A study of SARS-COV-2 outbreaks in US federal prisons: the linkage between staff, incarcerated populations, and community transmission

Background

Since the novel coronavirus SARS-COV-2 was first identified to be circulating in the US on January 20, 2020, some of the worst outbreaks have occurred within state and federal prisons. The vulnerability of incarcerated populations, and the additional threats posed to the health of prison staff and the people they contact in surrounding communities underline the need to better understand the dynamics of transmission in the inter-linked incarcerated population/staff/community sub-populations to better inform optimal control of SARS-COV-2.

Methods

We examined SARS-CoV-2 case data from 101 non-administrative federal prisons between 5/18/2020 to 01/31/2021 and examined the per capita size of outbreaks in staff and the incarcerated population compared to outbreaks in the communities in the counties surrounding the prisons during the summer and winter waves of the SARS-COV-2 pandemic. We also examined the impact of decarceration on per capita rates in the staff/incarcerated/community populations.

Results

For both the summer and winter waves we found significant inter-correlations between per capita rates in the outbreaks among the incarcerated population, staff, and the community.

Over-all during the pandemic, per capita rates were significantly higher in the incarcerated population than in both the staff and community (paired Student’s t-test p = 0.03 and p < 0.001, respectively). Average per capita rates of incarcerated population outbreaks were significantly associated with prison security level, ranked from lowest per capita rate to highest: High, Minimum, Medium, and Low security.

Federal prisons decreased the incarcerated population by a relative factor of 96% comparing the winter to summer wave (one SD range [90%,102%]). We found no significant impact of decarceration on per capita rates of SARS-COV-2 infection in the staff community populations, but decarceration was significantly associated with a decrease in incarcerated per capita rates during the winter wave (Negative Binomial regression p = 0.015).

Conclusions

We found significant evidence of community/staff/incarcerated population inter-linkage of SARS-COV-2 transmission. Further study is warranted to determine which control measures aimed at the incarcerated population and/or staff are most efficacious at preventing or controlling outbreaks.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-12813-w.

Geodemographic insights on the COVID-19 pandemic in the State of Wisconsin and the role of risky facilities

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to impact the United States. While age and comorbid health conditions remain primary concerns in the community-based transmission of the virus, empirical evidence continues to suggest that substantial variability exists in the geographic and geodemographic distribution of COVID-19 infection rates. The purpose of this paper is to provide an alternative, spatiotemporal perspective on the pandemic using the state of Wisconsin as a case study. Specifically, in this paper, we explore the geographic nuances of COVID-19 and its spread in Wisconsin using a suite of spatial statistical approaches. We link detected hot spots of COVID-19 to local geodemographic profiles and the presence of high-risk facilities, including federal and state correctional facilities. The results suggest that the virus disproportionately impacts several communities and geodemographic groups and that proximity to risky facilities correlates to increased community infection rates.

Factors influencing temporal patterns in crime in a large American city: A predictive analytics perspective

BACKGROUND

Improving the accuracy and precision of predictive analytics for temporal trends in crime necessitates a good understanding of the how exogenous variables, such as weather and holidays, impact crime.

METHODS

We examine 5.7 million reported incidents of crime that occurred in the City of Chicago between 2001 to 2014. Using linear regression methods, we examine the temporal relationship of the crime incidents to weather, holidays, school vacations, day-of-week, and paydays. We correct the data for dominant sources of auto-correlation, and we then employ bootstrap methods for model selection. Importantly for the aspect of predictive analytics, we validate the predictive capabilities of our model on an independent data set; model validation has been almost universally overlooked in the literature on this subject.

RESULTS

We find significant dependence of crime on time of year, holidays, and weekdays. We find that dependence of aggressive crime on temperature depends on the hour of the day, and whether it takes place outside or inside. In addition, unusually hot/cold days are associated with unusual fluctuations upwards/downwards in crimes of aggression, respectively, regardless of the time of year.

CONCLUSIONS

Including holidays, festivals, and school holiday periods in crime predictive analytics software can improve the accuracy and precision of temporal predictions. We also find that including forecasts for temperature may significantly improve short term crime forecasts for the temporal trends in many types of crime, particularly aggressive crime.

Detecting the contagion effect in mass killings; a constructive example of the statistical advantages of unbinned likelihood methods

Background

When attempting to statistically distinguish between a null and an alternative hypothesis, many researchers in the life and social sciences turn to binned statistical analysis methods, or methods that are simply based on the moments of a distribution (such as the mean, and variance). These methods have the advantage of simplicity of implementation, and simplicity of explanation.

However, when null and alternative hypotheses manifest themselves in subtle differences in patterns in the data, binned analysis methods may be insensitive to these differences, and researchers may erroneously fail to reject the null hypothesis when in fact more sensitive statistical analysis methods might produce a different result when the null hypothesis is actually false.

Here, with a focus on two recent conflicting studies of contagion in mass killings as instructive examples, we discuss how the use of unbinned likelihood methods makes optimal use of the information in the data; a fact that has been long known in statistical theory, but perhaps is not as widely appreciated amongst general researchers in the life and social sciences.

Methods

In 2015, Towers et al published a paper that quantified the long-suspected contagion effect in mass killings. However, in 2017, Lankford & Tomek subsequently published a paper, based upon the same data, that claimed to contradict the results of the earlier study. The former used unbinned likelihood methods, and the latter used binned methods, and comparison of distribution moments.

Using these analyses, we also discuss how visualization of the data can aid in determination of the most appropriate statistical analysis methods to distinguish between a null and alternate hypothesis. We also discuss the importance of assessment of the robustness of analysis results to methodological assumptions made (for example, arbitrary choices of number of bins and bin widths when using binned methods); an issue that is widely overlooked in the literature, but is critical to analysis reproducibility and robustness.

Conclusions

When an analysis cannot distinguish between a null and alternate hypothesis, care must be taken to ensure that the analysis methodology itself maximizes the use of information in the data that can distinguish between the two hypotheses.

The use of binned methods by Lankford & Tomek (2017), that examined how many mass killings fell within a 14 day window from a previous mass killing, substantially reduced the sensitivity of their analysis to contagion effects. The unbinned likelihood methods used by Towers et al (2015) did not suffer from this problem.

While a binned analysis might be favorable for simplicity and clarity of presentation, unbinned likelihood methods are preferable when effects might be somewhat subtle.

Quantifying the relative effects of environmental and direct transmission of norovirus

Norovirus is a common cause of outbreaks of acute gastroenteritis in health- and child-care settings, with serial outbreaks also frequently observed aboard cruise ships. The relative contributions of environmental and direct person-to-person transmission of norovirus have hitherto not been quantified. We employ a novel mathematical model of norovirus transmission, and fit the model to daily incidence data from a major norovirus outbreak on a cruise ship, and examine the relative efficacy of potential control strategies aimed at reducing environmental and/or direct transmission. The reproduction number for environmental and direct transmission combined is [Formula: see text] [6.1,9.5], and of environmental transmission alone is [Formula: see text] [0.9,2.6]. Direct transmission is overwhelmingly due to passenger-to-passenger contacts, but crew can act as a reservoir of infection from cruise to cruise. This is the first quantification of the relative roles of environmental and direct transmission of norovirus. While environmental transmission has the potential to maintain a sustained series of outbreaks aboard a cruise ship in the absence of strict sanitation practices, direct transmission dominates. We find that intensive promotion of good hand washing practices may prevent outbreaks. Isolation of ill passengers and cleaning are beneficial, but appear to be less efficacious at outbreak control.

Fear-related behaviors in situations of mass threat

This Disaster Health Briefing focuses on the work of an expanding team of researchers that is exploring the dynamics of fear-related behaviors in situations of mass threat. Fear-related behaviors are individual or collective behaviors and actions initiated in response to fear reactions that are triggered by a perceived threat or actual exposure to a potentially traumatizing event. Importantly, fear-related behaviors modulate the future risk of harm. Disaster case scenarios are presented to illustrate how fear-related behaviors operate when a potentially traumatic event threatens or endangers the physical and/or psychological health, wellbeing, and integrity of a population. Fear-related behaviors may exacerbate harm, leading to severe and sometimes deadly consequences as exemplified by the Ebola pandemic in West Africa. Alternatively, fear-related behaviors may be channeled in a constructive and life-saving manner to motivate protective behaviors that mitigate or prevent harm, depending upon the nature of the threat scenario that is confronting the population. The interaction between fear-related behaviors and a mass threat is related to the type, magnitude, and consequences of the population encounter with the threat or hazard. The expression of FRBs, ranging from risk exacerbation to risk reduction, is also influenced by such properties of the threat as predictability, familiarity, controllability, preventability, and intentionality.

The Role of Fear-Related Behaviors in the 2013-2016 West Africa Ebola Virus Disease Outbreak

The 2013-2016 West Africa Ebola virus disease pandemic was the largest, longest, deadliest, and most geographically expansive outbreak in the 40-year interval since Ebola was first identified. Fear-related behaviors played an important role in shaping the outbreak. Fear-related behaviors are defined as "individual or collective behaviors and actions initiated in response to fear reactions that are triggered by a perceived threat or actual exposure to a potentially traumatizing event. FRBs modify the future risk of harm." This review examines how fear-related behaviors were implicated in (1) accelerating the spread of Ebola, (2) impeding the utilization of life-saving Ebola treatment, (3) curtailing the availability of medical services for treatable conditions, (4) increasing the risks for new-onset psychological distress and psychiatric disorders, and (5) amplifying the downstream cascades of social problems. Fear-related behaviors are identified for each of these outcomes. Particularly notable are behaviors such as treating Ebola patients in home or private clinic settings, the "laying of hands" on Ebola-infected individuals to perform faith-based healing, observing hands-on funeral and burial customs, foregoing available life-saving treatment, and stigmatizing Ebola survivors and health professionals. Future directions include modeling the onset, operation, and perpetuation of fear-related behaviors and devising strategies to redirect behavioral responses to mass threats in a manner that reduces risks and promotes resilience.

Estimate of the reproduction number of the 2015 Zika virus outbreak in Barranquilla, Colombia, and estimation of the relative role of sexual transmission

BACKGROUND

In 2015, the Zika arbovirus (ZIKV) began circulating in the Americas, rapidly expanding its global geographic range in explosive outbreaks. Unusual among mosquito-borne diseases, ZIKV has been shown to also be sexually transmitted, although sustained autochthonous transmission due to sexual transmission alone has not been observed, indicating the reproduction number (R0) for sexual transmission alone is less than 1. Critical to the assessment of outbreak risk, estimation of the potential attack rates, and assessment of control measures, are estimates of the basic reproduction number, R0.

METHODS

We estimated the R0 of the 2015 ZIKV outbreak in Barranquilla, Colombia, through an analysis of the exponential rise in clinically identified ZIKV cases (n=359 to the end of November, 2015).

FINDINGS

The rate of exponential rise in cases was ρ=0.076days^-1, with 95% CI [0.066,0.087] days^-1. We used a vector-borne disease model with additional direct transmission to estimate the R0; assuming the R0 of sexual transmission alone is less than 1, we estimated the total R0=3.8 [2.4,5.6], and that the fraction of cases due to sexual transmission was 0.23 [0.01,0.47] with 95% confidence.

INTERPRETATION

This is among the first estimates of R0 for a ZIKV outbreak in the Americas, and also among the first quantifications of the relative impact of sexual transmission.

Modeling the role of healthcare access inequalities in epidemic outcomes

Urban areas, with large and dense populations, offer conditions that favor the emergence and spread of certain infectious diseases. One common feature of urban populations is the existence of large socioeconomic inequalities which are often mirrored by disparities in access to healthcare. Recent empirical evidence suggests that higher levels of socioeconomic inequalities are associated with worsened public health outcomes, including higher rates of sexually transmitted diseases (STD's) and lower life expectancy. However, the reasons for these associations are still speculative. Here we formulate a mathematical model to study the effect of healthcare disparities on the spread of an infectious disease that does not confer lasting immunity, such as is true of certain STD's. Using a simple epidemic model of a population divided into two groups that differ in their recovery rates due to different levels of access to healthcare, we find that both the basic reproductive number (R0) of the disease and its endemic prevalence are increasing functions of the disparity between the two groups, in agreement with empirical evidence. Unexpectedly, this can be true even when the fraction of the population with better access to healthcare is increased if this is offset by reduced access within the disadvantaged group. Extending our model to more than two groups with different levels of access to healthcare, we find that increasing the variance of recovery rates among groups, while keeping the mean recovery rate constant, also increases R0 and disease prevalence. In addition, we show that these conclusions are sensitive to how we quantify the inequalities in our model, underscoring the importance of basing analyses on appropriate measures of inequalities. These insights shed light on the possible impact that increasing levels of inequalities in healthcare access can have on epidemic outcomes, while offering plausible explanations for the observed empirical patterns.

Some models for epidemics of vector-transmitted diseases

Vector-transmitted diseases such as dengue fever and chikungunya have been spreading rapidly in many parts of the world. The Zika virus has been known since 1947 and invaded South America in 2013. It can be transmitted not only by (mosquito) vectors but also directly through sexual contact. Zika has developed into a serious global health problem because, while most cases are asymptomatic or very light, babies born to Zika - infected mothers may develop microcephaly and other very serious birth defects. We formulate and analyze two epidemic models for vector-transmitted diseases, one appropriate for dengue and chikungunya fever outbreaks and one that includes direct transmission appropriate for Zika virus outbreaks. This is especially important because the Zika virus is the first example of a disease that can be spread both indirectly through a vector and directly (through sexual contact). In both cases, we obtain expressions for the basic reproduction number and show how to use the initial exponential growth rate to estimate the basic reproduction number. However, for the model that includes direct transmission some additional data would be needed to identify the fraction of cases transmitted directly. Data for the 2015 Zika virus outbreak in Barranquilla, Colombia has been used to fit parameters to the model developed here and to estimate the basic reproduction number.

Per capita incidence of sexually transmitted infections increases systematically with urban population size: a cross-sectional study

OBJECTIVES

Rampant urbanisation rates across the globe demand that we improve our understanding of how infectious diseases spread in modern urban landscapes, where larger and more connected host populations enhance the thriving capacity of certain pathogens.

METHODS

A data-driven approach is employed to study the ability of sexually transmitted diseases (STDs) to thrive in urban areas. The conduciveness of population size of urban areas and their socioeconomic characteristics are used as predictors of disease incidence, using confirmed-case data on STDs in the USA as a case study.

RESULTS

A superlinear relation between STD incidence and urban population size is found, even after controlling for various socioeconomic aspects, suggesting that doubling the population size of a city results in an expected increase in STD incidence larger than twofold, provided that all other socioeconomic aspects remain fixed. Additionally, the percentage of African-Americans, income inequalities, education and per capita income are found to have a significant impact on the incidence of each of the three STDs studied.

CONCLUSIONS

STDs disproportionately concentrate in larger cities. Hence, larger urban areas merit extra prevention and treatment efforts, especially in low-income and middle-income countries where urbanisation rates are higher.

Mass Measurement of 56Sc Reveals a Small A = 56 Odd-Even Mass Staggering, Implying a Cooler Accreted Neutron Star Crust

We present the mass excesses of (52-57)Sc, obtained from recent time-of-flight nuclear mass measurements at the National Superconducting Cyclotron Laboratory at Michigan State University. The masses of 56Sc and 57Sc were determined for the first time with atomic mass excesses of -24.85(59)((-54)(+0))  MeV and -21.0(1.3)  MeV, respectively, where the asymmetric uncertainty for 56Sc was included due to possible contamination from a long-lived isomer. The 56Sc mass indicates a small odd-even mass staggering in the A = 56 mass chain towards the neutron drip line, significantly deviating from trends predicted by the global FRDM mass model and favoring trends predicted by the UNEDF0 and UNEDF1 density functional calculations. Together with new shell-model calculations of the electron-capture strength function of 56Sc, our results strongly reduce uncertainties in model calculations of the heating and cooling at the 56Ti electron-capture layer in the outer crust of accreting neutron stars. We find that, in contrast to previous studies, neither strong neutrino cooling nor strong heating occurs in this layer. We conclude that Urca cooling in the outer crusts of accreting neutron stars that exhibit superbursts or high temperature steady-state burning, which are predicted to be rich in A≈56 nuclei, is considerably weaker than predicted. Urca cooling must instead be dominated by electron capture on the small amounts of adjacent odd-A nuclei contained in the superburst and high temperature steady-state burning ashes. This may explain the absence of strong crust Urca cooling inferred from the observed cooling light curve of the transiently accreting x-ray source MAXI J0556-332.

Contagion in Mass Killings and School Shootings

Background

Several past studies have found that media reports of suicides and homicides appear to subsequently increase the incidence of similar events in the community, apparently due to the coverage planting the seeds of ideation in at-risk individuals to commit similar acts.

Methods

Here we explore whether or not contagion is evident in more high-profile incidents, such as school shootings and mass killings (incidents with four or more people killed). We fit a contagion model to recent data sets related to such incidents in the US, with terms that take into account the fact that a school shooting or mass murder may temporarily increase the probability of a similar event in the immediate future, by assuming an exponential decay in contagiousness after an event.

Conclusions

We find significant evidence that mass killings involving firearms are incented by similar events in the immediate past. On average, this temporary increase in probability lasts 13 days, and each incident incites at least 0.30 new incidents (p = 0.0015). We also find significant evidence of contagion in school shootings, for which an incident is contagious for an average of 13 days, and incites an average of at least 0.22 new incidents (p = 0.0001). All p-values are assessed based on a likelihood ratio test comparing the likelihood of a contagion model to that of a null model with no contagion. On average, mass killings involving firearms occur approximately every two weeks in the US, while school shootings occur on average monthly. We find that state prevalence of firearm ownership is significantly associated with the state incidence of mass killings with firearms, school shootings, and mass shootings.

Rates of influenza-like illness and winter school breaks, Chile, 2004-2010

To determine effects of school breaks on influenza virus transmission in the Southern Hemisphere, we analyzed 2004-2010 influenza-like-illness surveillance data from Chile. Winter breaks were significantly associated with a two-thirds temporary incidence reduction among schoolchildren, which supports use of school closure to temporarily reduce illness, especially among schoolchildren, in the Southern Hemisphere.

Mass measurements demonstrate a strong N=28 shell gap in argon

We present results from recent time-of-flight nuclear mass measurements at the National Superconducting Cyclotron Laboratory at Michigan State University. We report the first mass measurements of ^{48}Ar and ^{49}Ar and find atomic mass excesses of -22.28(31)  MeV and -17.8(1.1)  MeV, respectively. These masses provide strong evidence for the closed shell nature of neutron number N=28 in argon, which is therefore the lowest even-Z element exhibiting the N=28 closed shell. The resulting trend in binding-energy differences, which probes the strength of the N=28 shell, compares favorably with shell-model calculations in the sd-pf shell using SDPF-U and SDPF-MU Hamiltonians.

Proactive Spatiotemporal Resource Allocation and Predictive Visual Analytics for Community Policing and Law Enforcement

In this paper, we present a visual analytics approach that provides decision makers with a proactive and predictive environment in order to assist them in making effective resource allocation and deployment decisions. The challenges involved with such predictive analytics processes include end-users' understanding, and the application of the underlying statistical algorithms at the right spatiotemporal granularity levels so that good prediction estimates can be established. In our approach, we provide analysts with a suite of natural scale templates and methods that enable them to focus and drill down to appropriate geospatial and temporal resolution levels. Our forecasting technique is based on the Seasonal Trend decomposition based on Loess (STL) method, which we apply in a spatiotemporal visual analytics context to provide analysts with predicted levels of future activity. We also present a novel kernel density estimation technique we have developed, in which the prediction process is influenced by the spatial correlation of recent incidents at nearby locations. We demonstrate our techniques by applying our methodology to Criminal, Traffic and Civil (CTC) incident datasets.

Temporal variations in the effective reproduction number of the 2014 west Africa ebola outbreak

Background The rapidly evolving 2014 Ebola virus disease (EVD) outbreak in West Africa is the largest documented in history, both in terms of the number of people infected and in the geographic spread. The high morbidity and mortality have inspired response strategies to the outbreak at the individual, regional, and national levels. Methods to provide real-time assessment of changing transmission dynamics are critical to the understanding of how these adaptive intervention measures have affected the spread of the outbreak. Methods In this analysis, we use the time series of EVD cases in Guinea, Sierra Leone, and Liberia up to September 8, 2014, and employ novel methodology to estimate how the rate of exponential rise of new cases has changed over the outbreak using piecewise fits of exponential curves to the outbreak data. Results We find that for Liberia and Guinea, the effective reproduction number rose, rather than fell, around the time that the outbreak spread to densely populated cities, and enforced quarantine was imposed on several regions in the countries; this may indicate that enforced quarantine may not be an effective control measure. Conclusions If effective control measures are not put in place, and the current rate of exponential rise of new cases continues, we predict 4400 new Ebola cases in West Africa during the last half of the month of September, with an upper 95% confidence level of 6800 new cases.

Transmission potential of influenza A/H7N9, February to May 2013, China

BACKGROUND

On 31 March 2013, the first human infections with the novel influenza A/H7N9 virus were reported in Eastern China. The outbreak expanded rapidly in geographic scope and size, with a total of 132 laboratory-confirmed cases reported by 3 June 2013, in 10 Chinese provinces and Taiwan. The incidence of A/H7N9 cases has stalled in recent weeks, presumably as a consequence of live bird market closures in the most heavily affected areas. Here we compare the transmission potential of influenza A/H7N9 with that of other emerging pathogens and evaluate the impact of intervention measures in an effort to guide pandemic preparedness.

METHODS

We used a Bayesian approach combined with a SEIR (Susceptible-Exposed-Infectious-Removed) transmission model fitted to daily case data to assess the reproduction number (R) of A/H7N9 by province and to evaluate the impact of live bird market closures in April and May 2013. Simulation studies helped quantify the performance of our approach in the context of an emerging pathogen, where human-to-human transmission is limited and most cases arise from spillover events. We also used alternative approaches to estimate R based on individual-level information on prior exposure and compared the transmission potential of influenza A/H7N9 with that of other recent zoonoses.

RESULTS

Estimates of R for the A/H7N9 outbreak were below the epidemic threshold required for sustained human-to-human transmission and remained near 0.1 throughout the study period, with broad 95% credible intervals by the Bayesian method (0.01 to 0.49). The Bayesian estimation approach was dominated by the prior distribution, however, due to relatively little information contained in the case data. We observe a statistically significant deceleration in growth rate after 6 April 2013, which is consistent with a reduction in A/H7N9 transmission associated with the preemptive closure of live bird markets. Although confidence intervals are broad, the estimated transmission potential of A/H7N9 appears lower than that of recent zoonotic threats, including avian influenza A/H5N1, swine influenza H3N2sw and Nipah virus.

CONCLUSION

Although uncertainty remains high in R estimates for H7N9 due to limited epidemiological information, all available evidence points to a low transmission potential. Continued monitoring of the transmission potential of A/H7N9 is critical in the coming months as intervention measures may be relaxed and seasonal factors could promote disease transmission in colder months.

A deterministic model for influenza infection with multiple strains and antigenic drift

We describe a multiple strain Susceptible Infected Recovered deterministic model for the spread of an influenza subtype within a population. The model incorporates appearance of new strains due to antigenic drift, and partial immunity to reinfection with related circulating strains. It also includes optional seasonal forcing of the transmission rate of the virus, which allows for comparison between temperate zones and the tropics. Our model is capable of reproducing observed qualitative patterns such as the overall annual outbreaks in the temperate region, a reduced magnitude and an increased frequency of outbreaks in the tropics, and the herald wave phenomenon. Our approach to modelling antigenic drift is novel and further modifications of this model may help improve the understanding of complex influenza dynamics.

Climate change and influenza: the likelihood of early and severe influenza seasons following warmer than average winters

The 2012-13 influenza season had an unusually early and severe start in the US, succeeding the record mild 2011-12 influenza season, which occurred during the fourth warmest winter on record. Our analysis of climate and past US influenza epidemic seasons between 1997-98 to present indicates that warm winters tend to be followed by severe epidemics with early onset, and that these patterns are seen for both influenza A and B. We posit that fewer people are infected with influenza during warm winters, thereby leaving an unnaturally large fraction of susceptible individuals in the population going into the next season, which can lead to early and severe epidemics. In the event of continued global warming, warm winters such as that of 2011-12 are expected to occur more frequently. Our results thus suggest that expedited manufacture and distribution of influenza vaccines after mild winters has the potential to mitigate the severity of future influenza epidemics.

The influence of climatic conditions on the transmission dynamics of the 2009 A/H1N1 influenza pandemic in Chile

Background

The role of demographic factors, climatic conditions, school cycles, and connectivity patterns in shaping the spatio-temporal dynamics of pandemic influenza is not clearly understood. Here we analyzed the spatial, age and temporal evolution of the 2009 A/H1N1 influenza pandemic in Chile, a southern hemisphere country covering a long and narrow strip comprising latitudes 17°S to 56°S.

Methods

We analyzed the dissemination patterns of the 2009 A/H1N1 pandemic across 15 regions of Chile based on daily hospitalizations for severe acute respiratory disease and laboratory confirmed A/H1N1 influenza infection from 01-May to 31-December, 2009. We explored the association between timing of pandemic onset and peak pandemic activity and several geographical and demographic indicators, school vacations, climatic factors, and international passengers. We also estimated the reproduction number (R) based on the growth rate of the exponential pandemic phase by date of symptoms onset, estimated using maximum likelihood methods.

Results

While earlier pandemic onset was associated with larger population size, there was no association with connectivity, demographic, school or climatic factors. In contrast, there was a latitudinal gradient in peak pandemic timing, representing a 16-39-day lag in disease activity from the southern regions relative to the northernmost region (P < 0.001). Geographical differences in latitude of Chilean regions, maximum temperature and specific humidity explained 68.5% of the variability in peak timing (P = 0.01). In addition, there was a decreasing gradient in reproduction number from south to north Chile (P < 0.0001). The regional mean R estimates were 1.6-2.0, 1.3-1.5, and 1.2-1.3 for southern, central and northern regions, respectively, which were not affected by the winter vacation period.

Conclusions

There was a lag in the period of most intense 2009 pandemic influenza activity following a South to North traveling pattern across regions of Chile, significantly associated with geographical differences in minimum temperature and specific humidity. The latitudinal gradient in timing of pandemic activity was accompanied by a gradient in reproduction number (P < 0.0001). Intensified surveillance strategies in colder and drier southern regions could lead to earlier detection of pandemic influenza viruses and improved control outcomes.

Social contact patterns and control strategies for influenza in the elderly

Despite dramatic increases in influenza vaccination coverage in the elderly population over the past 30 years, influenza mortality rates have remained static in this age group. Children are believed to be the primary spreaders of diseases such as influenza due to their high degree of inter-contact in school settings, and several studies have examined control of influenza in the entire population, including the elderly, via targeted vaccination of school children. However, such vaccination programs are expensive, and fraught with difficulties of public perception of what may be seen as an unnecessary vaccination against a disease that is normally mild in the children themselves. In the study presented here, we examine the control of influenza in the elderly using simple social distancing measures during an influenza epidemic. The recent work of Glasser et al. characterizes daily contact interactions within the population in terms of preferential mixing between age group peers, co-workers, and parents and children. We expand upon this to include interactions between grandparents and grandchildren, and fit the parameters of this formulation to the recently published social contact survey data of Mossong et al. Using this formulation, we then model an influenza epidemic with an age-structured deterministic disease model and examine how reduction in contacts between grandchildren and grandparents affects the spread of influenza to the elderly. We find that over 50% of all influenza infections in the elderly are caused by direct contact with an infected child, and we determine that social distancing between grandparents and grandchildren is remarkably effective, and is capable of reducing influenza attack rates in the elderly by up to 60%.

The impact of school closures on pandemic influenza: Assessing potential repercussions using a seasonal SIR model

When a new pandemic influenza strain has been identified, mass-production of vaccines can take several months, and antiviral drugs are expensive and usually in short supply. Social distancing measures, such as school closures, thus seem an attractive means to mitigate disease spread. However, the transmission of influenza is seasonal in nature, and as has been noted in previous studies, a decrease in the average transmission rate in a seasonal disease model may result in a larger final size. In the studies presented here, we analyze a hypothetical pandemic using a SIR epidemic model with time- and age-dependent transmission rates; using this model we assess and quantify, for the first time, the the effect of the timing and length of widespread school closures on influenza pandemic final size and average peak time. We find that the effect on pandemic progression strongly depends on the timing of the start of the school closure. For instance, we determine that school closures during a late spring wave of an epidemic can cause a pandemic to become up to 20% larger, but have the advantage that the average time of the peak is shifted by up to two months, possibly allowing enough time for development of vaccines to mitigate the larger size of the epidemic. Our studies thus suggest that when heterogeneity in transmission is a significant factor, decisions of public health policy will be particularly important as to how control measures such as school closures should be implemented.

Modeling the effects of vaccination and treatment on pandemic influenza

In this paper, we demonstrate the uses of some simple mathematical models for the study of disease dynamics in a pandemic situation with a focus on influenza. These models are employed to evaluate the effectiveness of various control programs via vaccination and antiviral treatment. We use susceptible-, infectious-, recovered-type epidemic models consisting of ordinary differential equations. These models allow us to derive threshold conditions that can be used to assess the effectiveness of vaccine and drug use and to determine disease outcomes. Simulations are helpful for examining the potential consequences of control options under different scenarios. Particularly, results from models with constant parameters and models with time-dependent parameter functions are compared, demonstrating the significant differences in model outcomes. Results suggest that the effectiveness of vaccination and drug treatment can be very sensitive to factors including the time of introduction of the pathogen into the population, the beginning time of control programs, and the levels of control measures. More importantly, in some cases, the benefits of vaccination and antiviral use might be significantly compromised if these control programs are not designed appropriately. Mathematical models can be very useful for understanding the effects of various factors on the spread and control of infectious diseases. Particularly, the models can help identify potential adverse effects of vaccination and drug treatment in the case of pandemic influenza.

Antiviral treatment for pandemic influenza: assessing potential repercussions using a seasonally forced SIR model

When resources are limited, measures to control an incipient influenza pandemic must be carefully considered. Because several months are needed to mass-produce vaccines once a new pandemic strain has been identified, antiviral drugs are often considered the first line of defense in a pandemic situation. Here we use an SIR disease model with periodic transmission rate to assess the efficacy of control strategies via antiviral drug treatment during an outbreak of pandemic influenza. We show that in some situations, and independent of drug-resistance effects, antiviral treatment can have a detrimental impact on the final size of the pandemic. Antiviral treatment also has the potential to increase the size of the major peak of the pandemic, and cause it to occur earlier than it would have if treatment were not used. Our studies suggest that when a disease exhibits periodic patterns in transmission, decisions of public health policy will be particularly important as to how control measures such as drug treatment should be implemented, and to what end (i.e.; towards immediate control of a current epidemic peak, or towards potential delay and/or reduction of an anticipated autumn peak).

Pandemic H1N1 influenza: predicting the course of a pandemic and assessing the efficacy of the planned vaccination programme in the United States

We use data on confirmed cases of pandemic influenza A(H1N1), disseminated by the United States Centers for Disease Control and Prevention(US CDC), to fit the parameters of a seasonally forced Susceptible, Infective, Recovered (SIR) model. We use the resulting model to predict the course of the H1N1 influenza pandemic in autumn 2009, and we assess the efficacy of the planned CDC H1N1 vaccination campaign. The model predicts that there will be a significant wave in autumn, with 63% of the population being infected, and that this wave will peak so early that the planned CDC vaccination campaign will likely not have a large effect on the total number of people ultimately infected by the pandemic H1N1 influenza virus.

Pandemic H1N1 influenza: predicting the course of a pandemic and assessing the efficacy of the planned vaccination programme in the United States

We use data on confirmed cases of pandemic influenza A(H1N1), disseminated by the United States Centers for Disease Control and Prevention(US CDC), to fit the parameters of a seasonally forced Susceptible, Infective, Recovered (SIR) model. We use the resulting model to predict the course of the H1N1 influenza pandemic in autumn 2009, and we assess the efficacy of the planned CDC H1N1 vaccination campaign. The model predicts that there will be a significant wave in autumn, with 63% of the population being infected, and that this wave will peak so early that the planned CDC vaccination campaign will likely not have a large effect on the total number of people ultimately infected by the pandemic H1N1 influenza virus.

Experimental discrimination between charge 2e/3 top quark and charge 4e/3 exotic quark production scenarios

We present the first experimental discrimination between the 2e/3 and 4e/3 top quark electric charge scenarios, using top quark pairs (tt) produced in pp collisions at (square root) s = 1.96 TeV by the Fermilab Tevatron Collider. We use 370 pb;{-1} of data collected by the D0 experiment and select events with at least one high transverse momentum electron or muon, high transverse energy imbalance, and four or more jets. We discriminate between b- and b-quark jets by using the charge and momenta of tracks within the jet cones. The data are consistent with the expected electric charge, |q|=2e/3. We exclude, at the 92% C.L., that the sample is solely due to the production of exotic quark pairs QQ with |q|=4e/3. We place an upper limit on the fraction of QQ pairs rho<0.80 at the 90% C.L.

Measurement of the Bs(0) lifetime using semileptonic decays

We report a measurement of the Bs(0) lifetime in the semileptonic decay channel Bs(0) --> Ds- mu+ nuX (and its charge conjugate), using approximately 0.4 fb(-1) of data collected with the D0 detector during 2002-2004. Using 5176 reconstructed Ds- mu+ signal events, we have measured the Bs(0) lifetime to be tau(Bs(0))=1.398+/-0.044(stat)(-0.025)(+0.028)(syst) ps. This is the most precise measurement of the Bs(0) lifetime to date.

Search for pair production of scalar bottom quarks in pp collisions at square root of s = 1.96 TeV

A search for direct production of scalar bottom quarks (b) is performed with 310 pb(-1) of data collected by the D0 experiment in pp collisions at square root s = 1.96 TeV at the Fermilab Tevatron Collider. The topology analyzed consists of two b jets and an imbalance in transverse momentum due to undetected neutralinos (chi(1)0), with chi(1)0 assumed to be the lightest supersymmetric particle. We find the data consistent with standard model expectations, and set a 95% C.L. exclusion domain in the (m(b), m(chi(1)0)) mass plane, improving significantly upon the results from run I of the Tevatron.

Search for neutral, long-lived particles decaying into two muons in pp[over] collisions at sqrt[s]=1.96 TeV

We present a search for a neutral particle, pair produced in pp[over] collisions at sqrt[s]=1.96 TeV, which decays into two muons and lives long enough to travel at least 5 cm before decaying. The analysis uses approximately 380 pb(-1) of data recorded with the D0 detector. The background is estimated to be about one event. No candidates are observed, and limits are set on the pair-production cross section times branching fraction into dimuons + X for such particles. For a mass of 10 GeV and lifetime of 4x10(-11) s, we exclude values greater than 0.14 pb (95% C.L.). These results are used to limit the interpretation of NuTeV's excess of dimuon events.

Search for the standard model Higgs Boson in the pp[over]-->ZH-->nunu[over]bb[over] channel

We report a search for the standard model (SM) Higgs boson based on data collected by the D0 experiment at the Fermilab Tevatron Collider, corresponding to an integrated luminosity of 260 pb(-1). We study events with missing transverse energy and two acoplanar b jets, which provide sensitivity to the ZH production cross section in the nunu[over]bb[over] channel, and to WH production when the lepton from the W-->lnu decay is undetected. The data are consistent with the SM background expectation, and we set 95% C.L. upper limits on sigma(pp[over]-->ZH/WH)xB(H-->bb[over]) from 3.4/8.3 to 2.5/6.3 pb, for Higgs-boson masses between 105 and 135 GeV.

Search for associated higgs boson production WH-->WWW*-->l+/-nul'+/-nu'+X in pp collisions at square root s=1.96 Te V

We present a search for associated Higgs boson production in the process pp-->WH-->WWW*-->l;+/-nul'+/-nu'+X in final states containing two like-sign isolated electrons or muons (e+/-e;+/-, e+/-micro+/-, or micro+/-micro+/-). The search is based on D0 run II data samples corresponding to integrated luminosities of 360-380 pb-1. No excess is observed over the predicted standard model background. We set 95% C.L. upper limits on sigma(pp-->WH)xBr(H-->WW*) between 3.2 and 2.8 pb for Higgs boson masses from 115 to 175 GeV.

Search for neutral Higgs bosons decaying to tau pairs in pp[over ] collisions at sqrt[s]=1.96 TeV

A search for the production of neutral Higgs bosons Phi decaying into tau(+)tau(-) final states in pp[over ] collisions at a center-of-mass energy of 1.96 TeV is presented. The data, corresponding to an integrated luminosity of approximately 325 pb(-1), were collected by the D0 experiment at the Fermilab Tevatron Collider. Since no excess compared to the expectation from standard model processes is found, limits on the production cross section times branching ratio are set. The results are combined with those obtained from the D0 search for Phib(b[over ])-->bb[over ]b(b[over ]) and are interpreted in the minimal supersymmetric standard model.

Search for resonant second generation slepton production at the Fermilab Tevatron

We present a search for supersymmetry in the R-parity violating resonant production and decay of smuons and muon sneutrinos in the channels mu-->chi(1)(0)mu, mu-->chi(2,3,4)(0)mu, and nu(mu)-->chi(1,2)(+/-)mu. We analyzed 0.38 fb(-1) of integrated luminosity collected between April 2002 and August 2004 with the D0 detector at the Fermilab Tevatron Collider. The observed number of events is in agreement with the standard model expectation, and we calculate 95% C.L. limits on the slepton production cross section times branching fraction to gaugino plus muon, as a function of slepton and gaugino masses. In the framework of minimal supergravity, we set limits on the coupling parameter lambda(211)('), extending significantly previous results obtained in Run I of the Tevatron and at the CERN LEP collider.

Direct limits on the oscillation frequency

We report results of a study of the B(s)(0) oscillation frequency using a large sample of B(s)(0) semileptonic decays corresponding to approximately 1 fb(-1) of integrated luminosity collected by the D0 experiment at the Fermilab Tevatron Collider in 2002-2006. The amplitude method gives a lower limit on the B(s)(0) oscillation frequency at 14.8 ps(-1) at the 95% C.L. At delta m(s) = 19 ps(-1), the amplitude deviates from the hypothesis A= 0(1) by 2.5 (1.6) standard deviations, corresponding to a two-sided C.L. of 1% (10%). A likelihood scan over the oscillation frequency, delta m(s), gives a most probable value of 19 ps(-1) and a range of 17 < delta m(s) < 21 ps(-1)at the 90% C.L., assuming Gaussian uncertainties. This is the first direct two-sided bound measured by a single experiment. If delta m(s) lies above 22 ps(-1), then the probability that it would produce a likelihood minimum similar to the one observed in the interval 16-22 ps(-1) is (5.0 +/- 0.3)%.

Search for the Higgs boson in H --> WW(*) decays in pp collisions at square root of 1.96 TeV

We present a search for the standard model Higgs boson in H --> WW(*) decays with e+e-, e+/-mu-/+, and mu+mu- final states in pp collisions at a center-of-mass energy of square root of s = 1.96 TeV. The data, collected from April 2002 to June 2004 with the D0 detector, correspond to an integrated luminosity of 300-325 pb(-1), depending on the final state. The number of events observed is consistent with the expectation from backgrounds. Limits from the combination of all three channels on the Higgs boson production cross section times branching ratio sigma x BR(H --> WW(*) are presented.

Measurement of the lifetime difference in the B0(s) system

We present a study of the decay B0(s) --> J/psiphi. We obtain the CP-odd fraction in the final state at time zero, Rperpendicular = 0.16 +/- 0.10(stat) +/- 0.02 (syst), the average lifetime of the (B0(s), B0(s)) system, tau(B0(s)) = 1.39(+0.13)(-0.16)(stat)(+0.01)(-0.02)(syst) ps, and the relative width difference between the heavy and light mass eigenstates, DeltaGamma/Gamma tripple bond (GammaL - GammaH)/Gamma = 0.24(+0.28)(-0.38)(stat)(+0.03)(-0.04)(syst). With the additional constraint from the world average of the lifetime measurements using semileptonic decays, we find tau(B0(s)) = 1.39 +/- 0.06 ps and DeltaGamma/Gamma = 0.25(+0.14)(-0.15). For the ratio of the B0(s) and B0 lifetimes we obtain tau(B0(s))/tau(B0) = 0.91 +/- 0.09(stat) +/- 0.003(syst).

Measurement of semileptonic branching fractions of B mesons to narrow D** states

Using the data accumulated in 2002-2004 with the D0 detector in proton-antiproton collisions at the Fermilab Tevatron collider with a center-of-mass energy of 1.96 TeV, the branching fractions of the decays B --> D0(1)(2420)mu+ vmuX and B --> D2(*0)(2460)mu+ vmuX and their ratio have been measured: B(b --> B) x B(B --> D0(1)mu+ vmuX) x B(D0(*0) --> D*- pi+) = [0.087 +/- 0.007(stat) +/- 0.014(syst)]%; B(b --> B) x B(B --> D2(*0) mu+ vmuX) x B(D2(*0) --> D*- pi+) = [0.035 +/- 0.007(stat) +/- 0.008(syst)]% and [B(B --> D2(*0)mu+ vmuX) x B(D2(*0) --> D*- pi+)]/[B(B --> D0(1)mu+ vmuX) x B(D0(1) --> D*- pi+)] = 0.39 +/- 0.09(stat) +/- 0.12 (syst), where the charge conjugated states are always implied.

Search for large extra spatial dimensions in dimuon production with the d0 detector

We present the results of a search for the effects of large extra spatial dimensions in pp collisions at sqrt[s] = 1.96 TeV in events containing a pair of energetic muons. The data correspond to 246 pb(-1) of integrated luminosity collected by the D0 experiment at the Fermilab Tevatron Collider. Good agreement with the expected background was found, yielding no evidence for large extra dimensions. We set 95% C.L. lower limits on the fundamental Planck scale between 0.85 and 1.27 TeV within several formalisms. These are the most stringent limits achieved in the dimuon channel to date.

Search for supersymmetry via associated production of charginos and neutralinos in final states with three leptons

A search for associated production of charginos and neutralinos is performed using data recorded with the D0 detector at a pp center-of-mass energy of 1.96 TeV at the Fermilab Tevatron Collider. This analysis considers final states with missing transverse energy and three charged leptons, of which at least two are electrons or muons. No evidence for supersymmetry is found in a data set corresponding to an integrated luminosity of 320 pb-1. Limits on the product of the production cross section and leptonic branching fraction are set. For the minimal supergravity model, a chargino lower mass limit of 117 GeV at the 95% C.L. is derived in regions of parameter space with enhanced leptonic branching fractions.

Search for neutral supersymmetric Higgs Bosons in multijet events at sqrt[s]=1.96 TeV

We have performed a search for neutral Higgs bosons produced in association with bottom quarks in pp collisions, using 260 pb-1 of data collected with the D0 detector in Run II of the Fermilab Tevatron Collider. The cross sections for these processes are enhanced in many extensions of the standard model (SM), such as in its minimal supersymmetric extension at large tanbeta. The results of our analysis agree with expectations from the SM, and we use our measurements to set upper limits on the production of neutral Higgs bosons in the mass range of 90 to 150 GeV.

Production of WZ events in pp collisions at square root(s) = 1.96 TeV and limits on anomalous WWZ couplings

We present results from a search for WZ production with subsequent decay to l nu l' l' (l and l' = e or mu) using 0.30 fb(-1) of data collected by the D0 experiment between 2002 and 2004 at the Fermilab Tevatron. Three events with WZ decay characteristics are observed. With an estimated background of 0.71 +/- 0.08 events, we measure the WZ production cross section to be 4.5(-2.6)(+3.8) pb, with a 95% C.L. upper limit of 13.3 pb. The 95% C.L. limits for anomalous WWZ couplings are found to be -2.0 < delta kappaZ < 2.4 for form factor scale lambda = 1 TeV, and -0.48 < lambdaZ < 0.48 and -0.49 < delta g(1)(Z) < 0.66 for lambda = 1.5 TeV.

Search for Randall-Sundrum gravitons in dilepton and diphoton final states

We report the first direct search for the Kaluza-Klein (KK) modes of Randall-Sundrum gravitons using dielectron, dimuon, and diphoton events observed with the D0 detector operating at the Fermilab Tevatron pp(-) Collider at sqrt[s]=1.96 TeV. No evidence for resonant production of gravitons has been found in the data corresponding to an integrated luminosity of approximately equal to 260 pb(-1). Lower limits on the mass of the first KK mode at the 95% C.L. have been set between 250 and 785 GeV, depending on its coupling to standard model particles.