Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum

Falciparum malaria is clinically heterogeneous and the relative contribution of parasite and host in shaping disease severity remains unclear. We explored the interaction between inflammation and parasite variant surface antigen (VSA) expression, asking whether this relationship underpins the variation observed in controlled human malaria infection (CHMI). We uncovered marked heterogeneity in the host response to blood challenge; some volunteers remained quiescent, others triggered interferon-stimulated inflammation and some showed transcriptional evidence of myeloid cell suppression. Significantly, only inflammatory volunteers experienced hallmark symptoms of malaria. When we tracked temporal changes in parasite VSA expression to ask whether variants associated with severe disease rapidly expand in naive hosts, we found no transcriptional evidence to support this hypothesis. These data indicate that parasite variants that dominate severe malaria do not have an intrinsic growth or survival advantage; instead, they presumably rely upon infection-induced changes in their within-host environment for selection.

The appropriateness of a proton pump inhibitor prescription

Proton pump inhibitors (PPIs) are one of the most commonly prescribed groups of drug in Ireland, at great expense to the Irish healthcare executive. This study aims to evaluate the appropriateness of PPI prescriptions on admission and discharge in a tertiary referral hospital. All non-elective admissions in the Emergency Department in one week were included in the study. 102 patients in total were included, with 36 (35.4%) treated with a PPI on admission. Of these, only 3 (8.3%) had a clear indication noted as per current NICE guidelines. 18 new in-hospital PPI prescriptions were documented. 11 (61%) of which were present on discharge prescriptions. Continuing PPI prescription on discharge into the community may be inappropriate, costly and potentially harmful. Brief interventions aimed at reducing inappropriate PPI prescriptions have been shown to be effective at reducing the cost and potential harm of unnecessary treatment.

Tumour microenvironment of both early- and late-stage colorectal cancer is equally immunosuppressive

BACKGROUND

Tumour microenvironment (TME) of advanced colorectal cancer (CRC) suppresses dendritic cell (DC) maturation. Here, our aim was to determine how the microenvironment of early-stage tumours influences DCs.

METHODS

Tumour-conditioned media (TCM) was generated by culturing explant tumour tissue in vitro (n=50). Monocyte-derived DCs (MDDCs) of healthy donors or cancer patients were pretreated with TCM and stimulated with lipopolysaccharide (LPS). DC maturation was assessed by flow cytometry and cytokine production measured by ELISA.

RESULTS

TCM from both early- and late-staged tumours abrogated LPS-induction of IL-12p70 secretion, while increasing IL-10. The profile of inflammatory mediators in TCM was similar across stages, and all increased pSTAT3 expression by DCs.CRC patient DCs (n=31) secreted low levels of IL-12p70 and failed to upregulate expression of maturation markers in response to LPS. Furthermore, in vitro culture of autologous DCs with TCM did not change the hypo-responsiveness of patient DCs.

CONCLUSION

Our data demonstrates that the TME of all stages of CRC contains inflammatory mediators capable of suppressing local DCs. MDDCs obtained from CRC patients are hyporesponsive to stimuli such as LPS. Measures to reverse the negative influence of the TME on DCs will optimise cancer vaccines in both early- and late-stage CRC.

Design and initial characterization of a compact, ultra high vacuum compatible, low frequency, tilt accelerometer

A compact tilt accelerometer with high sensitivity at low frequency was designed to provide low frequency corrections for the feedback signal of the Advanced Laser Interferometer Gravitational Wave Observatory active seismic attenuation system. It has been developed using a Tungsten Carbide ceramic knife-edge hinge designed to avoid the mechanical 1/f noise believed to be intrinsic in polycrystalline metallic flexures. Design and construction details are presented; prototype data acquisition and control limitations are discussed. The instrument's characterization reported here shows that the hinge is compatible with being metal-hysteresis-free, and therefore also free of the 1/f noise generated by the dislocation Self-Organized Criticality in the metal. A tiltmeter of this kind will be effective to separate the ground tilt component from the signal of horizontal low frequency seismometers, and to correct the ill effects of microseismic tilt in advanced seismic attenuation systems.

A high precision, compact electromechanical ground rotation sensor

We present a mechanical rotation sensor consisting of a balance pivoting on a tungsten carbide knife edge. These sensors are important for precision seismic isolation systems, as employed in land-based gravitational wave interferometers and for the new field of rotational seismology. The position sensor used is an air-core linear variable differential transformer with a demonstrated noise floor of 1 × 10⁻¹¹ m/√Hz. We describe the instrument construction and demonstrate low noise operation with a noise floor upper bound of 5.7 × 10⁻⁹ rad/√Hz at 10 mHz and 6.4 × 10⁻¹⁰ rad/√Hz at 0.1 Hz. The performance of the knife edge hinge is compatible with a behaviorur free of noise from dislocation self-organized criticality.

Review article: the psychosexual impact of inflammatory bowel disease in male patients

BACKGROUND

Knowledge of the extent and the impact of sexual dysfunction and interpersonal relationships in men with inflammatory bowel disease is scarce.

AIMS

The aim of this review article was to summarise the current literature on sexual function in male patients with IBD and to provide a critical review of the IBD-related medical, surgical and psychological complications that can result in impaired quality of sexual health.

METHODS

To collect relevant articles, PubMed/Medline and Embase searches were performed using Boolean search phrases.

RESULTS

Reported rates of sexual dysfunction in male IBD patients range from 10% to 50%. Thirty-three to fifty per cent of patients report that sexual desire and satisfaction deteriorated after IBD diagnosis. Of those patients who were sexually inactive, half of these attributed lack of intercourse to underlying IBD. A striking finding reproduced in numerous studies is that disease activity relates strongly to impaired psychological function, and the most consistently reported risk factor for sexual problems in IBD patients is co-existing mood disorders. Hypogonadism is a complication of IBD and its therapies, the role of testosterone deficiency should be further explored as a potentially treatable and reversible factor in sexual dysfunction.

CONCLUSIONS

By understanding what factors contribute to poor sexual functioning in our patients, we can strive to minimise adverse psychosocial events. Further insight into this complex relationship requires an IBD-specific measure of sexual function in male patients. We recommend screening for and treating co-morbid depression, testosterone deficiency and striving for clinical remission to prevent psychosexual dysfunction in male patients with inflammatory bowel disease.

A national house-staff audit of medical prophylaxis in medical patients for the PREVENTion of Venous ThromboEmbolism (PREVENT-VTE)

We established a national audit to assess the thromboprophylaxis rate for venous thromoembolism (VTE) in at risk medical patients in acute hospitals in the Republic of Ireland and to determine whether the use of stickers to alert physicians regarding thromboprophylaxis would double the rate prophylaxis in a follow-up audit. 651 acute medical admission patients in the first audit and 524 in the second re-audit were recruited. The mean age was 66.5 yrs with similar numbers of male and female patients and 265 (22.6%) patients were active smokers. The first and second audits identified 549 (84%) and 487 (93%) of patients at-risk for VTE respectively. Of the at-risk patients, 163 (29.7%) and 132 (27.1%) received LMWH in the first and second audit respectively. Mechanical thromboprophylaxis was instigated in 75 (13.6%) patients in the first and 86 (17.7%) patients in the second audit. The placement of stickers in patient charts didn't produce a significant increase in the number of at risk patients treated in the second audit. There is unacceptably low adherence to the ACCP guidelines in Ireland and more complex intervention than chart reminders are required to improve compliance.

Characterization, stability, and plant effects of kiln-produced wheat straw biochar

Biochar is a promising technology for improving soil quality and sequestering C in the long term. Although modern pyrolysis technologies are being developed, kiln technologies often remain the most accessible method for biochar production. The objective of the present study was to assess biochar characteristics, stability in soil, and agronomic effects of a kiln-produced biochar. Wheat-straw biochar was produced in a double-barrel kiln and analyzed by solid-state C nuclear magneticresonance spectroscopy. Two experiments were conducted with biochar mixed into an Ap-horizon sandy loam. In the first experiment, CO efflux was monitored for 3 mo in plant-free soil columns across four treatments (0, 10, 50, and 100 Mg biochar ha). In the second experiment, ryegrass was grown in pots having received 17 and 54 Mg biochar ha combined with four N rates from 144 to 288 kg N ha. Our kiln method generated a wheat-straw biochar with carbon content composed of 92% of aromatic structures. Our results suggest that the biochar lost <0.16% C as CO over the 90-d incubation period. Biomass yields were not significantly modified by biochar treatments, except for a slight decrease at the 144 kg N ha rate. Foliar N concentrations were significantly reduced by biochar application. Biochar significantly increased soil water content; however, this increase did not result in increased biomass yield. In conclusion, our kiln-produced biochar was highly aromatic and appeared quite recalcitrant in soil but had no overall significant impact on ryegrass yields.

Particulate matter concentrations in residences: an intervention study evaluating stand-alone filters and air conditioners

This study, a randomized controlled trial, evaluated the effectiveness of free-standing air filters and window air conditioners (ACs) in 126 low-income households of children with asthma. Households were randomized into a control group, a group receiving a free-standing HEPA filter placed in the child's sleeping area, and a group receiving the filter and a window-mounted AC. Indoor air quality (IAQ) was monitored for week-long periods over three to four seasons. High concentrations of particulate matter (PM) and carbon dioxide were frequently seen. When IAQ was monitored, filters reduced PM levels in the child's bedroom by an average of 50%. Filter use varied greatly among households and declined over time, for example, during weeks when pollutants were monitored, filter use was initially high, averaging 84±27%, but dropped to 63±33% in subsequent seasons. In months when households were not visited, use averaged only 34±30%. Filter effectiveness did not vary in homes with central or room ACs. The study shows that measurements over multiple seasons are needed to characterize air quality and filter performance. The effectiveness of interventions using free-standing air filters depends on occupant behavior, and strategies to ensure filter use should be an integral part of interventions.

PRACTICAL IMPLICATIONS

Environmental tobacco smoke (ETS) increased particulate matter (PM) levels by about 14 μg/m3 and was often detected using ETS-specific tracers despite restrictions on smoking in the house as reported on questionnaires administered to caregivers. PM concentrations depended on season, filter usage, relative humidity, air exchange ratios, number of children, outdoor PM levels, sweeping/dusting, and presence of a central air conditioner (AC). Free-standing air filters can be an effective intervention that provides substantial reductions in PM concentrations if the filters are used. However, filter use was variable across the study population and declined over the study duration, and thus strategies are needed to encourage and maintain use of filters. The variability in filter use suggests that exposure misclassification is a potential problem in intervention studies using filters. The installation of a room AC in the bedroom, intended to limit air exchange ratios, along with an air filter, did not lower PM levels more than the filter alone.

Blackawton bees

BACKGROUND

Real science has the potential to not only amaze, but also transform the way one thinks of the world and oneself. This is because the process of science is little different from the deeply resonant, natural processes of play. Play enables humans (and other mammals) to discover (and create) relationships and patterns. When one adds rules to play, a game is created.

THIS IS SCIENCE

the process of playing with rules that enables one to reveal previously unseen patterns of relationships that extend our collective understanding of nature and human nature. When thought of in this way, science education becomes a more enlightened and intuitive process of asking questions and devising games to address those questions. But, because the outcome of all game-playing is unpredictable, supporting this 'messyness', which is the engine of science, is critical to good science education (and indeed creative education generally). Indeed, we have learned that doing 'real' science in public spaces can stimulate tremendous interest in children and adults in understanding the processes by which we make sense of the world. The present study (on the vision of bumble-bees) goes even further, since it was not only performed outside my laboratory (in a Norman church in the southwest of England), but the 'games' were themselves devised in collaboration with 25 8- to 10-year-old children. They asked the questions, hypothesized the answers, designed the games (in other words, the experiments) to test these hypotheses and analysed the data. They also drew the figures (in coloured pencil) and wrote the paper. Their headteacher (Dave Strudwick) and I devised the educational programme (we call 'i,scientist'), and I trained the bees and transcribed the childrens' words into text (which was done with smaller groups of children at the school's local village pub). So what follows is a novel study (scientifically and conceptually) in 'kids speak' without references to past literature, which is a challenge. Although the historical context of any study is of course important, including references in this instance would be disingenuous for two reasons. First, given the way scientific data are naturally reported, the relevant information is simply inaccessible to the literate ability of 8- to 10-year-old children, and second, the true motivation for any scientific study (at least one of integrity) is one's own curiousity, which for the children was not inspired by the scientific literature, but their own observations of the world. This lack of historical, scientific context does not diminish the resulting data, scientific methodology or merit of the discovery for the scientific and 'non-scientific' audience. On the contrary, it reveals science in its truest (most naive) form, and in this way makes explicit the commonality between science, art and indeed all creative activities.

PRINCIPAL FINDING

'We discovered that bumble-bees can use a combination of colour and spatial relationships in deciding which colour of flower to forage from. We also discovered that science is cool and fun because you get to do stuff that no one has ever done before. (Children from Blackawton)'.

Mitochondria and cell death

Mitochondria play a central role in both apoptosis and necrosis through the opening of the mitochondrial permeability transition pore (MPTP). This is thought to be formed through a Ca(2+)-triggered conformational change of the adenine nucleotide translocase (ANT) bound to matrix cyclophilin-D and we have now demonstrated this directly by reconstitution of the pure components. Opening of the MPTP causes swelling and uncoupling of mitochondria which, unrestrained, leads to necrosis. In ischaemia/reperfusion injury of the heart we have shown MPTP opening directly. Recovery of hearts correlates with subsequent closure, and agents that prevent opening or enhance closure protect from injury. Transient MPTP opening may also be involved in apoptosis by initially causing swelling and rupture of the outer membrane to release cytochrome c (cyt c), which then activates the caspase cascade and sets apoptosis in motion. Subsequent MPTP closure allows ATP levels to be maintained, ensuring that cell death remains apoptotic rather than necrotic. Apoptosis in the hippocampus that occurs after a hypoglycaemic or ischaemic insult is triggered by this means. Other apoptotic stimuli such as cytokines or removal of growth factors also involve mitochondrial cyt c release, but here there is controversy over whether the MPTP is involved. In many cases cyt c release is seen without any mitochondrial depolarization, suggesting that the MPTP does not open. Recent data of our own and others have revealed a specific outer-membrane cyt c-release pathway involving porin that does not release other intermembrane proteins such as adenylate kinase. This is opened by pro-apoptotic members of the Bcl-2 family such as BAX and prevented by anti-apoptotic members such as Bcl-X(L). Our own data suggest that this pathway may interact directly with the ANT in the inner membrane at contact sites.

THF gamma 2 stimulates cytokine release by peripheral blood mononuclear cells of patients with chronic hepatitis B virus infection

A recent study indicated that thymic hormones have antiviral effects in human hepatitis B virus infection and woodchuck hepatitis virus infection. These hormones are known to exert immunomodulatory effects on lymphocyte maturation and function; because these are abnormal in patients with chronic hepatitis B virus infection, we have examined the effects of a thymic hormone (THF gamma 2) on peripheral blood mononuclear cells from patients with chronic hepatitis B virus infection. THF gamma 2 (50 or 150 ng/ml) alone was without effect; in the presence of low doses of the mitogen phytohaemagglutinin, it had a broad effect in patients and controls. The effect on interleukin-2 production was greater in patients than controls with a significant increase in production at 150 ng/ml for patients alone (p = 0.037). Tumour necrosis factor alpha production was enhanced in all patients and controls, with a greater effect seen at 150 ng/ml THF gamma 2 than 50 ng/ml. There was no effect on interferon gamma production or on the expression of membrane markers of T-cell activation. THF gamma 2 has substantial immunomodulatory activity in chronic hepatitis B virus carriers and in vivo assessment of THF gamma 2 in chronic hepatitis B virus is indicated.