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The COVID-19 pandemic has highlighted the need to upgrade systems for infectious disease surveillance and forecasting and modeling of the spread of infection, both of which inform evidence-based public health guidance and policies. Here, we discuss requirements for an effective surveillance system to support decision making during a pandemic, drawing on the lessons of COVID-19 in the U.S., while looking to jurisdictions in the U.S. and beyond to learn lessons about the value of specific data types. In this report, we define the range of decisions for which surveillance data are required, the data elements needed to inform these decisions and to calibrate inputs and outputs of transmission-dynamic models, and the types of data needed to inform decisions by state, territorial, local, and tribal health authorities. We define actions needed to ensure that such data will be available and consider the contribution of such efforts to improving health equity.
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COVID-19 , Humanos , COVID-19/epidemiología , Estados Unidos/epidemiología , SARS-CoV-2 , Pandemias , Vigilancia de la Población , Salud PúblicaRESUMEN
Despite long-running efforts to increase gender diversity among tenured and tenure-track faculty in the U.S., women remain underrepresented in most academic fields, sometimes dramatically so. Here, we quantify the relative importance of faculty hiring and faculty attrition for both past and future faculty gender diversity using comprehensive data on the training and employment of 268,769 tenured and tenure-track faculty rostered at 12,112U.S. PhD-granting departments, spanning 111 academic fields between 2011 and 2020. Over this time, we find that hiring had a far greater impact on women's representation among faculty than attrition in the majority (90.1%) of academic fields, even as academia loses a higher share of women faculty relative to men at every career stage. Finally, we model the impact of five specific policy interventions on women's representation, and project that eliminating attrition differences between women and men only leads to a marginal increase in women's overall representation-in most fields, successful interventions will need to make substantial and sustained changes to hiring in order to reach gender parity.
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Docentes , Selección de Personal , Humanos , Femenino , Masculino , Docentes/estadística & datos numéricos , Estados Unidos , Universidades , Sexismo/estadística & datos numéricos , Movilidad LaboralRESUMEN
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus but delayed by up to two days to control omicron-era severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, while rapid tests are superior to reverse transcription quantitative polymerase chain reaction (RT-qPCR) to control founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Last, we illustrate the model's flexibility by quantifying trade-offs in the use of post-diagnosis testing to shorten isolation times.
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COVID-19 , SARS-CoV-2 , Humanos , COVID-19/transmisión , COVID-19/diagnóstico , COVID-19/virología , COVID-19/prevención & control , COVID-19/epidemiología , SARS-CoV-2/aislamiento & purificación , SARS-CoV-2/genética , Prueba de COVID-19/métodos , Enfermedades Transmisibles/transmisión , Enfermedades Transmisibles/diagnóstico , Enfermedades Transmisibles/virología , Gripe Humana/diagnóstico , Gripe Humana/virología , Gripe Humana/transmisión , Gripe Humana/epidemiología , Gripe Humana/prevención & control , Infecciones por Virus Sincitial Respiratorio/diagnóstico , Infecciones por Virus Sincitial Respiratorio/virología , Infecciones por Virus Sincitial Respiratorio/transmisión , Modelos TeóricosRESUMEN
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus (RSV), but delayed by up to 2d to control omicron-era SARS-CoV-2. Furthermore, while rapid tests are superior to RT-qPCR for control of founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Finally, we illustrate the model's flexibility by quantifying tradeoffs in the use of post-diagnosis testing to shorten isolation times.
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The COVID-19 pandemic demonstrated the poor ability of body temperature to reliably identify SARS-CoV-2-infected individuals, an observation that has been made before in the context of other infectious diseases. While acute infection does not always cause fever, it does reliably drive host transcriptional responses as the body responds at the site of infection. These transcriptional changes can occur both in cells that are directly harboring replicating pathogens and in cells elsewhere that receive a molecular signal that infection is occurring. Here, we identify a core set of approximately 70 human genes that are together upregulated in cultured human cells infected by a broad array of viral, bacterial, and fungal pathogens. We have named these "core response" genes. In theory, transcripts from these genes could serve as biomarkers of infection in the human body, in a way that is agnostic to the specific pathogen causing infection. As such, we perform human studies to show that these infection-induced human transcripts can be measured in the saliva of people harboring different types of infections. The number of these transcripts in saliva can correctly classify infection status (whether a person harbors an infection) 91% of the time. Furthermore, in the case of SARS-CoV-2 specifically, the number of core response transcripts in saliva correctly identifies infectious individuals even when enrollees, themselves, are asymptomatic and do not know they are infected.IMPORTANCEThere are a variety of clinical and laboratory criteria available to clinicians in controlled healthcare settings to help them identify whether an infectious disease is present. However, in situations such as a new epidemic caused by an unknown infectious agent, in health screening contexts performed within communities and outside of healthcare facilities or in battlefield or potential biowarfare situations, this gets more difficult. Pathogen-agnostic methods for rapid screening and triage of large numbers of people for infection status are needed, in particular methods that might work on an easily accessible biospecimen like saliva. Here, we identify a small, core set of approximately 70 human genes whose transcripts serve as saliva-based biomarkers of infection in the human body, in a way that is agnostic to the specific pathogen causing infection.
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Women remain underrepresented among faculty in nearly all academic fields. Using a census of 245,270 tenure-track and tenured professors at United States-based PhD-granting departments, we show that women leave academia overall at higher rates than men at every career age, in large part because of strongly gendered attrition at lower-prestige institutions, in non-STEM fields, and among tenured faculty. A large-scale survey of the same faculty indicates that the reasons faculty leave are gendered, even for institutions, fields, and career ages in which retention rates are not. Women are more likely than men to feel pushed from their jobs and less likely to feel pulled toward better opportunities, and women leave or consider leaving because of workplace climate more often than work-life balance. These results quantify the systemic nature of gendered faculty retention; contextualize its relationship with career age, institutional prestige, and field; and highlight the importance of understanding the gendered reasons for attrition rather than focusing on rates alone.
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Academic fields exhibit substantial levels of gender segregation. Here, we investigated differences in field-specific ability beliefs (FABs) as an explanation for this phenomenon. FABs may contribute to gender segregation to the extent that they portray success as depending on "brilliance" (i.e., exceptional intellectual ability), which is a trait culturally associated with men more than women. Although prior work has documented a relation between academic fields' FABs and their gender composition, it is still unclear what the underlying dynamics are that give rise to gender imbalances across academia as a function of FABs. To provide insight into this issue, we custom-built a new data set by combining information from the author-tracking service Open Researcher and Contributor ID (ORCID) with information from a survey of U.S. academics across 30 fields. Using this expansive longitudinal data set (Ns = 86,879-364,355), we found that women were underrepresented among those who enter fields with brilliance-oriented FABs and overrepresented among those who exit these fields. We also found that FABs' association with women's transitions across academic fields was substantially stronger than their association with men's transitions. With respect to mechanisms, FABs' association with gender segregation was partially explained by the fact that women encounter more prejudice in fields with brilliance-oriented FABs. With its focus on the dynamic patterns shaping segregation and its broad scope in terms of geography, career stage, and historical time, this research makes an important contribution toward understanding the factors driving gender segregation in academia. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
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Ocupaciones , Sexismo , Masculino , Humanos , Femenino , Factores SexualesRESUMEN
Faculty at prestigious institutions dominate scientific discourse, producing a disproportionate share of all research publications. Environmental prestige can drive such epistemic disparity, but the mechanisms by which it causes increased faculty productivity remain unknown. Here, we combine employment, publication, and federal survey data for 78,802 tenure-track faculty at 262 PhD-granting institutions in the American university system to show through multiple lines of evidence that the greater availability of funded graduate and postdoctoral labor at more prestigious institutions drives the environmental effect of prestige on productivity. In particular, greater environmental prestige leads to larger faculty-led research groups, which drive higher faculty productivity, primarily in disciplines with group collaboration norms. In contrast, productivity does not increase substantially with prestige for faculty publications without group members or for group members themselves. The disproportionate scientific productivity of elite researchers can be largely explained by their substantial labor advantage rather than inherent differences in talent.
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Emergence of a novel pathogen drives the urgent need for diagnostic tests that can aid in defining disease prevalence. The limitations associated with rapid development and deployment of these tests result in a dilemma: In efforts to optimize prevalence estimates, would tests be better used in the lab to reduce uncertainty in test characteristics or to increase sample size in field studies? Here, we provide a framework to address this question through a joint Bayesian model that simultaneously analyzes lab validation and field survey data, and we define the impact of test allocation on inferences of sensitivity, specificity, and prevalence. In many scenarios, prevalence estimates can be most improved by apportioning additional effort towards validation rather than to the field. The joint model provides superior estimation of prevalence, sensitivity, and specificity, compared with typical analyses that model lab and field data separately, and it can be used to inform sample allocation when testing is limited.
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Sensibilidad y Especificidad , Teorema de Bayes , Prevalencia , Tamaño de la MuestraRESUMEN
Faculty hiring and retention determine the composition of the US academic workforce and directly shape educational outcomes1, careers2, the development and spread of ideas3 and research priorities4,5. However, hiring and retention are dynamic, reflecting societal and academic priorities, generational turnover and efforts to diversify the professoriate along gender6-8, racial9 and socioeconomic10 lines. A comprehensive study of the structure and dynamics of the US professoriate would elucidate the effects of these efforts and the processes that shape scholarship more broadly. Here we analyse the academic employment and doctoral education of tenure-track faculty at all PhD-granting US universities over the decade 2011-2020, quantifying stark inequalities in faculty production, prestige, retention and gender. Our analyses show universal inequalities in which a small minority of universities supply a large majority of faculty across fields, exacerbated by patterns of attrition and reflecting steep hierarchies of prestige. We identify markedly higher attrition rates among faculty trained outside the United States or employed by their doctoral university. Our results indicate that gains in women's representation over this decade result from demographic turnover and earlier changes made to hiring, and are unlikely to lead to long-term gender parity in most fields. These analyses quantify the dynamics of US faculty hiring and retention, and will support efforts to improve the organization, composition and scholarship of the US academic workforce.
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Docentes , Selección de Personal , Universidades , Recursos Humanos , Educación de Postgrado/estadística & datos numéricos , Empleo/estadística & datos numéricos , Docentes/estadística & datos numéricos , Femenino , Humanos , Masculino , Selección de Personal/estadística & datos numéricos , Grupos Raciales/estadística & datos numéricos , Factores Socioeconómicos , Estados Unidos , Universidades/estadística & datos numéricos , Mujeres , Recursos Humanos/estadística & datos numéricosRESUMEN
Counting the number of species, items, or genes that are shared between two groups, sets, or communities is a simple calculation when sampling is complete. However, when only partial samples are available, quantifying the overlap between two communities becomes an estimation problem. Furthermore, to calculate normalized measures of ß-diversity, such as the Jaccard and Sorenson-Dice indices, one must also estimate the total sizes of the communities being compared. Previous efforts to address these problems have assumed knowledge of total community sizes and then used Bayesian methods to produce unbiased estimates with quantified uncertainty. Here, we address communities of unknown size and show that this produces systematically better estimates-both in terms of central estimates and quantification of uncertainty in those estimates. We further show how to use species, item, or gene count data to refine estimates of community size in a Bayesian joint model of community size and overlap.
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Teorema de Bayes , IncertidumbreRESUMEN
Despite the special role of tenure-track faculty in society, training future researchers and producing scholarship that drives scientific and technological innovation, the sociodemographic characteristics of the professoriate have never been representative of the general population. Here we systematically investigate the indicators of faculty childhood socioeconomic status and consider how they may limit efforts to diversify the professoriate. Combining national-level data on education, income and university rankings with a 2017-2020 survey of 7,204 US-based tenure-track faculty across eight disciplines in STEM, social science and the humanities, we show that faculty are up to 25 times more likely to have a parent with a Ph.D. Moreover, this rate nearly doubles at prestigious universities and is stable across the past 50 years. Our results suggest that the professoriate is, and has remained, accessible disproportionately to the socioeconomically privileged, which is likely to deeply shape their scholarship and their reproduction.
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Docentes , Becas , Humanos , Niño , Universidades , Factores SocioeconómicosRESUMEN
Screening programs that test only the unvaccinated population have been proposed and implemented to mitigate SARS-CoV-2 spread, implicitly assuming that the unvaccinated population drives transmission. To evaluate this premise and quantify the impact of unvaccinated-only screening programs, we introduce a model for SARS-CoV-2 transmission through which we explore a range of transmission rates, vaccine effectiveness scenarios, rates of prior infection, and screening programs. We find that, as vaccination rates increase, the proportion of transmission driven by the unvaccinated population decreases, such that most community spread is driven by vaccine-breakthrough infections once vaccine coverage exceeds 55% (omicron) or 80% (delta), points which shift lower as vaccine effectiveness wanes. Thus, we show that as vaccination rates increase, the transmission reductions associated with unvaccinated-only screening decline, identifying three distinct categories of impact on infections and hospitalizations. More broadly, these results demonstrate that effective unvaccinated-only screening depends on population immunity, vaccination rates, and variant.
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COVID-19 , SARS-CoV-2 , COVID-19/epidemiología , COVID-19/prevención & control , Vacunas contra la COVID-19 , Hospitalización , Humanos , Complicaciones Posoperatorias , VacunaciónRESUMEN
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths around the world within the past 2 years. Transmission within the United States has been heterogeneously distributed by geography and social factors with little data from North Carolina. Here, we describe results from a weekly cross-sectional study of 12,471 unique hospital remnant samples from 19 April to 26 December 2020 collected by four clinical sites within the University of North Carolina Health system, with a majority of samples from urban, outpatient populations in central North Carolina. We employed a Bayesian inference model to calculate SARS-CoV-2 spike protein immunoglobulin prevalence estimates and conditional odds ratios for seropositivity. Furthermore, we analyzed a subset of these seropositive samples for neutralizing antibodies. We observed an increase in seroprevalence from 2.9 (95% confidence interval [CI], 1.8 to 4.5) to 12.8 (95% CI, 10.6 to 15.2) over the course of the study. Latinx individuals had the highest odds ratio of SARS-CoV-2 exposure at 6.56 (95% CI, 4.66 to 9.44). Our findings aid in quantifying the degree of asymmetric SARS-CoV-2 exposure by ethnoracial grouping. We also find that 49% of a subset of seropositive individuals had detectable neutralizing antibodies, which was skewed toward those with recent respiratory infection symptoms. IMPORTANCE PCR-confirmed SARS-CoV-2 cases underestimate true prevalence. Few robust community-level SARS-CoV-2 ethnoracial and overall prevalence estimates have been published for North Carolina in 2020. Mortality has been concentrated among ethnoracial minorities and may result from a high likelihood of SARS-CoV-2 exposure, which we observe was particularly high among Latinx individuals in North Carolina. Additionally, neutralizing antibody titers are a known correlate of protection. Our observation that development of SARS-CoV-2 neutralizing antibodies may be inconsistent and dependent on severity of symptoms makes vaccination a high priority despite prior exposure.
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COVID-19 , SARS-CoV-2 , Anticuerpos Neutralizantes , Teorema de Bayes , COVID-19/epidemiología , Estudios Transversales , Humanos , North Carolina/epidemiología , Estudios Seroepidemiológicos , Glicoproteína de la Espiga del CoronavirusRESUMEN
Community testing programs focused on the unvaccinated population are being enacted in populations with mixed vaccination status to mitigate SARS-CoV-2 spread. Presumably, these policies assume that the unvaccinated are driving transmission, though it is not well understood how viral spread occurs in mixed-status populations. Here, we analyze a model of transmission in which a variable fraction of the population is vaccinated, with unvaccinated individuals proactively screened for infection. By exploring a range of transmission rates, vaccine effectiveness (VE) scenarios, and rates of prior infection, this analysis reveals principles of viral spread in communities of mixed vaccination status, with implications for screening policies. As vaccination rates increase, the proportion of transmission driven by the unvaccinated population decreases, such that most community spread is driven by breakthrough infections once vaccine coverage exceeds 55% (omicron) or 80% (delta), with additional variation dependent on waning or boosted VE. More broadly, the potential impacts of unvaccinated-only screening fall into three distinct parameter regions: (I) "flattening the curve" with little impact on cumulative infections, (II) effectively suppressing transmission, and (III) negligible impact because herd immunity is reached without screening. By evaluating a wide range of scenarios, this work finds broadly that effective mitigation of SARS-CoV-2 transmission by unvaccinated-only screening is highly dependent on vaccination rate, population-level immunity, screening compliance, and vaccine effectiveness against the current variant.
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BACKGROUND: The coronavirus disease 2019 pandemic spread to >200 countries in <6 months. To understand coronavirus spread, determining transmission rate and defining factors that increase transmission risk are essential. Most cases are asymptomatic, but people with asymptomatic infection have viral loads indistinguishable from those in symptomatic people, and they do transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, asymptomatic cases are often undetected. METHODS: Given high residence hall student density, the University of Colorado Boulder established a mandatory weekly screening test program. We analyzed longitudinal data from 6408 students and identified 116 likely transmission events in which a second roommate tested positive within 14 days of the index roommate. RESULTS: Although the infection rate was lower in single-occupancy rooms (10%) than in multiple-occupancy rooms (19%), interroommate transmission occurred only about 20% of the time. Cases were usually asymptomatic at the time of detection. Notably, individuals who likely transmitted had an average viral load approximately 6.5-fold higher than individuals who did not (mean quantification cycle [Cq], 26.2 vs 28.9). Although students with diagnosed SARS-CoV-2 infection moved to isolation rooms, there was no difference in time to isolation between cases with or without interroommate transmission. CONCLUSIONS: This analysis argues that interroommate transmission occurs infrequently in residence halls and provides strong correlative evidence that viral load is proportional to transmission probability.
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Infecciones Asintomáticas/epidemiología , COVID-19/transmisión , SARS-CoV-2/patogenicidad , Carga Viral , COVID-19/diagnóstico , COVID-19/epidemiología , COVID-19/virología , Humanos , Pandemias/prevención & control , Pandemias/estadística & datos numéricos , SARS-CoV-2/aislamiento & purificación , Estudiantes , Adulto JovenRESUMEN
Analysing social networks is challenging. Key features of relational data require the use of non-standard statistical methods such as developing system-specific null, or reference, models that randomize one or more components of the observed data. Here we review a variety of randomization procedures that generate reference models for social network analysis. Reference models provide an expectation for hypothesis testing when analysing network data. We outline the key stages in producing an effective reference model and detail four approaches for generating reference distributions: permutation, resampling, sampling from a distribution, and generative models. We highlight when each type of approach would be appropriate and note potential pitfalls for researchers to avoid. Throughout, we illustrate our points with examples from a simulated social system. Our aim is to provide social network researchers with a deeper understanding of analytical approaches to enhance their confidence when tailoring reference models to specific research questions.
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Proyectos de Investigación , Análisis de Redes SocialesRESUMEN
A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Molecular tests that detect viral RNAs or antigens will be unable to rise to this challenge unless testing capacity increases by at least an order of magnitude while decreasing turnaround times. Here, we evaluate an alternative strategy based on the monitoring of olfactory dysfunction, a symptom identified in 76-83% of SARS-CoV-2 infections-including those with no other symptoms-when a standardized olfaction test is used. We model how screening for olfactory dysfunction, with reflexive molecular tests, could be beneficial in reducing community spread of SARS-CoV-2 by varying testing frequency and the prevalence, duration, and onset time of olfactory dysfunction. We find that monitoring olfactory dysfunction could reduce spread via regular screening, and could reduce risk when used at point-of-entry for single-day events. In light of these estimated impacts, and because olfactory tests can be mass produced at low cost and self-administered, we suggest that screening for olfactory dysfunction could be a high impact and cost-effective method for broad COVID-19 screening and surveillance.
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Anosmia/diagnóstico , COVID-19/etiología , COVID-19/transmisión , Anosmia/epidemiología , Anosmia/virología , COVID-19/prevención & control , Prueba de Ácido Nucleico para COVID-19 , Control de Enfermedades Transmisibles , Análisis Costo-Beneficio , Humanos , Tamizaje Masivo/economía , Tamizaje Masivo/métodos , Modelos Teóricos , Prevalencia , Factores de Tiempo , Carga ViralRESUMEN
Background: Robust community-level SARS-CoV-2 prevalence estimates have been difficult to obtain in the American South and outside of major metropolitan areas. Furthermore, though some previous studies have investigated the association of demographic factors such as race with SARS-CoV-2 exposure risk, fewer have correlated exposure risk to surrogates for socioeconomic status such as health insurance coverage. Methods: We used a highly specific serological assay utilizing the receptor binding domain of the SARS-CoV-2 spike-protein to identify SARS-CoV-2 antibodies in remnant blood samples collected by the University of North Carolina Health system. We estimated the prevalence of SARS-CoV-2 in this cohort with Bayesian regression, as well as the association of critical demographic factors with higher prevalence odds. Findings: Between April 21st and October 3rd of 2020, a total of 9,624 unique samples were collected from clinical sites in central NC and we observed a seroprevalence increase from 2·9 (1·7, 4·3) to 9·1 (7·2, 11·1) over the study period. Individuals who identified as Latinx were associated with the highest odds ratio of SARS-CoV-2 exposure at 7·77 overall (5·20, 12·10). Increased odds were also observed among Black individuals and individuals without public or private health insurance. Interpretation: Our data suggests that for this care-accessing cohort, SARS-CoV-2 seroprevalence was significantly higher than cumulative total cases reported for the study geographical area six months into the COVID-19 pandemic in North Carolina. The increased odds of seropositivity by ethnoracial grouping as well as health insurance highlights the urgent and ongoing need to address underlying health and social disparities in these populations.