteria, BBV, varicella/measles and latent TB screening was inconsistent, as was advice for vaccinations, with few areas complying with specialty or consensus guidelines. Less than 10% of patients in one specialty were tested for HIV. In BME patients screening for HIV [60%], measles [0%] and varicella [40%] immunity and latent [30%] or active [20%] TB was low. Only 38% of patients receiving potent immunosuppression received Pneumocystis prophylaxis, with 3 of 4 specialties providing less than 15% of patients in this category with prophylaxis.

CONCLUSIONS

Compliance with guidelines to mitigate risks of infection from immunosuppressive therapies was either inconsistent or poor for most specialties. New approaches to highlight such risks and assist appropriate pre-immunosuppression screening are needed.

Meta-analysis of global livestock urine-derived nitrous oxide emissions from agricultural soils

Nitrous oxide (N2 O) is an air pollutant of major environmental concern, with agriculture representing 60% of anthropogenic global N2 O emissions. Much of the N2 O emissions from livestock production systems result from transformation of N deposited to soil within animal excreta. There exists a substantial body of literature on urine patch N2 O dynamics, we aimed to identify key controlling factors influencing N2 O emissions and to aid understanding of knowledge gaps to improve GHG reporting and prioritize future research. We conducted an extensive literature review and random effect meta-analysis (using REML) of results to identify key relationships between multiple potential independent factors and global N2 O emissions factors (EFs) from urine patches. Mean air temperature, soil pH and ruminant animal species (sheep or cow) were significant factors influencing the EFs reviewed. However, several factors that are known to influence N2 O emissions, such as animal diet and urine composition, could not be considered due to the lack of reported data. The review highlighted a widespread tendency for inadequate metadata and uncertainty reporting in the published studies, as well as the limited geographical extent of investigations, which are more often conducted in temperate regions thus far. Therefore, here we give recommendations for factors that are likely to affect the EFs and should be included in all future studies, these include the following: soil pH and texture; experimental set-up; direct measurement of soil moisture and temperature during the study period; amount and composition of urine applied; animal type and diet; N2 O emissions with a measure of uncertainty; data from a control with zero-N application and meteorological data.

Late HIV diagnosis and missed opportunities for testing: piloting a standardised, multi-source review process

Late diagnosis of human immunodeficiency virus (HIV) (CD4 < 350) remains common in the UK and missed opportunities (MOs) for testing are often evident. National guidelines recommend HIV clinics conduct look-back reviews in all patients presenting late; however, a standardised methodology is not available and reviews are not routinely performed. This multi-centre audit reviewed all new, late HIV diagnoses across three centres in North East England. A standardised review process (incorporating a shared regional pathology system and summary care records) was used to identify MOs. Of 45 late diagnoses reviewed (median age 45 years, 76% male, median CD4 cell count 134), 28 (62%) had one or more MO, with a median of 18 months from MO to presentation. Sixty-two per cent of MOs occurred in primary care and most (82%) consisted of indicator conditions. At HIV presentation, 27 (60%) suffered moderate harm, 16 (36%) presented with acquired immune deficiency syndrome (AIDS) and 10 (22%) suffered severe harm, including 3 (7%) who died. Despite challenges in eliciting full medical records, the comprehensive review process described, which incorporates two regional electronic records, was more effective than previous methodologies and identified more MOs. Many people present with late HIV infection or AIDS and increased efforts are needed to improve testing.

Nitrification represents the bottle-neck of sheep urine patch N2O emissions from extensively grazed organic soils

Extensively grazed grasslands are understudied in terms of their contribution to greenhouse gas (GHG) emissions from livestock production. Mountains, moorlands and heath occupy 18% of the UK land area, however, in situ studies providing high frequency N₂O emissions from sheep urine deposited to such areas are lacking. Organic soils typical of these regions may provide substrates for denitrification-related N₂O emissions, however, acidic and anoxic conditions may inhibit nitrification (and associated emissions from nitrification and denitrification). We hypothesised urine N₂O-N emission factors (EFs) would be lower than the UK country-specific and IPCC default value for urine, which is based on lowland measurements. Using automated GHG sampling chambers, N₂O emissions were determined from real sheep urine (930 kg N ha^-1) and artificial urine (920 kg N ha^-1) applied in summer, and from an artificial urine treatment (1120 kg N ha^-1) and a combined NO₃^- and glucose treatment (106 kg N ha^-1; 213 kg C ha^-1) in autumn. The latter treatment provided an assessment of the soils capacity for denitrification under non-substrate limiting conditions. The artificial urine-N₂O EF was 0.01 ± 0.00% of the N applied in summer and 0.00 ± 0.00% of the N applied in autumn. The N₂O EF for real sheep urine applied in summer was 0.01 ± 0.02%. A higher flux was observed in only one replicate of the real urine treatment, relating to one chamber where an increase in soil solution NO₃^- was observed. No lag phase in N₂O emission was evident following application of the NO₃^- and glucose treatment, which emitted 0.69 ± 0.15% of the N applied. This indicates nitrification rates are the bottle-neck for N₂O emissions in upland organic soils. We calculated the potential impact of using hill-grazing specific urine N₂O EFs on the UK inventory of N₂O emissions from sheep excreta, and found a reduction of ca. 43% in comparison to the use of a country-specific excretal EF.