Whole-genome sequencing (WGS) and whole-transcriptome sequencing (WTS), with the ability to provide comprehensive genomic information, have become the focal point of research interest as novel techniques that can support precision diagnostics in routine clinical care of patients with various cancer types, including hematological malignancies. This national multi-center study, led by Genomic Medicine Sweden, aims to evaluate whether combined application of WGS and WTS (WGTS) is technically feasible and can be implemented as an efficient diagnostic tool in patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). In addition to clinical impact assessment, a health-economic evaluation of such strategy will be performed.The study comprises four phases  including approximately 700 adult and pediatric Swedish AML and ALL patients. Results of WGS for tumor (90×) and normal/germline (30×) samples as well as WTS for tumors only will be compared to current standard of care diagnostics. Primary study endpoints are diagnostic efficiency and improved diagnostic yield. Secondary endpoints are technical and clinical feasibility for routine implementation, clinical utility, and health-economic impact.Data from this national multi-center study will be used to evaluate clinical performance of the integrated WGTS diagnostic workflow compared with standard of care. The study will also elucidate clinical and health-economic impacts of a combined WGTS strategy when implemented in routine clinical care.https://doi.org/10.1186/ISRCTN66987142], identifier [ISRCTN66987142].[ Although these methods provide clinically relevant information for individual patients, their detection/diagnostic capacities are hindered by low resolution, limited genomic coverage, and/or inability to identify novel genetic alterations, as well as the time and cost associated with performing multiple tests of the same sample. These challenges could potentially be overcome by using whole-genome sequencing (WGS), which covers the entire genome and thereby is capable of providing the most unbiased and comprehensive genetic information  and acute myeloid leukemias (AML) are associated with clinically relevant SNVs, CNAs, and SVs including gene fusions . Since iThe potential of a multi-modal sequencing approach as a clinical test was first evaluated in pediatric patients with various types of hematological malignancies and solid tumors at St. Jude Children’s Research Hospital . This stThe aim of this national multi-center study performed by Genomic Medicine Sweden (GMS), in close collaboration with the Clinical Genomics Platform at Science for Life Laboratory (SciLifeLab), is to evaluate whether application of WGS and WTS combined, collectively termed WGTS, is technically feasible and can be implemented as an efficient clinical tool with a high diagnostic accuracy in patients with ALL and AML. Specifically, the combined workflow of WGTS will be compared with current SoC methodologies to identify potential benefits and challenges of WGTS implementation in a routine diagnostic setting. This study will also address whether WGTS will improve the diagnostic yield and patient management as well as if these assays combined are cost-effective. The ultimate goal of this study is to evaluate if WGTS can replace current diagnostic SoC methods of patients with ALL and AML across Sweden. This manuscript outlines the conceptual and experimental designs for the study.The study is led by the Hematology Working Group within GMS. The study comprises 4 phases and includes a total of approximately 700 Swedish AML and ALL patients . The retThe prospective phase encompasses WGTS of prospectively collected samples from approximately 350 adult and pediatric ALL and AML patients . WGS wilThe real-time validation phase comprises WGTS of prospectively collected samples from approximately 100 ALL and AML patients, as described for the prospective phase . The aimDuring the follow-up phase, patient outcome data will be recorded for those included in the prospective and real-time validation phases. At least 2 years of follow-up after the last included patient will be required for meaningful health-economic analysis.Primary and secondary endpoints are listed in Diagnostic efficiency is based on(1)the percentage of patients for whom WGS detects (or excludes) all mandatory and highly recommended variants identified by cytogenetics, FISH, genomic arrays, NGS panels and/or multiplex ligation-dependent probe amplification (retrospective and prospective phases);(2)the percentage of patients for whom WTS detects all mandatory and highly recommended variants identified by RT-PCR or FISH (prospective phase); and(3)the percentage of patients for whom combined WGTS detects all mandatory and highly recommended variants identified by SoC diagnostics (prospective phase).In the real-time validation phase, percentages for WGS and WGTS will be recorded separately for tumor-only analysis (after 2–3 weeks) and tumor-normal analysis .Improved diagnostic yield is determined by the percentage of acute leukemia patients for whom genetic variants relevant for classification or risk stratification are identified by WGTS but not by SoC methods (prospective phase). This includes inconclusive cases by SoC and genetic variants that were missed by SoC technologies but also those that were not actively screened for with SoC. In the real-time validation phase, improved diagnostic yield will be recorded separately for tumor-only and tumor-normal analysis.Technical feasibility is assessed by the percentage of patients for whom WGTS analysis and interpretation are successfully completed without a strict time limit (prospective phase). Here we will also measure the percentage of samples where SoC tests or WGTS analysis were uninformative for mandatory and highly recommended variants.PML:RARA, FLT3-ITD).Clinical feasibility is tested during the real-time validation phase and refers to the percentage of patients for whom WGTS analysis is successfully reported within the required time frame for genetic diagnosis of acute leukemias . Of note, this does not include targeted molecular tests that need to be performed in AML within the first days after diagnosis to decide on targeted therapy  are/potentially could be changed based on variants detected by WGTS, but not SoC diagnostics. Specifically, the percentage of patients for whom WGTS findings lead to targeted treatment options and/or a change in treatment options not identified by SoC will be recorded. This information will be retrieved from registries and retrospective analysis of medical records .The health-economic evaluation consists of two analytic parts:(1)A micro-costing analysis which is performed to estimate and compare the average cost of SoC and WGTS.(2)Analysis of cost-effectiveness of WGTS (defined further below) in comparison with SoC will be estimated using economic simulation modeling.The seven Swedish sites  belonging to the Clinical Genomics Platform at SciLifeLab and corresponding Genomic Medicine Centers (GMCs) will participate in the study. While patients with acute leukemia will be recruited at all sites, sample processing, sequencing, and data analysis will be performed centrally at select locations .The retrospective cohort includes samples from 150 AML patients and 100 ALL patients for whom WGS has already been performed. For the prospective and real-time validation phases, the aim is to include a total of 450 consecutive adult and pediatric patients with a confirmed diagnosis of ALL or AML from any of the participating sites. This number corresponds approximately to the number of patients diagnosed with acute leukemias on average in Sweden within one year. The study will end after 15-18 months (depending on the patient recruitment rate) when the sample size has reached 450. The estimate of sample size at each site, based on the average number of patients diagnosed per year, is shown in All patients diagnosed with acute leukemia and analyzed with genetic SoC methods will be offered inclusion. Patients will be included if the patient/guardians provide informed written consent and as long as sufficient tumor material is available for SoC tests and WGS.A bone marrow sample will be used for chromosome banding and FISH analyses. From the same sample, DNA and RNA will be extracted using standard procedures at each participating site. In the event of limited material from a bone marrow sample, peripheral blood may be used. The expected tumor purity in bone marrow as well as peripheral blood samples is >80–90%. WGTS of leukemic samples will be performed using surplus DNA and RNA that remain after SoC tests in most cases, without requiring additional sampling.As germline material, a skin biopsy will be collected from which fibroblasts are cultured and DNA prepared. Alternatively, T-cells are isolated (adult AML) or a remission sample (taken at day 29) is used (adult ALL) as an alternative source of germline DNA. If a patient does not achieve remission, germline DNA will be extracted from a buccal swab sample also collected at day 29.The SoC methods used in AML include chromosome banding analysis to identify numerical and structural chromosomal aberrations, targeted FISH analysis to investigate stratifying structural variants, targeted NGS panel  and fragment analysis for selected mutations. Some of the fusion genes detected by FISH can alternatively be detected by RT-PCR. The SoC methods used in ALL includes chromosome banding analysis, FISH to identify fusion genes and/or genomic arrays to identify CNAs. For pediatric patients and young adults with ALL, multiplex ligation-dependent probe amplification may also be performed to detect CNAs.The methods included in SoC at each site are listed in All samples, regardless of tumor content, will be analyzed. WGS libraries will be prepared with the TruSeq PCR-Free kit . WTS libraries will be prepared with the TruSeq Stranded mRNA kit or Illumina Stranded mRNA Prep (Illumina). Input requirements are 1200 ng DNA at a concentration of 25 ng/μl and 500 ng RNA at a concentration of 10 ng/μl . If sufficient material is unavailable, individual sequencing centers may use alternative PCR-free methods with lower input requirements. Sequencing will be performed using the NovaSeq platform (Illumina) with paired-end 150 bp read length. For WGS, leukemia samples will be sequenced to a target of 90× coverage and the matched germline samples to 30× coverage. For WTS, we aim to generate 50 million read-pairs or more for each leukemia sample.Bioinformatic analysis of WGTS data will be performed at each sequencing site. The bioinformatic pipelines at each site are outlined in In all phases, data analysis and interpretation will be performed in two steps:1.Targeted analysis of genes/variants that are mandatory to include or exclude in SoC. The lists of mandatory genetic variants for AML  and ALL 2.Targeted analysis of an extended list of highly recommended genes/variants that is curated 1–2 times per year by the GMS Hematology Working Group. This list includes additional variants that are determined to be clinically relevant based on literature and other classifications .In the retrospective phase, matched tumor-normal WGS data will be analyzed to identify mandatory and highly recommended genetic variants in AML  and ALL,In the real-time validation phase, tumor-only analysis and interpretation will be performed according to step 1 within 2 weeks for pediatric acute leukemias and 3 weeks for adult acute leukemias, followed by tumor-normal analysis and final interpretation according to step 2 within 4 weeks (except for adult ALL where the remission sample will be collected at day 29).After the completion of patient recruitment, a retrospective explorative research analysis of the entire WGS and WTS datasets will be performed to identify novel genomic aberrations of clinical interest.For the whole study duration SoC will be the primary data source for subtype classification and the study data will be regarded as complementary information. Genetic variants of diagnostic, prognostic, and/or predictive impact detected by WGTS will be interpreted and recorded according to the standard procedure at each participating center.In the real-time validation phase, all mandatory variants detected by WGTS will be included in the first clinical report [after 2 (ALL) or 3 (AML) weeks], whereas highly recommended variants will be included the final clinical report (after 4 weeks), and may potentially influence classification/risk stratification and treatment.In the prospective phase, clinically relevant variants that are detected by WGTS, but not by SoC, will be reported to the hematologist/pediatric oncologist as a complementary clinical report after being verified with another clinically validated method . Thus, also in this phase, such variants may influence risk classification and treatment.During the prospective and real time validation phases, we will prepare a WGTS study report for each patient with the following information:•Availability of materials for SoC and WGTS.•Sequencing metrics .•Mandatory and highly recommended variants identified by both SoC and WGTS.•Mandatory and highly recommended variants that are identified by WGTS but not SoC, and if available results of verification experiments.•Mandatory and highly recommended variants that are identified by SoC but not WGTS, and if available results of verification experiments.•Potential impact of WGTS findings on classification, risk stratification and therapy selection.•For the real-time validation phase, turnaround time in calendar days from sample collection to first clinical report  and to the final report .During the real-time validation phase, in addition to a WGTS study report, we will include WGTS findings in the clinical report according to the standard clinical reporting practice. Also, national review meetings, including physicians, clinical scientists, and bioinformaticians will be held on a regular basis to discuss the findings and their clinical interpretation  and to harmonize the reports between sites.We have also prepared standardized templates for collection of metadata  to ensure that all sites collect the same information.The micro-costing analysis will be performed initially at two sites and ultimately at all four sites where WGTS is carried out . A generic micro-costing spreadsheet will be developed and applied to Swedish genetic laboratories estimating the average cost of SoC and WGTS. The micro-costing will capture the economic burden to each laboratory; including the costs of personnel, equipment/material, bioinformatic analysis and interpretation, storage and compute costs, test consumables as well as platforms used (for WGTS) and potentially iterative testing. An activity-based costing model will be applied to calculate the total cost of the included diagnostic techniques. The analysis will take into account that some rapid conventional testing will be required in parallel to WGTS.Cost-effectiveness of WGTS in comparison with SoC will be estimated using economic simulation modeling where the value of WGTS in quality adjusted life years is driven by the proportion of patients for whom management or therapy decision is/could be changed based on variants detected by WGTS, but not by SoC diagnostics. The outcome of patients where WGTS led to changes in risk stratification will be compared to the outcome of patients in risk groups defined by SoC only.Based on literature, study outcomes , and registry data , a simulation model will be built to estimate the diagnostic and the long-term cost for AML and ALL patients. The model will also be able to estimate the long-term health outcomes and the incremental cost effectiveness ratio of WGTS vs. SoC.Sequencing data will initially be stored at each university hospital/university and later on at the National Genomic Platform that is under development within GMS. Sequencing data from pediatric patients will also be stored at the Childhood Tumor Bank. In conjunction with publication, data will be stored at the European Genome-phenome Archive with restricted access. A data access committee that evaluates data requests will be formed within GMS.2 and unpaired t-tests. Diagnostic efficiency, sensitivity and specificity of WGTS for detection of mandatory and highly recommended genetic variants, as compared to SoC methods, will be assessed.In this study, our goal is to investigate all the patients with adult and pediatric acute leukemias who are diagnosed in Sweden during 12 months, i.e., 450 patients. Because a small proportion of patients (estimated to be less than 10%) is expected to be ineligible for the study , we will continue recruiting for up to 18 months to ensure the inclusion of 450 patients in the study. Bivariate relationships between variables will be assessed using χThe application of WGS may potentially generate incidental or secondary findings of genetic variants linked to inherited disease. Notably, however, this study will not actively search for germline variants not related to hematologic malignancies. In the consent form, adult patients have the opportunity to opt in or out to receive information regarding unsolicited findings on inherited diseases beyond hematological conditions.The study protocol was approved by the Swedish Ethical Review Authority for adult (2020-06673) and pediatric (2021-04135) acute leukemia patients. Data processing as well as the dissemination and exploitation of the study findings will take place in full compliance with EU data protection law.This GMS multi-center study, performed in close collaboration with the Clinical Genomics platform at SciLifeLab, will investigate diagnostic efficiency, improved diagnostic yield, technical and clinical feasibility, and clinical utility of a combined WGTS workflow, as a routine clinical test for patients with acute leukemias and determine whether WGTS may replace current, often laborious SoC technologies. Specifically, the study aims to determine whether all mandatory genetic aberrations stipulated in the treatment protocols/national guidelines can be detected by WGTS within a given time frame. The only exceptions are targeted molecular tests that need to be performed within days after diagnosis. Additionally, a health-economic evaluation will be conducted including both a micro-costing and a cost-effectiveness analysis.Clinical grade validation of short-read WGS in chronic lymphocytic leukemia (as a part of the Chronic Lymphocytic Leukemia Genomics England Pilot) demonstrated a high concordance  between WGS and targeted NGS for SNV and indel detection . ConcordCurrently, there is a debate regarding the appropriate sequencing depth as well as whether normal sample should be included in the WGS analysis. Yet, current consensus for correct somatic variant calling by WGS are read depths of 90–100× for tumor samples and 30× for the normal control . For cleIn the study by Duncavage et al., the cost of a WGS-based diagnostic approach was estimated to be $1,300–$1,900 . HoweverTo minimize the effects of inter-site heterogeneity in WGTS analysis, all sites will use the same type of sequencing instrument (NovaSeq) and reagents and the same gene lists will be used for variant prioritization. Although all sites will follow the same principles for data analysis, heterogenous in-house developed bioinformatic pipelines could potentially cause variability in variant calling and consequently affect study outcomes. Also, differences in variant filtering and interpretation procedures may give rise to differences. To evaluate this potential limitation, we will perform additional centralized data processing and analysis on all study samples, including analysis using the Illumina DRAGEN platform. This will allow us to pinpoint any major differences between sites due to the custom bioinformatic workflows. It will also provide an explorative option to identify any missed genetic aberrations in either the custom-developed tools or in DRAGEN, to guide further development of the analytic tools.Our study is limited in that slightly different SoC methods will be used at the participating sites. Most of the SoC methods are very similar between the sites , whereas others may differ . To ensure that SoC complies with the quality requirements all sites participate regularly in quality control rounds issued by CQAS and are yearly reviewed by the Swedish accreditation agency (SWEDAC). A significant fraction of the SoC investigations is also centrally reviewed annually to harmonize procedures. Thus, the final list of reported variants with SoC will be very similar regardless of which site performed the analysis and despite minor differences in methodology between sites. Moreover, annual updates of the national care programs will typically result in minor changes which are unlikely to have an impact on the current study. Similarly, the relevant clinical study protocols are not expected to change during the duration of the current study. Hence, although the SoC methods are slightly more heterogenous between sites than the WGTS approach , the study will provide a direct comparison between the WGTS approach and the current SoC for each individual patient.In summary, data from this national study will be used to (1) evaluate clinical performance of the integrated WGTS diagnostic strategy compared with SoC and (2) provide information regarding clinical and health-economic impacts of WGTS implementation in routine clinical care. We anticipate being able to disseminate our findings by 2022 and onward.The studies involving human participants were reviewed and approved by the Swedish Ethical Review Authority (2020-06673 and 2021-04135). Written informed consent to participate in this study was provided by the patient/guardians.EB, GB, CO-P, LC, TF, and RR designed the study and wrote the manuscript. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Drosophila melanogaster have provided insight into the neural circuit mechanisms underlying behavioral flexibility. Here we discuss how Drosophila behavior is modulated by internal and behavioral state, environmental context, and learning. We describe general principles of neural circuit organization and modulation that underlie behavioral flexibility, principles that are likely to extend to other species.Behavioral flexibility is critical to survival. Animals must adapt their behavioral responses based on changes in the environmental context, internal state, or experience. Studies in  Drosophila, but may also represent a distress signal from other flies  modulation by internal state; (2) modulation by behavioral state; (3) modulation by environmental context; and (4) behavioral flexibility in learning and memory  in the antenna and maxillary palp, which project to the antennal lobe of the brain Montell, . Differevia inputs from DANs, and these MBONs promote food-seeking when flies are hungry , a high-level integration center essential for learning and memory  neurons that seem to be specific for salt-sensing. Salt deprivation specifically modulates the Ppk23glut taste pathway, ensuring that salt preference is modulated without affecting responses to sugar or bitter  promote yeast consumption and suppress sugar intake after protein deprivation  promote feeding over courtship. Conversely, P1 neurons, previously identified as courtship command neurons, promote courtship over feeding. Tyramine acts as a satiety signal that modulates both of these pathways: tyramine inhibits the TyrRPLP neurons while activating P1 neurons, thus shifting the choice toward courtship over feeding.Another study investigated how male flies choose between feeding and mating when they are both food- and sex-deprived  or set of neurons (ISN cells) may be used to modulate multiple pathways in opposing ways. By simultaneously activating and inhibiting different pathways that promote competing behaviors, the balance can be shifted toward one behavior or another. This principle is also reminiscent of behavioral switches that can occur during a single internal state, such as switching from acetic acid aversion to attraction during hunger or switching from sugar to yeast preference during protein deprivation (see above). In all of these examples, competing behavioral pathways are modulated in opposing ways by internal state.vice versa .Similar to internal states such as hunger, an animal’s behavioral state can modulate how the animal responds to stimuli in the world. For instance, the same sensory cue may have different salience or even a different meaning depending on whether a fly is walking, flying, or stationary. Like modulation by internal state, flexibility due to behavioral state can reflect modulation of sensory processing, sensorimotor transformations, or motor responses. It is important to note that changes in behavioral state are likely to correspond with changes in internal state, whether it is the internal state that alters behavioral state  or Drosophila visual system, particularly in motion-sensing pathways. These results parallel findings in the mammalian visual system . In this case, the learned response is suppressed Early work suggested that extinction relies on distinct transcriptional and molecular signaling pathways from those that underlie initial associative learning , the neurons that encode sexual arousal state (recurrently connected NPF/pCd neurons), how the activity of state-encoding neurons is regulated over long timescales , and how these neurons modulate circuits for behavior (dopaminergic modulation of P1 neurons). In the future, we expect to see more examples detailing comprehensive circuit mechanisms underlying behavioral flexibility.Drosophila reveal another general principle: circuits can be modulated at different levels, from sensory responses to motor pathways. Why might modulation at a specific level be advantageous? Modulating sensory responses early in the circuit, such as the sensory neurons themselves, would result in global modulation of all behaviors elicited by that cue. This could be advantageous if it is critical for an animal to perceive a cue as more or less salient, such as hunger-dependent enhancement of sugar sensitivity, but it does not allow for control over which behaviors are modulated. In contrast, modulating motor or pre-motor pathways would enable an internal state to gate the activation of specific behaviors or motor programs. Some forms of behavioral state-dependent modulation occur downstream of descending neurons and are likely to represent modulation of motor pathways. State-dependent modulation can also act in between sensory and motor pathways to modulate the sensorimotor transformation. Examples of this include the arousal-dependent gating of courtship pursuit and flight-dependent responses to looming stimuli.Studies of behavioral flexibility in The examples of behavioral flexibility that we have described primarily fall under three categories: (1) gain changes modulating the strength of a behavior, (2) tuning changes modulating the preferred range of stimuli that produce a response, and (3) a behavioral switch that changes the response entirely . Shared Moreover, examples of behavioral flexibility that we currently describe as gain changes may actually represent a behavioral switch if a broader set of behaviors were monitored. For instance, the suppression of PER during walking, or the suppression of courtship after males have recently copulated, likely allows for other behaviors to be expressed instead. It is important for an animal to adequately prioritize mutually exclusive goals. Recent studies investigating the behavioral competition, such as choosing between feeding and mating, highlight the interactions between different behaviors and their underlying circuits. As the field moves toward studying broader repertoires of behavior in more naturalistic paradigms, more of these interactions will likely emerge.Drosophila has proven to be an excellent model system for dissecting the neural circuits underlying behavioral flexibility. Astounding progress has been made over the last decade in characterizing the synaptic wiring diagram of the fly nervous system and developing increasingly sophisticated genetic tools for circuit analysis. In parallel, methods for behavioral analysis and quantification have drastically improved (Pereira et al., Overall, All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


This rapid evidence review identifies and integrates evidence from epidemiology, microbiology and fluid dynamics on the transmission of SARS-CoV-2 in indoor environments.Searches were conducted in May 2020 in PubMed, medRxiv, arXiv, Scopus, WHO COVID-19 database, Compendex & Inspec. We included studies reporting data on any indoor setting except schools, any indoor activities and any potential means of transmission. Articles were screened by a single reviewer, with rejections assessed by a second reviewer. We used Joanna Briggs Institute and Critical Appraisal Skills Programme tools for evaluating epidemiological studies and developed bespoke tools for the evaluation of study types not covered by these instruments. Data extraction and quality assessment were conducted by a single reviewer. We conducted a meta-analysis of secondary attack rates in household transmission. Otherwise, data were synthesised narratively.We identified 1573 unique articles. After screening and quality assessment, fifty-eight articles were retained for analysis. Experimental evidence from fluid mechanics and microbiological studies demonstrates that aerosolised transmission is theoretically possible; however, we found no conclusive epidemiological evidence of this occurring. The evidence suggests that ventilation systems have the potential to decrease virus transmission near the source through dilution but to increase transmission further away from the source through dispersal. We found no evidence for faecal-oral transmission. Laboratory studies suggest that the virus survives for longer on smooth surfaces and at lower temperatures. Environmental sampling studies have recovered small amounts of viral RNA from a wide range of frequently touched objects and surfaces; however, epidemiological studies are inconclusive on the extent of fomite transmission. We found many examples of transmission in settings characterised by close and prolonged indoor contact. We estimate a pooled secondary attack rate within households of 11%  = 9, 13). There were insufficient data to evaluate the transmission risks associated with specific activities. Workplace challenges related to poverty warrant further investigation as potential risk factors for workplace transmission. Fluid mechanics evidence on the physical properties of droplets generated by coughing, speaking and breathing reinforce the importance of maintaining 2 m social distance to reduce droplet transmission.This review provides a snap-shot of evidence on the transmission of SARS-CoV-2 in indoor environments from the early months of the pandemic. The overall quality of the evidence was low. As the quality and quantity of available evidence grows, it will be possible to reach firmer conclusions on the risk factors for and mechanisms of indoor transmission. It is well established that SARS-CoV-2 is readily transmitted in indoor environments; however, questions remain about the relative importance of different transmission mechanisms, the risks associated with non-clinical indoor environments and activities and the role of ventilation and plumbing systems in mitigating or amplifying transmission. Although other reviews address aspects of these questions -3 there The purpose of this review is to integrate evidence from epidemiological, microbiological and fluid mechanics studies on the transmission of SARS-CoV-2 in indoor, non-clinical settings in order to answer ten specific questions:What evidence is there for aerosolised transmission?What evidence is there for faecal-oral transmission?What evidence is there regarding the role of ventilation systems in indoor transmission?What evidence is there regarding the role of plumbing systems in indoor transmission?What evidence is there regarding transmission via different indoor surfaces ?What evidence is there for the transmission in indoor residential settings?What evidence is there for transmission in indoor workplace settings?What evidence is there for transmission in other indoor settings ?Do particular activities convey greater risk ?What evidence is there for the appropriate length of distancing between people?We designed two separate search strategies: one to identify epidemiological and microbiological papers and the other focused on fluid mechanics papers (mechanistic studies). We searched PubMed, medRxiv, arXiv, Scopus, WHO COVID-19 database, Compendex & Inspec. Searches were collaboratively developed by two reviewers (MD and LG) and results exported on 20 and 21 May 2020. Full search details are in Appendix S1 in the We included studies reporting data on any indoor setting except schools, which is addressed elsewhere in a living systematic review , any indEpidemiological studies: We excluded studies of transmission within clinical settings and studies focusing purely on the clinical characteristics of cases. We also excluded statistical modelling studies aiming to predict future outcomes, as opposed to descriptive studies characterising past events.Microbiological studies: We included studies involving the testing of swabs taken from “real world” settings for the presence of SARS-CoV-2. As most of these were conducted in hospital settings, we included studies from both clinical and non-clinical settings. However, to maximise the transferability and generalisability of these findings to non-clinical indoor settings, we excluded microbiological studies of samples collected in areas of the hospital such as operating theatres and Intensive Care Units (ICU) where aerosol-generating procedures are routinely carried out. We also included laboratory studies investigating the persistence and viability of the virus under different controlled conditions.Mechanistic studies: We included articles reporting data on any respiratory virus, numerical simulation studies focusing on the mechanisms of transmission and studies investigating any mechanisms with potential to influence transmission in indoor environments, such as ventilation, air conditioning or plumbing systems.Articles were screened by two separate teams . Title and abstract and full text screening were conducted by one reviewer within each team, with rejections assessed by a second reviewer.Data extraction and quality assessment for each article was conducted by a single reviewer, as above. A range of critical appraisal tools was employed, according to study design: case series and case reports were evaluated using Joanna Briggs Institute checklists . We adaprma.uni function in the metafor package [2 and Cochrane’s Q were calculated to assess heterogeneity. For consistency, the same function was used to estimate confidence intervals for SAR in individual studies that were not included in pooled estimates. A fixed effects analysis was chosen because the number of studies was relatively small, and thus a simpler underlying model (fewer assumptions/parameters required) was likely to be better estimated: in addition, there is reasonably good theoretical and simulation evidence that fixed effects models are relatively robust to moderate heterogeneity [Data heterogeneity was such that results were synthesised narratively, except for the results on secondary attack rates within households, which were meta-analysed using a fixed effect model in R 3.6.3  using th package . I2 and ogeneity . There wAfter the removal of duplicates, a total of 1573 articles were identified. A total of 1447 were rejected through title and abstract screening and a further 68 were rejected at the full-text screening stage and quality assessment stage. Forty-one did not provide data relevant to study questions, 26 were poor quality and one article could not be retrieved. Fifty-eight articles were retained for analysis  and in the care home (P < 0.00001). We found two workplace studies which did not present sufficient data to estimate SARs but nevertheless provide insight into workplace transmission  difference in the numbers of droplets emitted between each of these levels and the next -79. TherThe four studies we found which report on transmission in communal contexts are consistent with the conveyance of risk through close contact daily living activities. It is striking that the SAR reported in the care home  is an orOur findings are consistent with the hypothesis that the main route of CoV-2 transmission is through person-to-person short-range transmission, which occurs through large respiratory droplets ejected while speaking, coughing and sneezing. The distance that these respiratory droplets travel before falling to the ground depends on (among other factors) how they were generated. The physical behaviour of droplets is well characterised: those generated by speaking fall to the ground within 1 m or closer to the speaker ; dropletThis rapid evidence review integrates evidence from epidemiological, microbiological and fluid mechanics perspectives on the transmission of covid-19 in indoor settings. We found epidemiological, mechanical and microbiological evidence consistent with person-to-person, short-range spread via mostly respiratory droplets that directly reach recipients either through the air or through touching contaminated surfaces and then transferring the virus on the hands to mucosal membranes. Evidence from numerical simulation and fluid mechanics studies, microbiological laboratory studies and environmental sampling studies suggest that aerosol transmission is theoretically possible and is another potential source of transmission but we did not find conclusive epidemiological evidence to confirm this. However, evidence from fluid mechanics experiments and numerical simulations indicate that ventilation can play an important role in reducing disease transmission through diluting and dispersing the concentrations of viral particles in the air. Although viral RNA can be detected in faeces of affected individuals, we found no evidence for the presence of live virus in faecal samples nor for transmission through infected faeces.Evidence from household, communal residential, community and workplace settings suggests that close and prolonged physical contact is important in transmission dynamics. Within households, the risk of transmission was higher between spouses than between other types of relative. Community and social settings associated with a higher risk of transmission are also those where people gather in close proximity indoors for prolonged periods. Churches and religious gatherings, sharing meals and bathing facilities, close physical contact and activities such as singing together have all been reported in conjunction with outbreaks. In contrast, there have been fewer reports of transmission in relation to more casual, short term social contact, although this may be because such contacts are subject to recall bias and harder to track and trace. Many of the workplace settings where outbreaks have occurred are characterised by close physical contact and prolonged time spent in crowded indoor spaces. Evidence from the study on outbreaks in meat and poultry processing plants  also higTo our knowledge, this is the only review focusing on indoor transmission across different indoor contexts and combining evidence from epidemiological, microbiological and fluid mechanics studies. The key advantage of bringing together evidence from different disciplines in this way is that it enables practical issues that are of direct and immediate importance to decision-makers to be addressed. Three recently published systematic reviews address similar questions: Koh and colleagues estimated a pooled secondary attack rate in household settings of 18.1%  – somewhat higher than our estimate, potentially reflecting the small number and poor quality of the primary studies we found on this topic. . This stOur findings have several implications for researchers, policymakers and the general public. First, we highlight important gaps in the evidence base: although aerosolised transmission is theoretically possible, whether this actually occurs in non-clinical indoor settings remains uncertain and many questions remain unanswered. It is still not known what quantity of live virus is required to present an infection risk or whether live virus is present in sufficient quantities in aerosolised particles to present a risk. Further research on these questions is urgently warranted. Although we excluded evidence from animal studies in this review, such studies should be included in future reviews, as they can potentially provide direct experimental evidence on airborne transmission . Second,This review has a number of limitations. Although the focus of this study is transmission of SARS-CoV-2 in indoor, non-clinical settings, most of the microbiological and environmental evidence was generated in clinical contexts because this is where most of this type of study have been conducted to date. Clearly such settings are very different from non-clinical, community contexts: for example, there is a higher risk of transmission via aerosol generating procedures (AGP) and greater numbers of individuals infected with SARS-CoV-2, so virus detection in these settings is likely higher than in non-clinical indoor settings. To maximise the transferability and generalisability of these findings to community settings, we attempted to extract and report only on samples taken from areas of hospitals accessible to visitors and the general public; however, this was not always possible, as the studies did not provide information on the extent to which AGPs were carried out in patient rooms. Therefore, these results must be treated with caution in applying them to non-clinical settings.The quality of the available epidemiological evidence was poor, so this makes any conclusions uncertain. In particular, there is significant variability in contact tracing approaches across different countries and even different regions within countries. Contact tracing of rapidly evolving infectious diseases inevitably contains case ascertainment biases, non-homogenous sampling over time and location, and uncontrolled correlation . There m


The aim of this study was to explore the perspectives of physiotherapists in four selected regions of sub-Saharan Africa regarding health system challenges impacting the integration of physiotherapy-led falls prevention services in the primary care of persons living with HIV (PLWH).Falls may pose a significant problem among younger PLWH in low- and middle-income countries. Physiotherapists’ role in optimising function and quality of life can do much in the prevention of falls in PLWH and reducing the harm that results. However, falls prevention strategies have not been implemented effectively especially in primary health care settings in sub-Saharan Africa. Physiotherapists’ account of the health system challenges they encounter may provide insights into potential strategies that may be considered in optimising fall prevention for PLWH in poorly resourced settings.A descriptive qualitative study was conducted in selected urban districts in the capital cities of four sub-Saharan African countries. In-depth interviews were conducted with 21 purposively selected physiotherapists involved in the primary care of PLWH. Audio recordings of interviews were transcribed verbatim and analysed using deductive thematic content analysis.The main results are presented in the theme ‘Health care system challenges’ and in nine categories informed by the WHO health system framework: lack of policies and clinical practice guidelines, shortage/Inaccessible falls prevention services, inadequate human resource, physiotherapists not adequately equipped in falls prevention, inaccessible/No facilities for BMD measurement, inefficient data capturing systems, lack of evidence regarding falls among PLWH, unclear physiotherapy role descriptions, inefficient referral system. Physiotherapists highlighted the need for more information and research regarding fall prevention for PLWH, promote their role in the primary care of PLWH and adopt a patient-centred approach to fall prevention. The PI was the main interviewer although a second interviewer (QL or KB) was present to ensure consistency and coherence throughout the interview process.All investigators were female physiotherapists and had experience in qualitative research. The interviewers revealed their identity and profession to prospective participants. Thus, it was expected that participants would be comfortable in using scientific or rehabilitation terminology in their responses.The research was conducted in primary health care (PHC) facilities in the urban districts of capital cities  of four sub-Saharan African countries . All four countries are classified as low-to-middle income countries (LMIC)  are presented below Table . Selecte‘…there is no specific policy to say physiotherapy, but there is a general guideline on the management of HIV. But not something which is strictly…referring to my profession alone, no.’ Participant 12, Zambia, general hospital.None of the countries had independent policy on physiotherapy-specific care of PLWH, including falls prevention in PLWH. This is exemplified in the following quote:Particularly in Botswana, where some hospitals are currently undergoing accreditation, some effort was being made on development and implementation of falls prevention policies for all hospitalised patients (which inherently include PLWH). Physiotherapy departments were expected to adapt these guidelines, but very few reported having departmental policies on generic falls prevention. As such, policies guiding falls prevention for community-dwelling PLWH were non-existent.‘…lack of access to appliances like wheelchairs, we have serious shortage of wheelchairs and then the other thing is like crutches, walking aids.’ Participant 2, Botswana, district hospital.‘Some people will tell you we don’t have money to buy assistive devices, we can’t afford to buy crutches or walking frames.’ Participant 19, Zimbabwe, referral hospital.Physiotherapists reported that fall prevention services were not available to PLWH at primary care level, due to the shortage of assistive devices in most facilities. Some participants from all the countries indicated that patients were unable to access required falls prevention services because they could not afford it.‘What we find is the role of physiotherapy within the whole spectrum of HIV and patient care is quite limited particularly by the authorities… or you find there are not many physiotherapists that are employed in that sector, and yet I think there is quite a big role to play.’ Participant 17, Zimbabwe, referral hospital.A disproportionate number of physiotherapists in our sample population was employed in the primary care of PLWH. One participant pointed out the lack of clear-cut role descriptions for involvement of physiotherapists in the care of PLWH, often resulting in physiotherapists being side-lined from the care of PLWH.There was also a lack of other health professionals at primary care level. Therefore, some of the specialist services were not available at their hospitals or clinics for physiotherapists to refer patients for further falls prevention services.‘We did one page of HIV training. I studied at Australia; they didn’t tell much on HIV. It was my first time seeing it when I started working in Botswana, so I just learnt through experience and asking colleagues.’ Participant 4, Botswana, district hospital.Most physiotherapists reported inadequate knowledge and skills in falls prevention for PLWH, citing inadequate prelicensure training. Physiotherapists from Botswana presented a unique scenario, in which the local non-existence of physiotherapy training schools meant they had to train in high-income countries, where HIV/AIDS is not a priority. These physiotherapists felt incompetent in caring for PLWH upon returning to Botswana.‘… maybe that is where this overlooking thing comes up because really when they do their HIV workshop, they don’t incorporate rehab staff or the physios.’ Participant 21, Zimbabwe, referral hospital.Unequal opportunities for professional training were reported. Most health facilities prioritised the training of medical doctors and pharmacists in the provision of care to PLWH while limited opportunities existed for physiotherapists.An absence of dual energy X-ray absorptiometry (DXA), considered the gold standard for measurement of BMD, was reported as a deterrent to physiotherapists’ ability to routinely assess the risk of bone demineralisation in their patients. Most reported using X-rays as the main diagnostic tool for osteoporosis, with limited use of computer topography (CT) due to its high cost.‘…I think maybe it’s also because when I treat them, I haven’t really tallied or taken statistics to compare those with HIV to those without really. So, I can’t really say I have seen more of the other than the other.’ Participant 1, Botswana, military hospital.Participants noted that inefficient capturing of statistics prevented physiotherapists from being able to notice trends indicating fall risk among PLWH.‘I don’t recall very clearly going into the details of it…I have seen there has been quite a few articles on the research of HIV management in the physiotherapy field, but I cannot recall touching on it so in-depth as an undergraduate.’ Participant 9, South Africa, district hospital.Participants further indicated poor coverage of information regarding care of PLWH, including falls prevention, in their undergraduate curricula. In these curricula, falls prevention was considered in the area of gerontology and not linked to HIV.‘Apparently here in Zimbabwe, maybe that is where this overlooking thing comes up because really when they do their HIV workshop, they don’t incorporate rehab staff or the physios. Participant 21, Zimbabwe, referral hospital.‘I don’t think we would ever get referral from a doctor saying that please assist this patient …because he is high risk of falling. That very rarely happens, I am going to go with one percent of referrals.’ Participant 7, South Africa, district hospital.Several participants highlighted how other health professionals were unaware of the roles that physiotherapists played in falls prevention or primary care of PLWH. As a result, physiotherapists were often excluded from HIV policy workshops while PLWH were not referred adequately for physiotherapy-led falls prevention.‘…we don’t screen our patients in the ward because then literally every single patient in the hospital would get some form of physiotherapy and then we are looking at four hundred patients getting physio on a daily basis which we do not have the capacity to do, so unfortunately we do work on a purely doctor referral basis.’ Participant 7, South Africa, district hospital.‘In our hospital the nurses are not allowed to refer to the allied health…but I am sure that the nurses do pick up the concern…they can verbally raise the concern with us and then we will advise them to speak to the doctor who will then refer the patients to us.’ Participant 9, South Africa, district hospital.Concerns were raised regarding the referral system between members of the multidisciplinary team (MDT) that could contribute to reducing falls risk in PLWH. The doctors remained the gatekeepers to the patients. The nurses could not refer to other members of the MDT, even though they were better positioned to identify patients at risk of falls.‘And as soon as the person is cleared medically and stable, they should get discharged whether they are able to walk or not. More or less that is what the hospital does.’ Participant 19, Zimbabwe, referral hospital.Another deficiency in the health care delivery system was failure to ensure community reintegration of patients and ensuring social and financial support. The doctors reportedly discharged patients before they had achieved sufficient mobility status and were at high risk of falls.To our knowledge, this is the first study to describe health system challenges as a barrier to integrating falls prevention into the primary care of PLWH, as perceived by physiotherapists from sub-Saharan African regions. It was clear that the provision of falls prevention services was suboptimal in all four investigated regions. This was partly attributed to gaps in the health system related to all six building blocks of the WHO health systems framework, namely leadership/governance, health care financing, health workforce, medical technology, information and research and service delivery. Mapping our findings against the established building blocks of a strong health system enabled us to propose potential strategies to implement falls prevention services targeted at PLWH into primary health care settings.et al., et al., et al.  by the allied health workforce in LMIC primary care settings have been identified (Dizon , et al.  develope, et al. .et al., et al., Despite this gap, our results also highlighted the potential positive outcomes of using the hospital accreditation system as a vehicle of CPG development and implementation. For example, physiotherapists reported that quality improvement initiatives in Botswana fostered the development of quality CPG for generic falls prevention by bench-marking against recognised standards of practice (Kredo et al., Participants voiced their concern regarding PLWH not being able to access falls prevention services due to cost or unavailability. The economic costs of falls prevention services associated with the purchase of assistive devices, attendance fees and transport costs are commonly-reported barriers to implementing falls prevention services – cited in over two-thirds of studies included in a systematic review (Child et al., et al., et al., et al., et al., et al., et al., Physiotherapists highlighted poor capturing of statistical data on falls occurring in PLWH as another gap in the health system as a barrier to falls prevention in PLWH. Their failure to document falls may be linked to their lack of routinely assessing for falls in PLWH or to patients failing to report fall incidences (Phelan et al. (The information and research on falls in PLWH may also be important in training physiotherapists and other health care professionals. The physiotherapists in our study perceived their prelicensure training and continuous professional development on falls prevention for PLWH as inadequate. Thus, most physiotherapists’ knowledge on falls prevention was based on what they were taught in another context, such as gerontology. An audit of the physiotherapy undergraduate curricula of eight South African academic institutions by Myezwa et al.  revealedThis study highlighted additional health system challenges stemming from other health care professionals’ poor understanding of the scope of physiotherapy practice in the primary care of PLWH, including falls prevention. This resulted in a disjointed pathway of care that negatively impacted health outcomes for the patients.et al., et al., et al., et al., Lack of other health professionals’ knowledge about physiotherapists’ role in HIV care resulted in the profession being misunderstood or undervalued (Cobbing et al., et al., Physicians not knowing what physiotherapists do for falls prevention may have contributed to physicians inadequately referring PLWH to physiotherapy as mentioned by a few physiotherapists in this study. An inadequate referral pathway was similarly reported in another South African study, (Maddocks An Irish study (Mackenzie and Clifford, et al. (et al., A limited understanding of physiotherapists’ role in PHC may have been demonstrated by the smaller proportion of physiotherapists involved in this study who were employed in PHC settings. In fact, only one of the physiotherapists was employed at an outpatient HIV clinic while less than a third worked in primary district hospitals. Cobbing et al.  highligh et al., . Governmet al. (et al., Physiotherapists’ role in PHC seems to be more appreciated in high-income countries. Deboer et al.  reported et al., . If physet al., Another gap in the health system affecting falls prevention for PLWH was the lack of some elements of patient-centred care. Some participants indicated poor socio-economic support from PLWH’s families as a hindrance to successful implementation of falls prevention services. A similar lack of caregiver support for patients’ fall management were raised in a Malaysian study, (Loganathan Purposive sampling was used to gain perspectives of physiotherapists working in primary care of PLWH. However, physiotherapists in Zimbabwe and Zambia were mostly employed in secondary and tertiary hospitals, while a disproportionate number of physiotherapists in South Africa worked in the private sector. Participants were restricted to the public sector but included the input of physiotherapists employed at general and referral hospitals because they were still the first line of contact for rehabilitation and would be the same physiotherapists who would need to implement falls prevention programs in the community perhaps by means of outreach visits to primary hospitals and HIV clinics. By doing so, the study gained additional information with regards to falls that occur in hospitalised PLWH. Perhaps maximum variation sampling would have better suited this population and allowed the researcher to assess differences in patterns of experience from physiotherapists engaging with PLWH at different levels of care.A strong patient-centred health system is essential for the management of the health needs of the community including PLWH. Findings from this study indicate that physiotherapists face various challenges from deficiencies within the health system when it comes to falls prevention for PLHW, including fragmented service delivery, shortage of competent human resources and budgetary constraints. Physiotherapists play a crucial role in re-integrating PLWH into communities and need to liaise with other health professionals to ensure patient-centred continuum of care for PLWH and effectively improve their QoL.


COVID-19-associated pulmonary aspergillosis (CAPA) has raised concerns about increased mortality, and a consensus has been recently prepared to define and manage this pathology. Voriconazole is currently recommended as first-line therapy for CAPA . Given tWe propose an empirical algorithm to optimize the management of measuring VTC of CAPA patients to avoid misdosing Fig. . First, Overall, these findings suggest that therapeutic management must take into account the high level of inflammation of CAPA patients. As it is based on parameters that are readily available in comparison with VTC, the empirical algorithm presented here, that must consider clinical and biological parameters of each patient, could be considered with the goal of improving patient management.


Human granulocytic anaplasmosis is a tick-borne disease with an increasing incidence associated with morbidity and mortality. Uncertainty remains whether a prophylactic dose of doxycycline is effective in prevention.We present a case of an 80-year-old female with syncope, resultant facial trauma, and fever two weeks after a tick bite for which she received prophylaxis. Workup revealed anaplasmosis, and treatment led to symptomatic improvement.We review the presenting symptoms, laboratory findings, and treatment of anaplasmosis, as well as give caution about the limitations in prescribing a prophylactic dose of doxycycline following a tick bite. Anaplasma phagocytophilum and transmitted by the Ixodes scapularis tick (1Human granulocytic anaplasmosis (HGA) is a tick-borne illness caused by the rickettsial bacterium ris tick .1 SymptoWe present a case of HGA that may have contributed to a syncopal episode leading to traumatic facial injury in a patient who had taken doxycycline prophylaxis for a tick bite.An 80-year-old female with history of mild chronic obstructive pulmonary disease, mitral valve prolapse, and herniated discs presented to the emergency department (ED) by private vehicle for a facial injury after being struck in the face by a dresser drawer. Leading up to the injury she reported feeling lightheaded, and at the point of losing consciousness she attempted to steady her balance by grabbing a dresser, causing it to fall on her chest pinning her against the wall for approximately five hours. She denied significant pain and noted that the top of her scalp superior to the laceration was insensate. She experienced persistent oozing from the wound and her nose since the injury. A 10-point review of systems was otherwise negative with the exception of fever during the preceding two days to a maximum of 103.3°F on the day of presentation. Notably, she had a tick, which she had removed approximately two weeks prior that was attached for about 24 hours. She was prescribed a one-time dose of 200 milligrams (mg) of doxycycline for Lyme disease prophylaxis, which she had taken on the day of removal by her primary care provider.Ehrlichia chaffeensis polymerase chain reaction [PCR]); Anaplasma phagocytophilum PCR; Babesia microti PCR; respiratory viral panel; coronavirus disease 2019 PCR; and lactic acid. Notable results are shown in On exam, vital signs were notable for heart rate of 102 beats per minute and were otherwise unremarkable. She had a six-centimeter laceration over her left upper forehead with evidence of an open fracture of the frontal sinus on exam with bone fragments visible within the wound. Given the mechanism of injury and her age, we ordered computed tomography of the head, maxillofacial, cervical spine, chest, abdomen, and pelvis, which demonstrated left frontal calvarial fractures. Lab work included the following: a complete blood count; complete metabolic panel; troponin; creatinine kinase; prothrombin time and international normalized ratio; tick panel (Lyme disease immunoglobulin G/immunoglobulin M, What do we already know about this clinical entity?Human granulocytic anaplasmosis is a tick-borne disease with an increasing incidence associated with morbidity and mortality.What makes this presentation of disease reportable?We discuss a rare disease with a presentation including a syncopal episode and traumatic injury found to have findings consistent with anaplasmosis.What is the major learning point?This report highlights the classic historical and laboratory findings of anaplasmosis with caution about limitations of doxycycline in Lyme disease prophylaxis.How might this improve emergency medicine practice?This case may lead to increased recognition of a rare tick-borne illness to assist with timely diagnosis and treatment.Anaplasma phagocytophilum PCR ultimately returned positive on hospital day two revealing the diagnosis. She was started on doxycycline 100 mg twice daily with improvement of symptoms and hematologic parameters, and she was subsequently discharged on hospital day six.During the hospital course, the patient continued to spike fevers and had worsening thrombocytopenia, hyponatremia, and leukopenia as demonstrated in Anaplasmosis typically presents with nonspecific symptoms including fever, chills, headaches, and myalgias with associated leukopenia, thrombocytopenia, and elevated transaminases.The presentation of HGA as syncope leading to a traumatic event is unusual. There is one report of HGA leading to encephalopathy leading to a motor vehicle crash causing injury.8The specific etiology of syncope in this case is unclear. The suspicion is that HGA could have led to orthostatic hypotension from high fevers leading to increased metabolic demands and dehydration. The patient had an elevated creatinine on presentation that had improved by hospital day two with resuscitation. Human granulocytic anaplasmosis has been previously associated with acute renal failure.10The treatment of choice is doxycycline, which typically leads to rapid improvement and is continued for 10 days per Infectious Diseases Society of America guidelines. A failure to respond to doxycycline within 48 hours should prompt evaluation for other causes including babesiosis.10There is no data regarding the effectiveness of a single 200-mg dose of doxycycline in preventing non-Lyme tick-borne illness. Doxycycline prophylaxis, a single dose of 200 mg, following a tick bite has been recommended for Lyme disease prevention with criteria as shown in Anaplasmosis is an emerging disease that is increasing in frequency in endemic areas. In the evaluation of fever, hematologic abnormalities, and elevated transaminases with the proper travel history or location, human granulocytic anaplasmosis should certainly be considered as a possible cause. The effectiveness of doxycycline in prophylaxis of HGA has not been evaluated, and the emergency clinician should be aware of its limitations.


OXTR genotypes in conferring either a risk or protective effect in autism, schizophrenia, and eating disorders (ED). There are numerous DNA variations of this receptor, with the most common DNA variation being in the form of the single nucleotide polymorphisms (SNPs). Two OXTR SNPs have been most studied in relation to ED: rs53576 and rs2254298. Each SNP has the same allelic variant that produces genotypes AA, AG, and GG. In this critical review we will evaluate the putative role of rs53576 and rs2254298 SNPs in ED. Additionally, this narrative review will consider the role of gene-environment interactions in the development of ED pathology.Oxytocin, a nine amino acid peptide synthesised in the hypothalamus, has been widely recognised for its role in anxiolysis, bonding, sociality, and appetite. It binds to the oxytocin receptor (OXTR)—a G-protein coupled receptor—that is stimulated by the actions of oestrogen both peripherally and centrally. Studies have implicated OXTR SNPs rs53576 and rs2254298 show independent associations between the A allele and restrictive eating behaviours. Conversely, the G allele of the OXTR rs53576 SNP is associated with binging behaviours, findings that were also evident in neuroanatomy. One study found the A allele of both OXTR SNPs to confer risk for more severe ED symptomatology while the G allele conferred some protective effect. An interaction between poor maternal care and rs2254298 AG/AA genotype conferred increased risk for binge eating and purging in women.The Individual OXTR SNP are unlikely in themselves to explain complex eating disorders but may affect the expression of and/or effectiveness of the OXTR. A growing body of G x E work is indicating that rs53576G homozygosity becomes disadvantageous for later mental health under early adverse conditions but further research to extend these findings to eating pathology is needed. The GWAS approach would benefit this area of knowledge. Oxytocin is a chemical made in the brain that affects human behaviour in areas from anxiety, bonding right through to appetite. Oxytocin works by binding to a specific cellular receptor. In humans, the genes that specify this receptor are found in slightly different versions that are inherited from each parent. Research has suggested that individuals who possess speicfic combinations of oxytocin receptor gene variants may be more susceptible to certain kinds of mental illness. This paper considers two different versions of the oxytocin receptor gene most studied in relation to eating disorders. The two different versions considered in this review do not seem to affect the structure of the oxytocin receptor itself. Together, research indicates that the presence or absence of a particular receptor gene variant in an individual might have some predictive capability in respect of potential susceptibility to eating disorders. However, further research is necessary as some of the findings are contradictory. In addition, environmental factors—such as poor maternal care early in life—have also been demonstrated to be important in determining whether an individual will develop an eating disorder. Research in this area would benefit from non-hypothesis driven studies. The nine-amino acid peptide oxytocin is synthesised mainly in the hypothalamus and secreted directly within the cerebrum but also released via the posterior pituitary gland to regulate a range of physiologic and metabolic processes . CentralOxytocin is an anorectic with multifarious hypophagic controls, including homeostatic satiety-related signalling between the peripheral and central nervous system, metabolic modulation, supraoptic nuclei metabolic feedback, and the reduction of feeding reward . Blockad2) OT, inhibited feeding in rats but also produced tolerance [The anorectic effects of chronic oxytocin administration have not been widely studied. However, repeated ICV injections of oxytocin agonist  hypoactivation of relevant neural reward and homeostatic circuitry was seen in AN and weight-recovered AN, that was associated with plasma concentration oxytocin and disordered eating psychopathology [Oxytocin concentrations have been studied in relation to eating disorders. Low-weight women with anorexia nervosa (AN) have lower serum oxytocin concentrations than healthy controls, and postprandial oxytocin concentrations were associated with ED psychopathology . Additioathology , 23.OXTR is stimulated by oestrogen both peripherally and in central hypothalamic sites with behavioural actions [OXTR is oestrogen sensitive remains unclear [OXTR expression [There is evidence to support that sensitivity to oxytocin, which is thought to be mediated by genetic and epigenetic alterations in the OXTR gene, might play a role in criterion eating disorder behaviours . The OXT actions –29; howe unclear . Nonethepression –41.OXTR is located on chromosome 3p25, spanning 17 kb, and containing three introns and four exons [OXTR are SNPs—the most common form of DNA variation—and occur when one nucleotide of a base pair is replaced by another nucleotide. The two most studied OXTR SNPs in relation to ED are rs53576 and rs2254298,  or heterozygous if different alleles are inherited derived from each parent (AG). There are, therefore, three genotypes for each of these SNP: GG, AG, and AA. Since rs53576 and rs2254298 are located in the non-coding third intron of the OXTR, there is no effect in the expression of the OXTR protein.In humans, the ur exons , 42. TheOXTR gene were first linked to human mental health, specifically in autism research, that extended the work demonstrating the links between the OXTR and sociability in voles. The hypothesis that variation in the OXTR was associated with deficits in social behaviour was substantiated by a study linking rs53576 and rs2254298 to autism [OXTR studies, research into the broader hypothesis that OXTR polymorphisms are associated with social dysfunction has increased and has been extended to explain other psychopathology, such as depression, schizophrenia and ED, as well as general social functioning [Variations in the o autism . Despitectioning –47.OXTR and ED has so far pursued only the candidate-gene approach. In addition to common genetic variation, rare gene mutation may identify critical mechanisms in pathology.Broadly, there are two approaches for identifying genetic risk factors associated to a specific phenotype. The first is the candidate-gene approach, which investigates pre-specified gene variations in relation to a specific phenotype. This hypothesis-driven approach differs from data-driven genome-wide association studies (GWAS) and quantitative trait locus mapping that analyse the DNA sequence of the entire genome to identify genetic risk factors for phenotypes, usually diseases that are common in the population. Research into the OXTR promoter have been reported in relation to disorders characterized by impairments in social cognition, including Autistic Spectrum Disorder, eating behaviour, such as anorexia nervosa, and problems with facial and emotional recognition [CD38 [In addition to genetic variation, changes in the activity of OXTR may be related to other non-genetic regulatory mechanisms of transcription, such as DNA methylation—an epigenetic mechanism involving the transfer of a methyl group onto the C5 position of the cytosine to form 5-methylcytosine. Epigenomic changes might alter DNA accessibility thereby regulating patterns of gene expression . Consistognition –52. Howeon [CD38 .OXTR rs53576 and rs2254298 SNPs and their role in clinical and non-clinical samples with, or displaying behaviours characteristic of, AN, BN or binge-eating disorder.The aim of this critical review is to explore research into OXTR SNPs, the oxytocin gene itself, oxytocin secretion, and oxytocin administration were excluded from this review. Studies examining the OXTR gene and parturition have also been excluded, given the upregulation of oxytocin in the third trimester. Research that relies on salivary or plasma oxytocin concentrations has also been omitted as the validity of these measurements is not decided.Research was included in this review if it was written in English, peer-reviewed and explored rs53576 or rs2254298 and ED behaviours together  of Nucleotide Sequence Variation  for stud Catalog  was alsoOXTR SNPs and ED behaviours: two in clinical cohorts and two using ED pathology in the general population. Despite this paucity of research, the emerging results are broadly consistent.Only six studies have addressed the association between OXTR GG genotype in the rs53576 were more likely to have self-induced vomiting or used laxatives for weight loss [A large-scale hypothesis-free investigation of pregnant women from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort found that participants with the ght loss . HoweverOXTR SNPs rs53576 and rs2254298, maternal care and eating behaviours [p = .01) The SNP rs2254298 was most strongly associated with restrictive eating behaviour, in particular the A allele, with A-allele carriers and homozygotes having increased odds of engaging in restrictive eating and purging behaviours . Poor maternal care was independently positively associated with binging and purging but only interacted significantly with the rs2254298 A allele, carriers of which were four times more likely to engage in binging/purging (p = .03). The study’s strengths lie in its large sample size and longitudinal design, which allowed for evaluation of eating behaviours over time; however, the authors recognise that given the low frequency of certain eating behaviours, the sample may not have been sufficiently powered to identify small associations.In a community sample comprised of 3698 women recruited as part of the ALSPAC, Micali et al. investigated the relationship between the haviours . The stuOXTR SNPs, which included rs53576 and rs2254298, the G allele of rs53576 was positively correlated with BN [OXTR gene SNPs and AN or BN.In a clinical sample of 90 women with bulimia nervosa (BN) examining six  with BN . HoweverOXTR SNPs in a sample of 124 females with and without ED found a positive correlation between rs53576 and rs2254298 in the A-allele carriers and the severity of ED symptomatology [A study investigating the link between ED symptomatology and five OXTR SNPs, including rs53576 and rs2254298, reported no significant effects with respect to either SNP [A further exploratory study in a community sample of 460 adults examined the association between overeating and seven ther SNP . HoweverOXTR rs53576 or rs2254298 and ED  [If an increased risk for a phenotype is conferred by an environmental factor, then a gene by environment (G x E) interaction applies. Only Micali et al. in their abovementioned study also addressed G x E interactions in relation to a disordered eating phenotype . They fop = .03) .OXTR rs53576 and rs2254298 SNPs. A longitudinal study of 192 children examined OXTR rs53576 and its interaction with socioeconomic status to predict the risk of childhood obesity [OXTR rs53576 × childhood adversity interaction have been investigated using fMRI and found to map to the ventral striatum in the reward area of the brain [OXTR polymorphisms and childhood environment on eating behaviours would be useful.A number of environmental factors that relate indirectly to ED or allied phenotypes, such as obesity, have also been explored via G x E studies of the  obesity . Authors obesity . This fi obesity –65. Alth obesity , the neuhe brain . In GG hhe brain . Intereshe brain . Given the brain , 69–81, he brain –86, so fThere are a number of difficulties regarding reliability, interpretation, and validity of candidate-gene association studies. Results are often not replicated, and it is not known how often failure to replicate has resulted in failure to publish. In addition, small sample sizes in both original and replication studies create problems of lack of power highlighted as particular problem for both candidate-gene research and neuroscience .OXTR SNPs. Few studies compare data between women and men, despite evidence of sex-specific effects [There are specific issues pertaining to candidate-gene research using  effects –91 and fOXTR SNPs are unlikely in themselves to explain complex eating disorders but may form part of a haplotype with other OXTR SNPs to affect the expression of and/or effectiveness of the OXTR. A growing body of G x E work is indicating that rs53576G homozygosity becomes disadvantageous for later mental health under early adverse conditions but further research to extend these findings to eating pathology is needed. Eating disorders are not genetic monoliths but complex behaviours arising from multigenetic-environment interactions over time and the GWAS approach would benefit this area of knowledge.Understanding an aetiologic role for oxytocin in the development of ED is important, not only for researchers, but also for clinicians and patients, with potential new treatment avenues becoming an option for the latter group. However, despite the association of rs53576 and rs2254298 with eating patterns in a non-clinical population study, so far, these SNPs have not been identified in genome-wide association studies examining eating behaviours or obesity. Individual


This paper aims to provide an analytical insight on the current state of knowledge on gender-based violence among people with disabilities, a topic where the level of data is relatively low. We briefly discuss the current research on: (a) the prevalence, risk factors and the theoretical approaches for gender-based violence among people with disabilities. (b) Service provision among people with disabilities who experience gender-based violence. (c) We also highlight areas where further research is required, the applicable theoretical approaches and provide an example on how Sweden is attempting to bridge this knowledge gap through implementing the Disability and Intimate-partner violence project (DIS-IPV) project. Gender-based violence (GBV) defined, as any physical, sexual and psychological harm remains a major public health problem despite numerous written political commitments, policies and programmes ,2. SociaThe few existing studies on GBV among PWDs indicate that PWDs are at equal or greater risk of GBV compared to their peers without disabilities –14. PWDsLooking at Sweden, GBV research among PWDs is still limited here as well. The existing data suggest that the nature of violence experienced differs by type of disability and gender . Men witThe health consequences of GBV among PWDs are yet another understudied area both globally and in Sweden. Intimate partner violence is associated with negative mental and physical health; effects include chronic gastrointestinal, gynaecologic, cardiovascular and mental health issues ,16. CorrFactors that increase the vulnerability of PWDs are multifaceted. Gender role attitudes are one of the key determinants that increase GBV vulnerability among women with disabilities ,18. SeveThe social context of disability is yet another key exposure to GBV among PWDs. Disabilities that require dependency on others for support are exploited by perpetrators to exercise power and control, which increases vulnerability to GBV . A studyStructural barriers increase the vulnerability to GBV among PWDs ,18. SuchWe identified two theoretical approaches that can prove useful in understanding GBV among PWDs. The first approach is using the intersectionality approach that views social identities such as gender, ability, race and sexuality as interdependent and interconnected . Such idThe second approach combines the social model of disability with the material feminism . The socEvidence indicates that GBV-related services offered to survivors by professional service providers can reduce the risk to severe and fatal violence , and thaIn Sweden, people exposed to GBV seeking professional help mainly turn to health care, to the social services and to non-governmental women’s shelters . Sweden’To address this research gap, we are currently implementing “the Disability and Intimate Partner Violence (DIS-IPV)“ project in Sweden. We focus on intimate partner violence (IPV) because it is one of the frequently reported forms of GBV among PWDs. The aim of this project is to advance knowledge on the needs of PWDs exposed to IPV by assessing how existing services address their needs. The findings of this project will help to strengthen access and improve the quality of IPV services in this population. This project reaches out to PWDs exposed to IPV and to service providers, including health-care professionals, police, social workers and staff at shelters responsible for delivering GBV-related services. Our study uses a mixed methods approach of in-depth interviews and a cross-sectional survey for data collection. We use the intersectionality framework to understand how factors related to gender and disability influence access to IPV-related services. Combining the social model and the material feminist framework is ideal in identifying gender inequalities in service provision that affect adequate access to services among women with disabilities. We anticipate a rich collection of experiences that we will analyse and share with the public health services and scholars in Sweden and elsewhere.GBV is rooted in gender inequalities and thus research on GBV among PWDs requires application of frameworks that consider the dimensions of gender and disability. Relevant analytical frameworks should put into account the gender power relations that create subordination of people with disabilities. The intersectionality framework allows underpinning the complex multidimensional factors that expose women PWDs to GBV. In addition, combining the social model and the material feminist framework is ideal as it clearly illustrates that all women whether with disability or not have vulnerabilities that are used by perpetrators to exert power and control; however, disability adds an additional layer of vulnerability. The identified research gaps include a lack of data on GBV prevalence, risk factors and consequences. Existing research on GBV does not fully encompass all PWDs as it lacks disaggregation by gender, type of disabilities and other social categories such as ethnicity-racialization, sexual identity orientation or expression. We identified a critical need to evaluate how existing services address the needs of PWDs exposed to GBV because this evidence is almost non-existent. Future research on all aspects of GBV among PWDs will provide policy-relevant empirical evidence valuable in fostering political commitment and subsequent comprehensive public health engagement.


Although colorectal cancer (CRC) screening is effective in reducing CRC mortality, screening rates in vulnerable populations served by community health centers (CHCs) remain below national targets. CHCs in North Carolina are challenged to reach CRC screening targets as they tend to be under-resourced, have limited capacity to implement and sustain population health interventions, and typically operate independently from one another and from regional colonoscopy providers. The Scaling Colorectal Cancer Screening Through Outreach, Referral, and Engagement (SCORE) project is designed to address barriers to CRC screening in partnership with CHCs by implementing a multilevel intervention that includes centralized support infrastructure for mailed fecal immunochemical test (FIT) outreach and patient navigation to follow-up colonoscopy. This paper describes protocols for the SCORE implementation trial.We will conduct a type 2 hybrid effectiveness-implementation trial that will assess effectiveness at increasing CRC screening and follow-up rates while also assessing implementation outcomes. The planned trial sample will include 4000 CHC patients who are at average CRC risk and due for screening. Participants will be randomized 1:1 to receive either usual care or a multilevel intervention that includes mailed FIT outreach and patient navigation support to follow-up colonoscopy for those with abnormal FIT. The primary effectiveness outcome is completion of any CRC screening test at six months after randomization. We will also conduct a multilevel assessment of implementation outcomes and determinants.This hybrid effectiveness-implementation trial will evaluate the effectiveness and implementation of an intervention that provides centralized infrastructure for mailed FIT screening and patient navigation for CHCs that operate independently of other healthcare facilities. Findings from this research will enhance understanding of the effectiveness of a centralized approach and factors that determine successful implementation in vulnerable patient populations.ClinicalTrials.gov (identifier NCT04406714).The trial was registered on May 28, 2020, at  Contributions to the literatureThis study will rigorously evaluate a strategy of providing centralized support for two screening interventions—mailed FIT outreach and patient navigation—for two independent community health care systems. This study will examine the effectiveness and cost-effectiveness of this strategy in this context.This study will elucidate implementation barriers and facilitators related to implementing a centralized CRC screening program in a rural region with high CRC incidence and mortality.This study will demonstrate application of the Consolidated Framework for Implementation Research for understanding barriers and facilitators to implementing a centrally supported mailed FIT outreach and patient navigation program.Despite the availability of effective colorectal cancer (CRC) screening tests and national recommendations for their routine use , CRC remIn North Carolina, as in many parts of the USA, screening rates are particularly low among vulnerable and marginalized populations . The 201The United States Preventive Services Task Force (USPSTF) recommends several tests to screen for CRC, including colonoscopy and fecal blood tests such as fecal immunochemical testing (FIT), for patients ages 50–75 years . Mailed Inadequate follow-up after an abnormal (positive) FIT represents a key challenge to effective FIT-based CRC screening. To realize the potential of FIT as a screening modality, it is essential that a positive FIT is followed by a diagnostic (follow-up) colonoscopy. Regrettably, research suggests only 52–58% of patients served by CHCs complete a follow-up colonoscopy after a positive FIT result –22. Furtscreening colonoscopy completion  observation); (2) time logs; (3) self-administered questionnaires and guided interviews with clinic staff to assess labor investment for usual care activity, as well as intervention activity ; (4) self-administered questionnaires to assess study staff time spent on implementation activities that happen periodically , (5) review of meeting minutes to assess time spent in meetings to plan and monitor implementation, and (6) administrative/financial data to assess materials investments . We will not include time and resources used to develop existing CRC screening tools and patient-facing materials, but we will include such costs as pertinent to adapting these materials for the SCORE intervention and CHC settings. We will conduct in-depth interviews with patients with positive FIT results to understand the amount of time and opportunity costs associated with seeking follow-up colonoscopy and other care.Feasibility and fidelity. Using interviews, we will assess patient and clinician stakeholder perceptions that the SCORE intervention can be carried out successfully in the CHCs (feasibility) and the degree to which the SCORE intervention is delivered as intended (fidelity). We will also use tracking and call log data in the REDCap database to evaluate adherence to a set of prescribed protocols for implementing mailed FIT outreach and patient navigation. As part of our fidelity assessment, we will report the number of items mailed by date as part of the mailed FIT outreach component as well as when and how patients were notified of their FIT result. For the navigation component, we will report adherence to protocols for contacting patients to invite them into the navigation program, as well as dosage  for each patient in the intervention arm with a positive FIT result. We will conduct periodic reflections [lections  with CHCMultilevel implementation determinants. The Consolidated Framework for Implementation Research (CFIR) [h (CFIR)  guided tWe will use electronic health records, a REDCap database, surveys, interviews, observation, and periodic reflections to collect data for the SCORE project. Table REDCap database. Study personnel at UNC Lineberger will maintain a secure REDCap database that they populate with data from the clinics’ EHRs . Study personnel also will enter data related to intervention delivery into the REDCap database, including FIT outreach , FIT results, patient contact with the team, and patient navigation efforts.Electronic health records. Demographic, health history, and screening history data for eligible patients will be obtained via query of each clinic’s EHR and stored in the SCORE project’s REDCap database. Study personnel will assess CRC screening outcomes via manual EHR chart review and enter the data into REDCap. Study personnel will obtain FIT results and dates associated with sample collection and processing from the commercial laboratory’s online portal and will enter the data into the REDCap database.Surveys. We will conduct two brief surveys: a provider survey and a contextual determinants survey. We will administer the surveys at least six months after the SCORE trial launches to allow providers and clinic staff to have some experience with the SCORE intervention.To develop the provider survey, the study team drew upon items in existing instruments –49 as weAs part of an ACCSIS consortium-wide effort to assess factors that are posited to facilitate or impede implementation of a new CRC screening program , we co-developed a brief contextual determinants survey that we will administer to clinic staff who help implement quality improvement initiatives including SCORE. Survey items were drawn from existing surveys that applied CFIR constructs to assess the multilevel factors that influence CRC screening , 46, 47.Interviews. We will conduct semi-structured interviews with up to 20 clinician stakeholders  to facilitate interpretation of survey findings and to identify additional factors that may determine successful implementation. We used CFIR to guide the development of the provider interview guide [ew guide . We willObservation. We will conduct periodic episodes of direct observation (time and motion study) to assess costs of delivering the mailed FIT outreach component.Periodic reflections. Periodic reflections will be conducted approximately monthly as part of project meetings with CHC staff and program implementers, as well as with individual project staff. Reflections will aid in both understanding factors influencing implementation and capturing clinic-level adaptations to the intervention. The guide for these discussions was adapted from a template developed by Finley and colleagues [lleagues .We will follow the intention-to-treat principle  for our Cost data for the intervention and usual care alternatives will be aggregated across data sources, by activity, guided by our process flow diagrams. Costs will be categorized as fixed or variable and personnel or non-personnel (supplies/equipment) for micro-costing summaries. Calculations will report the total cost of the SCORE intervention, as well as cost per person reached and cost per person screened, compared to usual care. Sensitivity analyses will separately assess the value of reminder mailings and cost differentials by key groups .Interviews and periodic reflections will be audio-recorded and transcribed. We will use qualitative software  to organize and manage the data. The interview guide will serve as the foundation for developing an a priori codebook based on CFIR, with emergent codes added to the codebook as needed after reviewing and writing memos on the transcripts. Two team members will read and briefly summarize the interviews/reflections, will code separately, and meet to discuss codes and come to agreement on interpretation. Conflicting interpretations will be resolved through discussion with the larger team, as needed. We will use memo writing  and dataThe study statistician (XT) performed formal power calculations for the primary study outcome comparing CRC screening completion for the usual care arm vs. the intervention arm for each stratum defined by patient insurance status . These calculations assume equal numbers of participants at each site, in each arm, and in each stratum. Based on previous research , we aimeWe have presented a protocol describing planned pragmatic research to assess the effectiveness and implementation outcomes of a centralized intervention to improve CRC screening among vulnerable patient populations served by CHCs. Although previous research demonstrates that mailed FIT outreach and follow up is effective and can be implemented in large, integrated health care systems , the plaIn carrying out this research, we foresee encountering challenges common to pragmatic implementation studies, particularly when conducted in low-resource contexts. Some of the anticipated potential challenges include staffing turnover within CHCs, regulatory barriers to data sharing, changes in EHR systems, changing priorities and resources at the CHC level, and the emergence of new technologies, policies, and/or clinical guidelines relevant to CRC screening. Nevertheless, we also expect that the need to adapt our interventions and strategies in response to dynamic contextual challenges will also provide opportunities to study these adaptations rigorously, and this in turn will yield greater understanding of these complex implementation issues.The proposed study will take place as part of a larger consortium in collaboration with scientific partners from the National Cancer Institute, RTI International, and other funded research sites across the United States. As such, it will contribute to a “bigger picture” understanding of how to improve implementation of interventions to improve CRC screening in diverse, vulnerable populations in a variety of contexts. Thus, we anticipate that the individual and collective findings will accelerate progress in the fields of both cancer prevention and control and implementation science. We intend to disseminate these findings through publications in peer-reviewed journals and presentations at meetings with scientific and key stakeholder audiences.