Applying narrative medicine to prepare empathetic healthcare providers in undergraduate pharmacy education in Singapore: a mixed methods study.

BACKGROUND: Narrative medicine demonstrated positive impact on empathy in medicine and nursing students. However, this pedagogical approach had not been evaluated in pharmacy education. This study sought to apply and evaluate the narrative medicine approach in extending empathy in Asian undergraduate pharmacy students. METHODS: Narrative medicine was applied through workshops which used narratives of people with different experiences and perspectives. First-year undergraduate pharmacy students who volunteered and attended these workshops formed the intervention group (N = 31) and the remaining first-year cohort formed the control group (N = 112). A sequential explanatory mixed methods approach was adopted in which quantitative methods were first used to measure impact on pharmacy students' empathy using the Jefferson Scale of Empathy- Health Professions Student (JSE-HPS), and qualitative methods (i.e. group interviews) were then used to assess pharmacy students' emotional responses to narratives, and the perspectives of pharmacy students and faculty of this pedagogical approach. RESULTS: There was no difference in JSE-HPS scores between intervention and control groups across baseline (i.e. upon matriculation), pre-intervention, and post-intervention timepoints. Pharmacy students in the intervention group had lower scores in Factor 3 ("Standing in People's Shoes") following the intervention. Five themes, guided by internal and external factors in cognition, emerged from the Group Interviews: (1) incongruence between students' motivation and faculty's perception, (2) learning context, (3) academic context, (4) cognitive system, and (5) affective system. Themes 1, 4 and 5 referred to internal factors such as students' motivation, perceived learnings, and feelings. Themes 2 and 3 referred to external factors including workshop materials, activities, content, and facilitation. CONCLUSION: This study is the first to demonstrate that pharmacy students engaged with the narrative medicine approach as narratives elicited emotional responses, exposed them to diverse perspectives, and deepened their appreciation of the importance of empathy and complexities of understanding patients' perspectives. Scaffolded educational interventions using narratives and real-life patient encounters, alongside longitudinal measurements of empathy, are necessary to bring about meaningful and sustained improvements in empathy.

Differences in clinical presentations of patients seeking care for treatment-resistant depression across sexual orientations and gender identities.

BACKGROUND: Sexual and/or gender minority (SGM) individuals experience higher rates and greater severity of depressive disorders than non-SGM persons. SGM individuals are more likely than non-SGM individuals to seek mental health treatment and to present to treatment with unique characteristics that should be accounted for when considering treatment recommendations. Patients seeking care for treatment-resistant depression (TRD) are offered a variety of evidence-based interventions ranging in modality and invasiveness (eg, psychotherapy and neuromodulation). METHODS: The current study used data from a TRD clinical research program to examine whether SGM (N = 52) and non-SGM (N = 202) patients differed in their clinical presentations and the treatment recommendations offered to them. RESULTS: We found that SGM patients were younger, had a more severe history of childhood trauma, and reported greater current suicidality than non-SGM patients. There were no significant differences in treatment recommendations between groups. CONCLUSIONS: This study adds to nascent literature investigating clinical characteristics of SGM populations seeking mental health care and provides foundational evidence for the unique treatment considerations necessary for SGM individuals seeking treatment for TRD. Research into whether treatment outcomes differ for SGM and non-SGM individuals with TRD is encouraged, given clinical differences in trauma history and suicidality.

Monozygotic twins with identical premature timing of acne onset: A Case report.

Acne vulgaris, a common dermatological condition that affects most adolescents and young adults, can indicate an underlying pathology if present prematurely in mid-childhood. Premature acne can be caused by premature adrenarche secondary to non-classical congenital adrenal hyperplasia (NC-CAH), a condition arising from 21-hydroxylase deficiency. This report describes a pair of monozygotic twin brothers with identical premature onset of acne, who were found to have an identical homozygous mutation in the promoter region of the CYP21A2 gene. While it is widely known that NCCAH is associated with genetic changes, the drive behind onset of adrenarche are widely unknown. As such, this report provokes thoughts on whether adrenarche could be influenced by adrenal genetic polymorphisms.

The impact of adverse childhood experiences on adult depression severity and treatment outcomes.

BACKGROUND: Past research has established that adverse childhood experiences (ACE) are correlated with depression severity. The purpose of the present study was to examine how the number and nature of ACE exposure is associated with symptomatology and treatment outcomes in adult patients with treatment resistant depression (TRD). METHODS: Participants include 454 patients with a diagnosis of major depression or persistent depressive disorder. A one-way analysis of variance (ANOVA) was used to assess whether number of ACEs was associated with certain outcomes. Linear regression analyses were performed to model the associations between the five ACE subtypes (e.g., sexual abuse, physical violence, injury/illness, childhood grief, and parental upheaval) and symptom severity. Logistic regression analyses were then used to model the association between ACE subtypes and history of lifetime suicide attempt(s) and inpatient admission(s). RESULTS: Greater ACE exposure was associated with more severe symptomatology and treatment outcomes, but these differences were only seen between patients reporting no ACEs versus 3+ ACEs. Only the subtypes of violence and illness/injury were significant predictors of more severe symptomatology. The ACE subtypes of sexual trauma and violence uniquely predicted a lifetime suicide attempt(s), and only the subtype of sexual trauma predicted lifetime inpatient admission(s). LIMITATIONS: Limitations of the present study include retrospective adult assessments of childhood trauma, lack of data on ACE severity and timing, and the cross-sectional reporting of multiple study measures. CONCLUSIONS: Exposure to multiple ACE subtypes, particularly sexual and physical trauma, is associated with depression symptom severity, and history of suicidality, and inpatient admission(s).

Simulation and social network analysis provide insight into the acquisition of tool behaviour in hybrid macaques.

The pathways through which primates acquire skills are a central focus of cultural evolution studies. The roles of social and genetic inheritance processes in skill acquisition are often confounded by environmental factors. Hybrid macaques from Koram Island (Thailand) provide an opportunity to examine the roles of inheritance and social learning to skill acquisition within a single ecological setting. These hybrids are a cross between tool-using Burmese long-tailed (Macaca fascicularis aurea) and non-tool-using common long-tailed macaques (Macaca fascicularis fascicularis). This population provides an opportunity to explore the roles of social learning and inheritance processes while being able to exclude underlying ecological factors. Here, we investigate the roles of social learning and inheritance in tool use prevalence within this population using social network analysis and simulation. Agent-based modelling (ABM) is used to generate expectations for how social/asocial learning and inheritance structure the patterning in a social network. The results of the simulation show that various transmission mechanisms can be differentiated based on associations between individuals in a social network. The results provide an investigative framework for discussing tool use transmission pathways in the Koram social network. By combining ABM, network analysis, and behavioural data from the field we can investigate the roles social learning and inheritance play in tool acquisition of wild primates.

Tranexamic acid, as an adjunct to oxytocin prophylaxis, in the prevention of postpartum haemorrhage in women undergoing elective caesarean section: A single-centre double-blind randomised controlled trial.

OBJECTIVE: To evaluate the effectiveness of tranexamic acid (TXA) in reducing blood loss during elective caesarean sections in women with and without risk factors for postpartum haemorrhage (PPH). DESIGN: A double-blind, randomised placebo-controlled trial. SETTING: An academic tertiary referral centre in Singapore. POPULATION: Multiethnic women aged 21 years or older undergoing elective caesarean section. METHODS: Randomisation to intravenous TXA or normal saline (placebo) 10 minutes before skin incision. MAIN OUTCOME MEASURES: Calculated estimated blood loss (cEBL), derived from blood volume and haematocrit levels. RESULTS: Between June 2020 and October 2021, 200 women were randomised to the placebo or TXA groups. Women who received prophylactic TXA had a significantly lower mean cEBL compared with those receiving placebo (adjusted mean difference -126.4 mL, 95% CI -243.7 to -9.1, p = 0.035). The effect was greatest in those at high risk for PPH, with a reduction in cEBL (mean difference -279.6 mL, 95% CI -454.8 to -104.3, p = 0.002) and a lower risk of cEBL ≥500 mL (risk ratio [RR] 0.54, 95% CI 0.36-0.83, p = 0.007) and cEBL ≥1000 mL (RR 0.44, 95% CI 0.20-0.98, p = 0.016). Subgroup analysis showed benefit for women with preoperative haemoglobin <10.5 g/dL (mean difference -281.9 mL, 95% CI -515.0 to -48.8, p = 0.019). There was no significant difference in need for additional medical or surgical interventions. There were no maternal or neonatal adverse outcomes. CONCLUSION: Prophylactic TXA should be considered in women with risk factors for PPH, and those most likely to benefit are those with preoperative haemoglobin <10.5 g/dL.

Depression and anxiety in older adults with cancer: Systematic review and meta-summary of risk, protective and exacerbating factors.

OBJECTIVE: To systematically evaluate the risk factors of depression and anxiety in older adults with cancer. METHOD: This PRISMA-adherent systematic review (PROSPERO CRD42022372747) involved a systematic database search for prospective and retrospective cohort studies. RESULTS: We included 33 cohort studies with 31 evaluating depression and seven evaluating anxiety. Systematic synthesis yielded various protective and exacerbating factors for depression and anxiety amongst older adults with cancer. These factors span a range of domains: (1) Cancer and associated treatment-related factors; (2) Medical, physical and functional factors; (3) Demographic factors and; (4) Social and lifestyle factors. At the individual-level, the most significant factors were the presence of chronic medical comorbidities, having pre-existing psychological symptoms, and poor baseline physical and functional status. Within the social unit, the degree of social support and presence of a partner were most significant. CONCLUSION: The deleterious impact comorbid psychological symptoms can have on older adults with cancer can be profound. In this review, we highlight a range of protective and exacerbating factors identified from cohort studies that may enable policymakers to tailor and individualise interventions to manage depression, anxiety and associated burden in this vulnerable population. The relative paucity of studies evaluating anxiety highlights an important research gap.

Alzheimer's disease: Ablating single master site abolishes tau hyperphosphorylation.

Hyperphosphorylation of the neuronal tau protein is a hallmark of neurodegenerative tauopathies such as Alzheimer's disease. A central unanswered question is why tau becomes progressively hyperphosphorylated. Here, we show that tau phosphorylation is governed by interdependence- a mechanistic link between initial site-specific and subsequent multi-site phosphorylation. Systematic assessment of site interdependence identified distinct residues (threonine-50, threonine-69, and threonine-181) as master sites that determine propagation of phosphorylation at multiple epitopes. CRISPR point mutation and expression of human tau in Alzheimer's mice showed that site interdependence governs physiologic and amyloid-associated multi-site phosphorylation and cognitive deficits, respectively. Combined targeting of master sites and p38α, the most central tau kinase linked to interdependence, synergistically ablated hyperphosphorylation. In summary, our work delineates how complex tau phosphorylation arises to inform therapeutic and biomarker design for tauopathies.

Mortality among healthcare workers in Indonesia during 18 months of COVID-19.

The impact of SARS-CoV-2 infections upon Indonesian health care workers (HCWs) is unknown due to the lack of systematic collection and analysis of mortality data specific to HCWs in this setting. This report details the results of a systematic compilation, abstraction and analysis of HCW fatalities in Indonesia during the first 18 months of COVID-19. HCW who passed away between March 2020 and July 2021 were identified using Pusara Digital, a community-based digital cemetery database dedicated to HCW. We calculated the mortality rates and death risk ratio of HCWs versus the general population. The analysis indicates that at least 1,545 HCWs died during the study period. Death rates among males and females HCWs were nearly equivalent (51% vs. 49%). The majority were physicians and specialists (535, 35%), nurses (428, 28%), and midwives (359, 23%). Most deaths occurred between the ages of 40 to 59 years old, with the median age being 50 years (IQR: 39-59). At least 322 deaths (21%) occurred with pre-existing conditions, including 45 pregnant women. During the first 18 months of COVID-19 in Indonesia, we estimated a minimum HCW mortality rate of 1.707 deaths per 1,000 HCWs. The provincial rates of HCW mortality ranged from 0.136 (West Sulawesi) to 5.32 HCW deaths per 1,000 HCWs (East Java). The HCW mortality rate was significantly higher than that of the general population (RR = 4.92, 95% CI 4.67-5.17). The COVID-19 pandemic in Indonesia resulted in the loss of many hundreds of HCWs, the majority of whom were senior healthcare workers. The HCW mortality rate is five times that of the general population. A national systematic surveillance of occupational mortality is urgently needed in this setting.

Fractal generation in a two-dimensional active-nematic fluid.

Active fluids, composed of individual self-propelled agents, can generate complex large-scale coherent flows. A particularly important laboratory realization of such an active fluid is a system composed of microtubules, aligned in a quasi-two-dimensional (2D) nematic phase and driven by adenosine-triphosphate-fueled kinesin motor proteins. This system exhibits robust chaotic advection and gives rise to a pronounced fractal structure in the nematic contours. We characterize such experimentally derived fractals using the power spectrum and discover that the power spectrum decays as k-ß for large wavenumbers k. The parameter ß is measured for several experimental realizations. Though ß is effectively constant in time, it does vary with experimental parameters, indicating differences in the scale-free behavior of the microtubule-based active nematic. Though the fractal patterns generated in this active system are reminiscent of passively advected dye in 2D chaotic flows, the underlying mechanism for fractal generation is more subtle. We provide a simple, physically inspired mathematical model of fractal generation in this system that relies on the material being locally compressible, though the total area of the material is conserved globally. The model also requires that large-scale density variations are injected into the material periodically. The model reproduces the power-spectrum decay k-ß seen in experiments. Linearizing the model of fractal generation about the equilibrium density, we derive an analytic relationship between ß and a single dimensionless quantity r, which characterizes the compressibility.

Ultra-brief right unilateral electroconvulsive therapy for the treatment of late-life bipolar disorder.

BACKGROUND: Bipolar Affective Disorder (BPAD) accounts for 10-25% of all mood disorders in the geriatric population and 5% of all inpatient admissions to geropsychiatric units. Electroconvulsive therapy (ECT) is an effective treatment for all phases of BPAD, though only a few studies have focused on BPAD in the geriatric population. This study examines the safety and efficacy of ultra-brief right unilateral (UBRUL) ECT for patients with late-life bipolar depression (BD). METHODS: A retrospective chart review was conducted of patients with late-life BD who received UBRUL ECT treatments. Symptomatic response was measured using pre- and post-ECT Quick Inventory of Depressive Symptomatology (QIDS-SR16) and Beck Depression Inventory (BDI-II) scores. Clinical improvement and cognitive change were measured using Clinical Global Impression-Improvement (CGI-I) and Electroconvulsive Cognitive Assessment (ECCA) scores. RESULTS: Twenty-Seven elderly patients (mean age 69.1 ± 7.7 years) were included in the analysis. Baseline QIDS-SR16 was 17.3 ± 5.3 and BDI-II 30.0 ± 9.2. 80.0% (16/20) and 57.1% (4/7) of patients achieved response (50.0% decline) in their QIDS-SR16 and BDI-II scores, respectively. Remission rates in QIDS-SR16 (post-ECT scores ≤5) and BDI-II (post-ECT scores ≤12) were 65.0% (13/20) and 42.9% (3/7), respectively. Mean QIDS-SR16 and BDI-II scores were reduced by a statistically significant 68.2% and 50.5%, respectively (two-tailed, paired p-values <0.01) after ECT. CGI-I of ≤2 was attained by 85.2% (23/27) of patients. 85.7% (12/14) of patients saw no change or improvement in ECCA scores. LIMITATIONS: Inherent complications of chart review regarding quality, availability, and homogeny of data. CONCLUSIONS: UBRUL ECT is a safe and effective treatment for patients presenting with late-life BD.

Presenting symptoms of COVID-19 and clinical outcomes in hospitalised older adults.

BACKGROUND: In July 2020, a COVID-19 outbreak was recognised in the geriatric wards at a subacute campus of the Royal Melbourne Hospital affecting patients and staff. Patients were also admitted to this site after diagnosis in residential care. AIMS: To describe the early symptoms and the outcomes of COVID-19 in older adults. METHODS: Patients diagnosed with COVID-19 at the facility in July or August 2020 were identified and their medical records were examined to identify symptoms present before and after their diagnosis and to determine their outcomes. RESULTS: Overall, 106 patients were identified as having COVID-19, with median age of 84.3 years (range 41-104 years); 64 were diagnosed as hospital inpatients after a median length of stay of 49 days, 31 were transferred from residential aged care facilities with a known diagnosis and 11 were diagnosed after discharge. There were 95 patients included in an analysis of symptom type and timing onset. Overall, 61 (64.2%) were asymptomatic at the time of diagnosis of COVID-19, having been diagnosed through screening initiated on site. Of these, 88.6% developed symptoms of COVID-19 within 14 days. The most common initial symptom type was respiratory, but there was wide variation in presentation, including fever, gastrointestinal and neurological symptoms, many initially not recognised as being due to COVID-19. Of 104 patients, 32 died within 30 days of diagnosis. CONCLUSIONS: COVID-19 diagnosis is challenging due to the variance in symptoms. In the context of an outbreak, asymptomatic screening can identify affected patients early in the disease course.

Experiences and needs of parents of palliative paediatric oncology patients: A meta-synthesis.

INTRODUCTION: Despite palliative care being offered to paediatric cancer patients, it has limited utilisation and often excludes parental support. Therefore, this review aims to consolidate evidence regarding experiences and needs of parents of end-of-life palliative paediatric oncology patients. METHODS: Six electronic databases were searched as follows: CINAHL, The Cochrane Library, Embase, PubMed, Scopus and PsycINFO. Included studies were appraised using the Critical Appraisal Skills Programme Checklist. They were then analysed using a two-step approach comprising firstly meta-summaries followed by meta-synthesis for generating fresh insights to the topic. RESULTS: Thirteen studies were included. Three themes emerged as follows: (1) normalising the pain; (2) failure as a parent; and (3) importance of communication and social support. Parental experiences included moving on despite the pain and harbouring hopes for their children. However, parents felt immense guilt and a sense of failure in carrying out their parental roles. Effective communication with healthcare providers, availability of family support and religion were necessary to help them cope. CONCLUSIONS: Given the emotional challenges faced by parents, healthcare policies and practices should be revised to include parental support in paediatric palliative care services. Future healthcare communication trainings should consider parental need for sensitivity in communication, empathy and kindness from healthcare professionals.

Functions of p38 MAP Kinases in the Central Nervous System.

Mitogen-activated protein (MAP) kinases are a central component in signaling networks in a multitude of mammalian cell types. This review covers recent advances on specific functions of p38 MAP kinases in cells of the central nervous system. Unique and specific functions of the four mammalian p38 kinases are found in all major cell types in the brain. Mechanisms of p38 activation and downstream phosphorylation substrates in these different contexts are outlined and how they contribute to functions of p38 in physiological and under disease conditions. Results in different model organisms demonstrated that p38 kinases are involved in cognitive functions, including functions related to anxiety, addiction behavior, neurotoxicity, neurodegeneration, and decision making. Finally, the role of p38 kinases in psychiatric and neurological conditions and the current progress on therapeutic inhibitors targeting p38 kinases are covered and implicate p38 kinases in a multitude of CNS-related physiological and disease states.

Reduction of advanced tau-mediated memory deficits by the MAP kinase p38γ.

Hyperphosphorylation of the neuronal tau protein contributes to Alzheimer's disease (AD) by promoting tau pathology and neuronal and cognitive deficits. In contrast, we have previously shown that site-specific tau phosphorylation can inhibit toxic signals induced by amyloid-ß (Aß) in mouse models. The post-synaptic mitogen-activated protein (MAP) kinase p38γ mediates this site-specific phosphorylation on tau at Threonine-205 (T205). Using a gene therapeutic approach, we draw on this neuroprotective mechanism to improve memory in two Aß-dependent mouse models of AD at stages when advanced memory deficits are present. Increasing activity of post-synaptic kinase p38γ that targets T205 in tau reduced memory deficits in symptomatic Aß-induced AD models. Reconstitution experiments with wildtype human tau or phosphorylation-deficient tauT205A showed that T205 modification is critical for downstream effects of p38γ that prevent memory impairment in APP-transgenic mice. Furthermore, genome editing of the T205 codon in the murine Mapt gene showed that this single side chain in endogenous tau critically modulates memory deficits in APP-transgenic Alzheimer's mice. Ablating the protective effect of p38γ activity by genetic p38γ deletion in a tau transgenic mouse model that expresses non-pathogenic tau rendered tau toxic and resulted in impaired memory function in the absence of human Aß. Thus, we propose that modulating neuronal p38γ activity serves as an intrinsic tau-dependent therapeutic approach to augment compromised cognition in advanced dementia.

Renal functional effects of the highly selective AT2R agonist, ß-Pro7 Ang III, in normotensive rats.

Recently, we designed a group of peptides by sequential substitution of the naturally occurring α-amino acid throughout the Ang III peptide sequence with the corresponding ß-amino acid. ß-Amino acid substitution at the proline residue of Ang III (ß-Pro7-Ang III) resulted in a highly selective AT2R ligand, demonstrating remarkable selectivity for the AT2R in both binding and functional studies. To provide additional functional evidence for the suitability of ß-Pro7 Ang III as a novel AT2R agonist, we tested effects of acute systemic administration of ß-Pro7-Ang III on renal hemodynamic and excretory function in anesthetized normotensive male and female rats. We also compared the natriuretic effects of acute intrarenal administration of native Ang III and ß-Pro7-Ang III in the presence of systemic AT1R blockade in anesthetized female rats to allow for the differentiation of systemic versus direct intrarenal natriuretic actions of ß-Pro7-Ang III. In both male and female rats, acute systemic administration of ß-Pro7-Ang III elicited renal vasodilatation and natriuresis. Notably, greater renal vasodilatory effects were observed in female versus male rats at the highest dose of ß-Pro7-Ang III administered. Moreover, intra-renal administration of ß-Pro7-Ang III produced significant natriuretic effects in female rats and, like Ang III, evoked AT2R translocation to the apical plasma membrane in renal proximal tubular cells. Taken together, our findings support the use of ß-Pro7-Ang III as a novel AT2R agonist and experimental tool for exploring AT2R function and its potential as a therapeutic target. Furthermore, our findings provide further evidence of a sex-specific influence of AT2R stimulation on renal function.

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic.

The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still ongoing, which is exacerbated by discrepancies in reporting. To uncover locations with lingering outbreaks, we investigated travel-associated Zika cases to identify transmission not captured by reporting. We uncovered an unreported outbreak in Cuba during 2017, a year after peak transmission in neighboring islands. By sequencing Zika virus, we show that the establishment of the virus was delayed by a year and that the ensuing outbreak was sparked by long-lived lineages of Zika virus from other Caribbean islands. Our data suggest that, although mosquito control in Cuba may initially have been effective at mitigating Zika virus transmission, such measures need to be maintained to be effective. Our study highlights how Zika virus may still be "silently" spreading and provides a framework for understanding outbreak dynamics. VIDEO ABSTRACT.

Autoimmunity in psychotic disorders. Where we stand, challenges and opportunities.

Psychotic disorders are debilitating mental illnesses associated with abnormalities in various neurotransmitter systems. The development of disease-modifing therapies has been hampered by the mostly unknown etiologies and pathophysiologies. Autoantibodies against several neuronal antigens are responsible for autoimmune encephalitis. These autoantibodies disrupt neurotransmission within the brain, resulting in a wide range of psychiatric and neurologic manifestations, including psychosis. The overlap of symptoms of autoimmune encephalitis with psychotic disorders raised the question as to whether autoantibodies against a number of receptors, ion channel and associated proteins could ultimately be responsible for some forms of psychosis. Here we review our current knowledge, on antibody mediated autoimmunity in psychotic disorders, the different diagnostic methods and their limitations, as well as on varying therapeutic approaches targeting the immune system.

Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.

Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.