Dual anti-viral treatment for persistent COVID-19 in immunocompromised hemato-oncological patients is associated with a favorable prognosis and minor side effects

In hemato-oncological patients, COVID-19 can present as a persistent infection with ongoing symptoms and viral replication over a prolonged period of time. Data are scarce on the preferred treatment options for these patients. We describe our experience with a five-day course of dual anti-viral treatment with remdesivir and nirmatrelvir/ritonavir for hemato-oncological immunocompromised patients with persistent COVID-19. Fifteen patients with a history of lymphoma, CLL, and MM were included. Eight were male, median age was 74. All patients had an immediate clinical and virological response. In 73 % of patients, PCR for SARS-CoV-2 became negative at the end of treatment and the rest had an increase in PCR cycle threshold (CT) values, with a median increase of 6 cycles. After a follow-up of three months, 60 % of patients remained in full clinical and virological remission. None required invasive mechanical ventilation or died. The side effects we observed, neutropenia, lactatemia and elevated transaminases, were mild and almost all transient in nature. We conclude that dual anti-viral treatment appears to be a valid treatment option for persistent COVID-19.

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections

The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised individuals, but limited data from these cases hinders comprehensive analyses. Here, we harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings. The probability of observing high-fitness RBD mutations was 10-20 times higher in chronic infections than in global transmission chains. The majority of RBD mutations in BA.1/BA.2 chronic-like clades bore predictive value, i.e., went on to display global success. Finally, we used our LM to infer hundreds of additional chronic-like clades in the absence of metadata. Our approach allows mining extensive sequencing data and providing insights into future evolutionary patterns of SARS-CoV-2.

Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation

RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may lead to widely divergent estimates of viral mutation rates, as well as difficulties in inferring the fitness effects of mutations. Here, we develop, test, and apply an approach aimed at inferring the mutation rate and key parameters that govern natural selection, from haplotype sequences covering full-length genomes of an evolving virus population. Our approach employs neural posterior estimation, a computational technique that applies simulation-based inference with neural networks to jointly infer multiple model parameters. We first tested our approach on synthetic data simulated using different mutation rates and selection parameters while accounting for sequencing errors. Reassuringly, the inferred parameter estimates were accurate and unbiased. We then applied our approach to haplotype sequencing data from a serial passaging experiment with the MS2 bacteriophage, a virus that parasites Escherichia coli. We estimated that the mutation rate of this phage is around 0.2 mutations per genome per replication cycle (95% highest density interval: 0.051-0.56). We validated this finding with two different approaches based on single-locus models that gave similar estimates but with much broader posterior distributions. Furthermore, we found evidence for reciprocal sign epistasis between four strongly beneficial mutations that all reside in an RNA stem loop that controls the expression of the viral lysis protein, responsible for lysing host cells and viral egress. We surmise that there is a fine balance between over- and underexpression of lysis that leads to this pattern of epistasis. To recap, we have developed an approach for joint inference of the mutation rate and selection parameters from full haplotype data with sequencing errors and used it to reveal features governing MS2 evolution.

Trans* people’s access to gender-affirming health care: A European comparison

Background

Trans* people's life satisfaction is correlated with established legal frameworks for gender recognition and access to trans*-specific health care (Transgender Europe [TGEU], 2021). TGEU's guidelines to human rights-based principles of trans*-specific health care highlight bodily integrity/autonomy, free self-determination of gender, quality, specialized and decentralized care, and the right to determine reproductive paths as important pillars of gender affirming health care. We conducted a policy comparison across Europe regarding access to gender-affirming health care to assess how adherence to human rights-based principles could be strengthened.

Methods

We compared access to health care across four main domains: legal framework (e.g., legally recognised genders), insurance coverage (e.g., out of pocket costs), access barriers (e.g., legal requirements to access gender-affirming surgery), and health care offers (e.g., hormone replacement therapy). Criteria were developed in guided brainstorming sessions. Three researchers rated 28 countries across 28 items based on available policy documents.

Results

The majority of European countries prescribes a medicalised gender-affirming process rather than a self-decided process. Psychiatric diagnosis is also required in most countries to access gender-affirming health care. Gender-affirming health care is partly financed by statutory health insurance in most of the countries. Not all countries authorise full gender-affirming health care. Especially where statutory health insurance-covered gender-affirming health care relied centralised on single outpatient clinics or hospitals, waiting times between 6-24 months are found.

Conclusions

Many European countries fail to fully comply with TGEU's guidelines to human rights-based principles of trans* health care. Given the negative impact of access barriers on life satisfaction, European countries should target these shortfalls in ensuring gender-affirming health care.

Key messages

• Non- or only partly covered trans* health care contributes to health inequality.

• Regarding trans* people, European countries need to strengthen human-rights based access to gender-affirming health care.

Drivers of adaptive evolution during chronic SARS-CoV-2 infections

In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence.

Analysis of mutations that arise in chronic SARS-CoV-2 infections shows both overlap and differences with mutations present in pandemic viral variants of concern, highlighting their distinct drivers of evolution.

CellTrackVis: analyzing the performance of cell tracking algorithms

Live-cell imaging is a common data acquisition technique used by biologists to analyze cell behavior. Since manually tracking cells in a video sequence is extremely time-consuming, many automatic algorithms have been developed in the last twenty years to accomplish the task. However, none of these algorithms can yet claim robust tracking performance at the varying of acquisition conditions (e.g., cell type, acquisition device, cell treatments). While many visualization tools exist to help with cell behavior analysis, there are no tools to help with the algorithm's validation. This paper proposes CellTrackVis, a new visualization tool for evaluating cell tracking algorithms. CellTrackVis allows comparing automatically generated cell tracks with ground truth data to help biologists select the best-suited algorithm for their experimented pipeline. Moreover, CellTackVis can be used as a debugging tool while developing a new cell tracking algorithm to investigate where, when, and why each tracking error occurred.

Inoculation route-dependent Lassa virus dissemination and shedding dynamics in the natural reservoir - Mastomys natalensis

Lassa virus (LASV), a Risk Group-4 zoonotic haemorrhagic fever virus, affects sub-Saharan African countries. Lassa fever, caused by LASV, results in thousands of annual deaths. Although decades have elapsed since the identification of the Natal multimammate mouse (Mastomys natalensis) as a natural reservoir of LASV, little effort has been made to characterize LASV infection in its reservoir. The natural route of infection and transmission of LASV within M. natalensis remains unknown, and the clinical impact of LASV in M. natalensis is mostly undescribed. Herein, using an outbred colony of M. natalensis, we investigate the replication and dissemination dynamics of LASV in this reservoir following various inoculation routes. Inoculation with LASV, regardless of route, resulted in a systemic infection and accumulation of abundant LASV-RNA in many tissues. LASV infection in the Natal multimammate mice was subclinical, however, clinical chemistry values were transiently altered and immune infiltrates were observed histologically in lungs, spleens and livers, indicating a minor disease with coordinated immune responses are elicited, controlling infection. Intranasal infection resulted in unique virus tissue dissemination dynamics and heightened LASV shedding, compared to subcutaneous inoculation. Our study provides important insights into LASV infection in its natural reservoir using a contemporary infection system, demonstrating that specific inoculation routes result in disparate dissemination outcomes, suggesting intranasal inoculation is important in the maintenance of LASV in the natural reservoir, and emphasizes that selection of the appropriate inoculation route is necessary to examine aspects of viral replication, transmission and responses to zoonotic viruses in their natural reservoirs.

Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component, and there is accumulating evidence that whole-genome sequencing of the virus may provide more objective insight.

METHODS

We report a large nosocomial outbreak in 1 of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that 1 of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole-genome sequencing of the virus of 14 infected individuals involved in the outbreak.

RESULTS

Surprisingly, the results of whole-genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, 1 of which led to a cluster of 10 of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the 1 that arose from our initial investigation.

CONCLUSIONS

These results underscore the important added value of using whole-genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals

The BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vaccine sera in laboratory assays. We performed a matched cohort study to examine the distribution of VOCs in infections of BNT162b2 mRNA vaccinees from Clalit Health Services (Israel) using viral genomic sequencing, and hypothesized that if vaccine effectiveness against a VOC is reduced, its proportion among breakthrough cases would be higher than in unvaccinated controls. Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.

In-vivo engineering of B cells elicits memory retention and allows for secretion of broadly neutralizing antibodies in mice

A potential single-shot HIV therapy may be transplanted engineered B cells allowing strong secretion of broadly neutralizing antibodies (bNAbs). However, extensive, and expensive ex-vivo manipulations performed in specialized facilities hinders clinical potential of this approach. Furthermore, allogeneic B cell therapy necessitates MHC-II compatibility to receive mandatory T-cell help.

To overcome these limitations, we engineer B cells in-vivo. In particular, we demonstrate that a single, systemic dose of dual AAV, one coding for CRISPR/Cas9 and another coding for a bNAb donor cassette, allows for site specific integration in B cells. Following immunizations, we show memory retention and bNAb secretion at high titers. Antibodies secreted by the engineered B cells were found to be of multiple isotypes and IgGs could neutralize autologous and heterologous pseudoviruses. We found engineered B cell subsets in the spleen and blood. We detected homing of in-vivo engineered cells to germinal centers and bone marrow. Biodistribution of the donor AAV over time and as compared to a CRISPR- group, indicated expansion of engineered B cells in lymphatic tissues. We determined minimal CRISPR/Cas9 off-target cleavage, using unbiased, highly sensitive, CHANGE-Seq analysis. Finally, we diminished on-target, non-productive double-strand breaks at undesired tissues by expressing Cas9 from a B cell specific promoter.

Eliciting a specific, neutralizing serological response to hypervariable viruses is a long-standing challenge in medicine. B cell engineering provides an opportunity to express therapeutic antibodies to generate an adaptive and evolving immunity.

Biased Mutation and Selection in RNA Viruses

RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based data set spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases toward U rather than A in genomes of all viruses. In +ssRNA viruses, we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses, the genomic mutational bias toward U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.

Globally defining the effects of mutations in a picornavirus capsid

The capsids of non-enveloped viruses are highly multimeric and multifunctional protein assemblies that play key roles in viral biology and pathogenesis. Despite their importance, a comprehensive understanding of how mutations affect viral fitness across different structural and functional attributes of the capsid is lacking. To address this limitation, we globally define the effects of mutations across the capsid of a human picornavirus. Using this resource, we identify structural and sequence determinants that accurately predict mutational fitness effects, refine evolutionary analyses, and define the sequence specificity of key capsid-encoded motifs. Furthermore, capitalizing on the derived sequence requirements for capsid-encoded protease cleavage sites, we implement a bioinformatic approach for identifying novel host proteins targeted by viral proteases. Our findings represent the most comprehensive investigation of mutational fitness effects in a picornavirus capsid to date and illuminate important aspects of viral biology, evolution, and host interactions.

A virus is made up of genetic material that is encased with a protective protein coat called the capsid. The capsid also helps the virus to infect host cells by binding to the host receptor proteins and releasing its genetic material. Inside the cell, the virus hitchhikes the infected cell’s machinery to grow or replicate its own genetic material.

Viral capsids are the main target of the host’s defence system, and therefore, continuously change in an attempt to escape the immune system by introducing alterations (known as mutations) into the genes encoding viral capsid proteins. Mutations occur randomly, and so while some changes to the viral capsid might confer an advantage, others may have no effect at all, or even weaken the virus.

To better understand the effect of capsid mutations on the virus’ ability to infect host cells, Mattenberger et al. studied the Coxsackievirus B3, which is linked to heart problems and acute heart failure in humans. The researchers analysed around 90% of possible amino acid mutations (over 14,800 mutations) and correlated each mutation to how it influenced the virus’ ability to replicate in human cells grown in the laboratory.

Based on these results, Mattenberger et al. developed a computer model to predict how a particular mutation might affect the virus. The analysis also identified specific amino acid sequences of capsid proteins that are essential for certain tasks, such as building the capsid. It also included an analysis of sequences in the capsid that allow it to be recognized by another viral protein, which cuts the capsid proteins into the right size from a larger precursor. By looking for similar sequences in human genes, the researchers identified several ones that the virus may attack and inactivate to support its own replication.

These findings may help identify potential drug targets to develop new antiviral therapies. For example, proteins of the capsid that are less likely to mutate will provide a better target as they lower the possibility of the virus to become resistant to the treatment. They also highlight new proteins in human cells that could potentially block the virus in cells.

A Bayesian Framework for Inferring the Influence of Sequence Context on Point Mutations

The probability of point mutations is expected to be highly influenced by the flanking nucleotides that surround them, known as the sequence context. This phenomenon may be mainly attributed to the enzyme that modifies or mutates the genetic material, because most enzymes tend to have specific sequence contexts that dictate their activity. Here, we develop a statistical model that allows for the detection and evaluation of the effects of different sequence contexts on mutation rates from deep population sequencing data. This task is computationally challenging, as the complexity of the model increases exponentially as the context size increases. We established our novel Bayesian method based on sparse model selection methods, with the leading assumption that the number of actual sequence contexts that directly influence mutation rates is minuscule compared with the number of possible sequence contexts. We show that our method is highly accurate on simulated data using pentanucleotide contexts, even when accounting for noisy data. We next analyze empirical population sequencing data from polioviruses and HIV-1 and detect a significant enrichment in sequence contexts associated with deamination by the cellular deaminases ADAR 1/2 and APOBEC3G, respectively. In the current era, where next-generation sequencing data are highly abundant, our approach can be used on any population sequencing data to reveal context-dependent base alterations and may assist in the discovery of novel mutable sites or editing sites.

Drivers of within-host genetic diversity in acute infections of viruses

Genetic diversity is the fuel of evolution and facilitates adaptation to novel environments. However, our understanding of what drives differences in the genetic diversity during the early stages of viral infection is somewhat limited. Here, we use ultra-deep sequencing to interrogate 43 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV. Hundreds to thousands of virus templates were sequenced per sample, allowing us to reveal dramatic differences in within-host genetic diversity among virus populations. We found that increased diversity was mostly driven by presence of multiple divergent genotypes in HIV and CMV samples, which we suggest reflect multiple transmitted/founder viruses. Conversely, we detected an abundance of low frequency hyper-edited genomes in RSV samples, presumably reflecting defective virus genomes (DVGs). We suggest that RSV is characterized by higher levels of cellular co-infection, which allow for complementation and hence elevated levels of DVGs.

The few days or weeks following infection with a virus, termed acute infection, are critical for virus establishment. Here we sought to characterize what leads to differences in the genetic diversity of different viruses sampled during acute infection. We performed ultra-deep sequencing of hundreds to thousands viral genomes from forty-three samples spanning three pathogenic human viruses: HIV, RSV and CMV. We found major differences in the genetic diversity of these different viruses, and in different patients infected with the same virus. We investigated the factors responsible for these differences. We found that the DNA virus CMV was less diverse, most likely since it has a lower mutation rate than the RNA viruses HIV and RSV. We also found that the samples with the highest genetic diversity, which included one CMV sample and two HIV samples, bore evidence for multiple genotype infection. In other words, patients from whom these samples were taken were infected with two different “strains” of the virus. Finally, we also found evidence that viral genomes of HIV, and in particular RSV, are edited by the innate immune system of the host, leading to the presence of defective virus genomes.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Associations between ADHD and emotional problems from childhood to young adulthood: a longitudinal genetically sensitive study

BACKGROUND

Attention deficit/hyperactivity disorder (ADHD) is associated with emotional problems, and their co-occurrence often leads to worse outcomes. We investigated the developmental associations between ADHD and emotional problems from childhood to early adolescence and examined the genetic and environmental contributions to their developmental link. We further tested whether this developmental association remained across the transition to young adulthood.

METHODS

We used data from the Environmental Risk (E-Risk) Longitudinal Twin Study, a cohort of 2,232 British twins. In childhood, ADHD and emotional problems were assessed at ages 5, 7, 10 and 12 with mothers' and teachers' reports. At age 18, we used self-reported symptoms according to DSM-5 criteria for ADHD, and DSM-IV for anxiety and depression.

RESULTS

Longitudinal analyses showed that earlier ADHD was associated with later emotional problems consistently across childhood. However, earlier emotional problems were not associated with later ADHD symptoms. The developmental association between ADHD and later emotional problems in childhood was entirely explained by common genetic factors. Consistent with results in childhood, earlier symptoms of ADHD were associated with later emotional problems during the transition to young adulthood.

CONCLUSIONS

Our findings demonstrate that ADHD symptoms are predictors of the development of emotional problems, from childhood up to young adulthood, through shared genetic influences. Interventions targeting ADHD symptoms might prevent the development of emotional problems. Clinicians treating youth with ADHD must be aware of their risk for developing emotional problems and ought to assess, monitor and treat emotional problems alongside ADHD symptoms from childhood to adulthood.

Similarities and intersections – A comprehensive view in three studies

Background

Various groups face difficulties in access to, and usage of health care. Research on marginalization in health care, and programs aiming to reduce inequalities usually focus on one single group at a time. Regarding the heterogeneity of groups defined by a few social characteristics, our aim was to question the specificity of barriers, and similarities between different groups.

Methods

The results of a mixed methods study focusing on elderly people with Turkish migration background were compared to the interim results of a qualitative study focusing on transgender persons, and the interim results of a qualitative study focusing persons with trauma related psychiatric diagnoses.

Results

1) While relevant barriers in access to, and usage of health care seem to be group-specific at the first view, their underlying mechanisms of emergence are analogous. 2) Beside more obvious similarities, 3) further barriers arise by the combination of more than the mainly addressed characteristics of the different groups.

Conclusions

Barriers analogous or similar among different groups lead to underlying structural or professionality-related issues. If different dimensions of marginalization intersect, they may be disguised by a concentration on single characteristics. To target health inequalities on the long term, a closer look on similarities between groups facing health inequalities could improve the development of programs for a broader range of persons.

Key messages

The comparison of different marginalized groups is useful to identify and target systematic inequalities in health care. Researchers and stakeholders should consider mechanisms of multiple marginalization.

Competition between social cheater viruses is driven by mechanistically different cheating strategies

Cheater viruses, also known as defective interfering viruses, cannot replicate on their own yet replicate faster than the wild type upon coinfection. While there is growing interest in using cheaters as antiviral therapeutics, the mechanisms underlying cheating have been rarely explored. During experimental evolution of MS2 phage, we observed the parallel emergence of two independent cheater mutants. The first, a point deletion mutant, lacked polymerase activity but was advantageous in viral packaging. The second synonymous mutant cheater displayed a completely different cheating mechanism, involving an altered RNA structure. Continued evolution revealed the demise of the deletion cheater and rise of the synonymous cheater. A mathematical model inferred that while a single cheater is expected to reach an equilibrium with the wild type, cheater demise arises from antagonistic interactions between coinfecting cheaters. These findings highlight layers of parasitism: viruses parasitizing cells, cheaters parasitizing intact viruses, and cheaters may parasitize other cheaters.

Determination of Bronopol, Bronidox, and Methyldibromo Glutaronitrile in Cosmetics by Liquid Chromatography with Electrochemical Detection

A method for the simultaneous determination of methyldibromo glutaronitrile, bronopol, and broni-dox in cosmetics, based on liquid chromatography with electrochemical detection, is described. The method is suitable for both aqueous products and emulsions. The detection limit is better than 0.002% for all analytes. Recoveries from an emulsion, spiked to concentrations of 0.03% of the analytes, were 100.4% for bronopol [relative standard deviation (RSD), 0.43%], 97.1% for bronidox (RSD, 0.83%), and 98.4% for methyldibromo glutaronitrile (RSD, 1.7%). Repeatabilities were calculated from 10 replicate analyses of commercial samples. The repeatability for bronopol from an emulsion containing 0.047% bronopol was 0.0027% (RSD, 1.99%); for bronidox from a lotion containing 0.027% bronidox, 0.0014% (RSD, 1.86%); and for methyldibromo glutaronitrile from an emulsion containing 0.031% methyldibromo glutaronitrile, 0.0019% (RSD, 2.16%). A ruggedness test showed that sample amount influenced the results for all 3 analytes. The results obtained for bronidox also depended on detection parameters and composition of extraction solvent. The method was applied to 138 cosmetic products and performed trouble free during these analyses. Bronopol was found in 14 samples, and bronidox was found in 4 samples, including a baby hair lotion, in which it is prohibited. Methyldibromo glutaronitrile was present in 27 samples, including creams, lotions, and sun protection cosmetics.

Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations

One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, rendering the detection of true variants difficult. Here, we propose a new statistical approach named AssociVar, which differentiates between true mutations and sequencing errors from direct RNA/DNA sequencing using MinION. Our strategy relies on the assumption that sequencing errors will be dispersed randomly along sequencing reads, and hence will not be associated with each other, whereas real mutations will display a non-random pattern of association with other mutations. We demonstrate our approach using direct RNA sequencing data from evolved populations of the MS2 bacteriophage, whose small genome makes it ideal for MinION sequencing. AssociVar inferred several mutations in the phage genome, which were corroborated using parallel Illumina sequencing. This allowed us to reconstruct full genome viral haplotypes constituting different strains that were present in the sample. Our approach is applicable to long read sequencing data from any organism for accurate detection of bona fide mutations and inter-strain polymorphisms.

Quantitative Determination of Paralytic Shellfish Poisoning Toxins in Shellfish Using Prechromatographic Oxidation and Liquid Chromatography with Fluorescence Detection: Collaborative Study

A collaborative study was conducted for the determination of paralytic shellfish poisoning (PSP) toxins in shellfish. The method used liquid chromatography with fluorescence detection after prechromatographic oxidation of the toxins with hydrogen peroxide and periodate. The PSP toxins studied were saxitoxin (STX), neosaxitoxin (NEO), gonyautoxins 2 and 3 (GTX2,3; together), gonyautoxins 1 and 4 (GTX1,4; together), decarbamoyl saxitoxin (dcSTX), B-1 (GTX5), C-1 and C-2 (C1,2; together), and C-3 and C-4 (C3,4; together). B-2 (GTX6) toxin was also included, but for qualitative identification only. Mussels, both blank and naturally contaminated, were mixed and homogenized to provide a variety of PSP toxin mixtures and concentration levels. The same procedure was followed with clams, oysters, and scallops. Twenty-one test samples in total were sent to 21 collaborators who agreed to participate in the study. Results were obtained from 18 laboratories representing 14 different countries. It is recommended that the method be adopted First Action by AOAC INTERNATIONAL.

Transnational medication management by elderly migrants – a mixed-methods approach

Background

Many elderly people of Turkish origin choose a transnational lifestyle and commute between Germany and Turkey every few months. These circular migrants often suffer from chronic diseases. The transnational lifestyle can lead to discontinuities in long-term medication and irregular check-ups. If continuity of care is not ensured transnationally, health risks arise.

Methods

In a mixed-methods study 8 expert-interviews with general practitioners and 25 guideline interviews were conducted with circular migrants to analyze their medication adherence. Additional quantitative analyses were conducted based on data from a German statutory health insurance popular with migrants to investigate discontinuities of prescribed medication.

Results

Cross-border care involves different health risks with regard to medication adherence. For example, patients in Germany rarely receive the amount of medication they need for their stay in Turkey and there are discontinuities in medication delivery. The multi-perspective insight into the patients’ experiences of medical care and the view of general practitioners shows strong variations of preferred strategies to handle the challenges of transnational medication management. Single strategies, such as leaving the health insurance card in one state for prescription and sending of medication through family members or asking for higher amounts of medication to store before travel, lead to frustration both at GPs’ and patients’ sides. GPs experience high pressure by the health system’s structure in providing good care for the patients, especially in providing enough time for information transfer between GPs and patients.

Conclusions

Transnational solutions for health care, and in particular medication care, such as an interprofessional collaborative care across borders or transnational e-health records need to be developed.

Key messages

A transnational lifestyle can lead to discontinuities in the provision of medication. Transnational, inter-professional cooperation is needed to ensure continuity of health care for circular migrants.

The influence of culturalisation on GP consultations and in research on GP care

Background

General practitioners (GPs) have a gatekeeping function in the healthcare system. Research shows that patients of Turkish origin in Germany manage to access specialist care less often than non-immigrant patients. Underlying could be problems related to interactions with the GP. Focusing on interaction instead of individual patients’ characteristics might help identifying underappreciated barriers in health care.

Methods

We conducted a scoping review to identify research on interaction-related aspects of GP consultations of people of Turkish origin. Goffman’s interactional theory was used for operationalisation. Analysis focused on the process of consultation from the perspectives of patients, GPs, and interpreters. Additionally, noticeable issues in researchers’ perspectives on migrants’ utilization of health care were identified.

Results

Patients of Turkish origin expect similar professional performances from their GPs as patients without a migration background. If informal interpreters take part, misinformation might remain unrecognised. Frequently, GPs experience insecurity, which sometimes results in lower empathy and prejudice-based, unprofessional reactions or misdiagnoses. Researchers’ interpretations refer partly to unfounded explanations such as a homogeneous Turkish culture or somatization tendencies of Turkish patients.

Conclusions

Difficulties in GP care of patients of Turkish origin, and access barriers to specialist care, arise less from culture-bound performances of these patients as from culturalising expectations and performances of GPs. Researchers often show similar expectations and interpretations. Such culturalising interpretations should be avoided in future research.

Key messages

Difficulties in GP care of patients of Turkish origin, and access barriers to specialist care, arise less from culture-bound performances of these patients as from culturalising expectations of GPs. Future research should avoid culturalising interpretations.

Inferring population genetics parameters of evolving viruses using time-series data

With the advent of deep sequencing techniques, it is now possible to track the evolution of viruses with ever-increasing detail. Here, we present Flexible Inference from Time-Series (FITS)-a computational tool that allows inference of one of three parameters: the fitness of a specific mutation, the mutation rate or the population size from genomic time-series sequencing data. FITS was designed first and foremost for analysis of either short-term Evolve & Resequence (E&R) experiments or rapidly recombining populations of viruses. We thoroughly explore the performance of FITS on simulated data and highlight its ability to infer the fitness/mutation rate/population size. We further show that FITS can infer meaningful information even when the input parameters are inexact. In particular, FITS is able to successfully categorize a mutation as advantageous or deleterious. We next apply FITS to empirical data from an E&R experiment on poliovirus where parameters were determined experimentally and demonstrate high accuracy in inference.

Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

[This corrects the article DOI: 10.1371/journal.pgen.1007420.].

Associations between abuse/neglect and ADHD from childhood to young adulthood: A prospective nationally-representative twin study

Child maltreatment has consistently been found to be associated with attention deficit/hyperactivity disorder (ADHD). However, the robustness of this association and the direction of the link between maltreatment and ADHD remain unclear. We used data from the Environmental Risk (E-Risk) Longitudinal Twin Study, a cohort of 2232 British twins, to investigate the associations between exposure to abuse/neglect and ADHD in childhood and in young adulthood, and to test their robustness and specificity. We also aimed to test longitudinal associations between abuse/neglect and ADHD from childhood to young adulthood, controlling for confounders. Results indicated strong associations between abuse/neglect and ADHD in childhood and also in young adulthood. In childhood, the association was concentrated among children with comorbid conduct disorder. Longitudinal analyses showed that childhood ADHD predicted abuse/neglect in later years. This association was again concentrated among individuals with comorbid conduct disorder. Abuse/neglect in childhood was not associated with later ADHD in young adulthood after adjusting for childhood ADHD. Our study does not provide support of a causal link between child abuse/neglect and adult ADHD but highlights the possibility of a long-term effect of disruptive behaviors on the risk for experiencing abuse/neglect. These findings emphasize the need for clinicians treating people with ADHD, especially those with comorbid conduct disorder, to be aware of their increased risk for experiencing abuse/neglect. Interventions aimed at reducing risks of abuse/neglect should also focus on the environment of individuals with disruptive behaviors.

Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

HIV has a high mutation rate, which contributes to its ability to evolve quickly. However, we know little about the fitness costs of individual HIV mutations in vivo, their distribution and the different factors shaping the viral fitness landscape. We calculated the mean frequency of transition mutations at 870 sites of the pol gene in 160 patients, allowing us to determine the cost of these mutations. As expected, we found high costs for non-synonymous and nonsense mutations as compared to synonymous mutations. In addition, we found that non-synonymous mutations that lead to drastic amino acid changes are twice as costly as those that do not and mutations that create new CpG dinucleotides are also twice as costly as those that do not. We also found that G→A and C→T mutations are more costly than A→G mutations. We anticipate that our new in vivo frequency-based approach will provide insights into the fitness landscape and evolvability of not only HIV, but a variety of microbes.

Surface-dominated conduction up to 240 K in the Kondo insulator SmB6 under strain

SmB₆ is a strongly correlated mixed-valence Kondo insulator with a newly discovered surface state, proposed to be of non-trivial topological origin. However, the surface state dominates electrical conduction only below T^∗ ≈ 4 K (ref. ), limiting its scientific investigation and device application. Here, we report the enhancement of T^∗ in SmB₆ under the application of tensile strain. With 0.7% tensile strain we report surface-dominated conduction at up to a temperature of 240 K, persisting even after the strain has been removed. This can be explained in the framework of strain-tuned temporal and spatial fluctuations of f-electron configurations, which might be generally applied to other mixed-valence materials. We note that this amount of strain can be induced in epitaxial SmB₆ films via substrate in potential device applications.

The Evolutionary Pathway to Virulence of an RNA Virus

Paralytic polio once afflicted almost half a million children each year. The attenuated oral polio vaccine (OPV) has enabled world-wide vaccination efforts, which resulted in nearly complete control of the disease. However, poliovirus eradication is hampered globally by epidemics of vaccine-derived polio. Here, we describe a combined theoretical and experimental strategy that describes the molecular events leading from OPV to virulent strains. We discover that similar evolutionary events occur in most epidemics. The mutations and the evolutionary trajectories driving these epidemics are replicated using a simple cell-based experimental setup where the rate of evolution is intentionally accelerated. Furthermore, mutations accumulating during epidemics increase the replication fitness of the virus in cell culture and increase virulence in an animal model. Our study uncovers the evolutionary strategies by which vaccine strains become pathogenic and provides a powerful framework for rational design of safer vaccine strains and for forecasting virulence of viruses. VIDEO ABSTRACT.

The Relationship Between Executive Functions and Quality of Life in Adults With ADHD

OBJECTIVE

Adult ADHD is associated with impaired quality of life (QoL) and deficient executive function (EF). Given the absence of studies examining the relationship between EF and health-related quality of life (HRQL) in this population, the purpose of the present study was to do so, by the use of rating scales and tests.

METHOD

Adults with ADHD ( n = 81) completed ADHD and EF questionnaires and a neuropsychological battery.

RESULTS

Small to large significant correlations were found between EF ratings and HRQL for most of the variables. No significant correlations were found between all but one EF test and HRQL. Both ADHD symptoms and EF rating, but not the EF test, were found to have a unique contribution to the HRQL.

CONCLUSION

These results strengthen the ecological validity of the EF rating scales and their utility in identifying EF deficits with real-world implications for adults with ADHD.