CIDID Seminar: Alison Feder
Sep
8
10:00am10:00am

CIDID Seminar: Alison Feder

Intra-patient evolutionary dynamics of immunodeficiency viruses across time and space

SPEAKER: Alison Feder

Graduate Student
Department of Biology
Stanford University

ABSTRACT

HIV’s high mutation rates and large population sizes make it incredibly adaptable, especially to the antiretroviral drugs used in its treatment. However, as treatments have improved over the course of the epidemic, there has been a shift from HIV evolving resistance predictably and quickly in each patient to resistance emerging rarely, if at all. By studying the manner in which drug resistance emerges, we can gain broader insights into how HIV evolves within its host. I’ll explore two questions: 1) how has intra-patient drug resistance evolution changed over the course of the epidemic and 2) what role does population spatial structure play in influencing the intra-patient dynamics. In answer to the first question, I will present data from 6717 historical HIV sequences from the Stanford HIV Drug Resistance Database that suggest that as treatments have improved over the decades, there has been a transition from soft sweeps of many drug resistance mutations simultaneously to hard sweeps of single drug resistant types. This supports more broadly a prediction from theory that when adaptation is likely (as when drugs failed frequently), sweeps should be soft. In answer to the second question, I will present data from four Simian-HIV infected macaques sampled in multiple tissues over the course of their infection and treatment. I will use these data to estimate selection, migration and population size and suggest how their interaction may explain equivocal evidence of compartmentalization from the HIV literature.
 

Streaming video: the seminar will be broadcast live once the event has started. The video recording may also be viewed at a later date. [link]

Download flyer: [link]

 

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9th Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID 2017)
Jul
10
to Jul 26

9th Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID 2017)

  • University of Washington (map)
  • Google Calendar ICS

The 9th Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID 2017) will be held July 10-26, 2017 at the University of Washington in Seattle, Washington USA.

The Institute consists of a series of two-and-a-half day workshops designed to introduce infectious disease researchers to modern methods of statistical analysis and mathematical modeling and to introduce statisticians and mathematical modelers to the statistical and dynamic problems posed by modern infectious disease data. Prerequisites are minimal, and the modular nature of the Institute enables participants to design a program best suited to their backgrounds and interests. Most participants will likely take two or three modules.

Individuals attending the Institute will receive certificates of course completion in recognition of their participation.

Check back in January 2017 for more details and registration information. 

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May
25
to May 26

Immunology and Evolution of Influenza Symposium

  • Emory University School of Medicine (map)
  • Google Calendar ICS

Registration: please click here to register


View the main symposium page for list of speakers, agenda, and hotel information: [link]

Overview:
The Immunology and Evolution of Influenza Symposium is jointly sponsored by the Center for Inference and Dynamics of Infectious Diseases, funded by NIGMS, and the Center for Modeling Immunity to Influenza Infection, funded by NIAID. The Symposium will integrate both immunological and epidemiological approaches to modeling influenza strain variation.  The Symposium will start on May 25th at 8:30am and finish at noon on May 26th.

Registration: there is no registration fee, however you must register by 12pm noon (Eastern time) Friday, May 19th in order to attend. Please use the link above to complete your registration. 

 

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CIDID Seminar - Micaela Martinez
Apr
21
10:30am10:30am

CIDID Seminar - Micaela Martinez

The Finest Tuned Clocks: Biological Rhythms & Epidemics

 

Speaker: Micaela E. Martinez, Ph.D.

Associate Research Scholar
Dept. of Ecology & Evolutionary Biology
Princeton University

Abstract

Life on earth has evolved under day-night and seasonal cycles. These environmental cycles pose organisms with challenges and opportunities. Biological clocks have evolved as a mechanism for organisms to internalize time, giving them them the ability to anticipate, and prepare for, predictable changes in their environment. Circadian clocks, for example, are ubiquitous in eukaryotes, and circannual (i.e., seasonal) clocks are found throughout the animal kingdom. I will present research I have completed, and projects I have underway, to characterize cycles in disease transmission, human physiology, and immunity that have realized effects on human health and disease interventions. I will largely focus on two research areas. First, I will discuss the population-level interface of human phenology and infectious disease ecology, revealing the seasonal clockwork of epidemics using big demographic and epidemiological data, combined with dynamic models and cutting-edge statistical inference methods. Second, I will detail a clinical study I’m conducting through the NIH Director’s High-Risk High-Reward research program, in which I aim to discover the biological rhythms in human physiology and immunology that contribute to cycles of infection, birth, and mortality, as well as the evolution of rhythms in parasites, and thus may be leveraged by evolutionary medicine.  

Download flyer: [pdf]

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CIDID Seminar: Nicolas Rodrigue
Mar
30
10:30am10:30am

CIDID Seminar: Nicolas Rodrigue

Recent advances in methods for detecting adaptation in protein-coding DNA

Seminar Speaker: Nicolas Rodrigue, PhD

Assistant Professor
Department of Biology
Carleton University, Canada

Abstract: Statistical modelling of the long-term evolution of protein-coding DNA is an active area of research in molecular phylogenetics.  Several recent works have adopted a mutation-selection framework, whereby the substitution process is specified from a set of parameters controlling a point-mutation process, and another set of (potentially site-specific) parameters controlling the probability of fixation of mutations.  We have previously discussed using such a model as "a more relevant background against which to distinguish positive selection" (Rodrigue, Philippe & Lartillot, PNAS, 2010), and have recently used simulations to illustrate the potential of the approach (Rodrigue & Lartillot, MBE, 2017).  This lecture will outline the rationale of such a model, present results of its large-scale applications over several thousand protein-coding genes, and discuss on-going expansions to the mutation-selection framework.

Streaming video: the seminar will be broadcast live once the event has started. The video recording may also be viewed at a later date. [link]

Download flyer: [pdf]

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CIDID Seminar: Simon Hay
Mar
17
10:30am10:30am

CIDID Seminar: Simon Hay

A deep dive into the methods underlying model-based geostatistics and their application

Speaker: Professor Simon Iain Hay

Professor of Global Health
Director of Geospatial Science, Institute for Health Metrics & Evaluation (IHME)

University of Washington

Abstract: IHME's Director of Geospatial Science, Professor Simon Hay, will provide a deep dive into the methods underlying model-based geostatistics (MBG), particularly in relation to how MBG is being used to estimate (and map) under-5 mortality at a resolution of 5x5 km. He will focus on the types of data and methodological advancements and challenges faced by IHME's Geospatial Analysis team as they seek to produce accurate, spatially-granular estimates of under-5 mortality in 46 countries in sub-Saharan Africa, and eventually in Asia and the Americas. The methods described are also being applied more broadly to undernutrition and priority diseases for childhood survival (diarrhea, lower respiratory infection, and malaria). Additionally, Professor Simon Hay will illustrate the applications of geospatial analysis in assessing progress towards Sustainable Development Goals.

Streaming video: the seminar will be broadcast live once the event has started. The video recording and may also be viewed at a later date. [link]

Download flyer: [pdf]

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AAAS Annual Meeting - Zika and Dengue
Feb
19
1:00pm 1:00pm

AAAS Annual Meeting - Zika and Dengue

The Analysis and Control of Zika and Dengue Virus Epidemics

The Zika epidemic has been declared by the World Health Organization to be a “public health emergency of international concern,” and dengue continues to be a global public health menace. Both viruses are spread by the same Aedes mosquito vector, which now exposes nearly half of the world population to these viruses. In addition, Zika can be spread sexually from male-to-female and possibly through other types of direct contact. These epidemics can be controlled through improved vector control and new vaccines. This session describes the statistical and mathematical methods being developed and used to evaluate the effectiveness of these interventions. Based on their potential levels of effectiveness, the panelists will discuss how these interventions may be used to control Zika, dengue, and other arboviruses spread by Aedes now and in the future.

Organizer:  Ira M. Longini Jr., University of Florida
Moderator:  Natalie Dean, University of Florida
Discussant:  Ira M. Longini Jr., University of Florida

Speakers:
Nicholas P. Jewell, University of California, Berkeley
Testing the Efficacy of Wolbachia Against Dengue Virus Transmission With Randomized Trials

M. Elizabeth Halloran, University of Washington
The Design and Analysis of Vaccine Trials for Zika and Dengue

Gonzalo Vazquez-Prokopec, Emory University
Vector Control Approaches for Immediate Response to Zika Outbreaks

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CIDID Seminar: Nathan Grubaugh
Jan
13
10:30am10:30am

CIDID Seminar: Nathan Grubaugh

Dynamics of arthropod-borne virus evolution during transmission

Seminar Speaker: Nathan D. Grubaugh, PhD

Postdoctoral Fellow
Department of Immunology and Microbial Science
The Scripps Research Institute

Abstract:  Arthropod-borne viruses (arboviruses), such as Zika, chikungunya, and West Nile virus (WNV), pose as continuous threats to emerge and cause large epidemics. Often these events are associated with novel virus variants optimized for local transmission, which first arise as minorities within a host. Thus the conditions that regulate the frequency of intrahost variants are important determinants of emergence. For arboviruses, these conditions are complex as they cycle between the different environments of their arthropod vectors and vertebrate hosts. First, I will describe the forces that alter WNV genetic diversity during transmission. Next, we will explore the fitness costs and benefits of replicating different enzootic mosquito vectors and avian hosts. The general theme is that in mosquitoes, the WNV genetic repertoire dramatically changes due to repeated bottles and to escape the innate immune response, RNA interference. The consequence, however, is that the diversity generated in mosquitoes decreases its fitness in birds, and thus most WNV variants are rapidly purged upon transmission. Lastly, I will compare these results to a tick-borne virus (Powassan virus) to demonstrate how vector ecology can be a determinate of evolution. The results presented here highlight the complex evolutionary forces that a novel arbovirus variant must overcome to alter infection phenotypes at the population level.

 

Streaming video: the seminar will be broadcast live once the event has started. The video recording may also be viewed at a later date. [video link]

Download flyer: [pdf]

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CIDID Seminar: Bradley Efron
Oct
13
3:30pm 3:30pm

CIDID Seminar: Bradley Efron

  • University of Washington, School of Public Health (map)
  • Google Calendar ICS

NOTE: This seminar is co-sponsored with the University of Washington Department of Biostatistics.

Confidence densities, uninformative priors, and the bootstrap

Seminar Speaker: Bradley Efron, PhD

Professor of Statistics and Biomedical Data Science
Stanford University

Abstract

There have been a series of conferences around the world under the label "BFF", standing for Bayesian, Frequentist, and Fiducial. I will give a version of the keynote talk at the most recent one. A general problem of BFF interest goes as follows: A family of densities with vector parameter "mu" has yielded data "X", from which the statistician wishes to infera real-valued parameter theta = t(mu). For example X might be multi-variate normal, X~N(m,V), and theta the trace of V. A statistical holy grail task is to find a convincing posterior density of theta given X, when there is no prior information on the distribution of mu. A suite of more or less related answers have been proposed: uninformative priors, matching priors, fiducial methods, and confidence densities (the last being derivatives of confidence distributions.) This talk reviews the various theories, connecting them to bootstrap methods for their implementation.

Download flyer: [pdf]

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CIDID Seminar: Louise Moncla
Sep
28
10:30am10:30am

CIDID Seminar: Louise Moncla

  • Fred Hutch, B1-072/074 Weintraub Bldg (map)
  • Google Calendar ICS

The interplay of selective bottlenecks and random chance during avian influenza virus evolution in mammals

SPEAKER: Louise Moncla

PhD Candidate, Department of Pathobiological Sciences,
University of Wisconsin School of Veterinary Medicine

ABSTRACT:

 Zoonotic influenza viruses periodically emerge to cause pandemics. Transmission bottlenecks define the starting genetic material available for onward within-host influenza evolution. However, the relative roles of natural selection, genetic drift and founder effects during influenza transmission are not well understood. It was recently shown that avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among ferrets by acquiring mutations in hemagglutinin (HA) and polymerase. We traced the within-host evolutionary pathway by which this avian-like virus evolved mammalian replication and transmission. During initial infection, within-host HA diversity increased dramatically. The first transmission event was a loose genetic bottleneck, during which 2 polymerase mutations became fixed in the population without conferring a detectable replication advantage. After further evolution, the transmission bottleneck imposed a selective sweep on HA. Intriguingly, our data suggest that the stringency and evolutionary forces governing between-host bottlenecks may change throughout host adaptation. These data unify previous findings from diverse experimental designs and systems that have historically seemed in conflict. To explore this hypothesis, we are developing novel uses for long-read technologies that provide linkage information for all sites across a gene segment. We will use these techniques to dissect within-host influenza population dynamics at a finer scale.

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CIDID Seminar: Jeffrey B. Joy
Sep
15
10:30am10:30am

CIDID Seminar: Jeffrey B. Joy

Evolutionary genetics of HCV: from population to patient

SPEAKER: Jeffrey B. Joy, PhD

BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
Department of Medicine, University of British Columbia, Vancouver, BC, Canada

ABSTRACT:
Hepatitis C virus (HCV) represents a health crisis of global proportions with an estimated 185 million infected persons worldwide including approximately 4.6 million infections of predominantly HCV genotype 1a within North America. Despite the advent of curative HCV therapies many challenges remain at all levels of the epidemic hierarchy. One such challenge concerns resolving the controversy surrounding the timing of the initial spread of hepatitis C genotype 1a in North America. In particular, how and when HCV reached extraordinary prevalence in specific demographic groups has remained unclear. Secondly, natural HCV polymorphisms conferring resistance to direct acting antiviral therapy exist however the frequency of these variants at the population level is uncertain. A third problem facing treatment of HCV particularly in high risk populations is that identification and treatment of individuals with mixed HCV infections (infection with 2 or more distinct viral variants) is challenging and the detection of such mixed infections remains complex. Finally, HCV therapy rapidly leads to undetectable viral load, and consequently the loss of any ability to closely monitor what is happening to the virus in vivo until a patient relapses or achieves sustained virological response. In this talk I will apply evolutionary genetic methods to the abundance of available sequence data at the both the population level and longitudinally within individual patients to contribute to resolving these controversies and problems and provide practical insights into HCV epidemic dynamics at multiple scales. 

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Simulating Intervention Trials in Infectious Diseases Workshop
Aug
24
to Aug 25

Simulating Intervention Trials in Infectious Diseases Workshop

  • Fred Hutch, Sze Conference Room, Thomas Building (map)
  • Google Calendar ICS

Agenda: [pdf]
Map of Fred Hutch campus and conference room location: [pdf]
Map to dinner location: [pdf]


This workshop is co-sponsored with the Center for Communicable Disease Dynamics (Harvard). 

Background:
Testing interventions for the control of infectious diseases raises several distinctive issues that are not generally present in interventions for non-communicable diseases. Many infectious disease control interventions have indirect effects, changing the transmission risk of those receiving the intervention and also of those not receiving it. Moreover, the urgency and in some cases high lethality of infectious diseases motivates innovative designs for trials to balance concerns of maintaining scientific validity, obtaining an answer rapidly, and performing the trial in a way that is ethically and culturally acceptable. All of these concerns were at the forefront in the case of Ebola, but they have also arisen in many other contexts. The use of novel designs in particular raises questions about the effect measures being estimated and their relationships to familiar quantities such as measures of direct efficacy and indirect effectiveness. While some of these issues can be addressed analytically, many require simulation to incorporate the details of the setting and the associated transmission dynamics and logistics.

 

For more information, please contact Stephanie Shadbolt: sshadbolt@fredhutch.org

 

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CIDID Seminar: Stephanie Spielman
Jul
21
10:30am10:30am

CIDID Seminar: Stephanie Spielman

Uncovering the properties and limitations of models of sequence evolution

Speaker: Stephanie Spielman, PhD

Institute for Genomics and Evolutionary Medicine
Temple University

ABSTRACT

Natural selection leaves signatures of its activity in DNA. As sequencing increasingly assumes a central role in modern biological research, we have an unprecedented opportunity to elucidate the myriad ways in which evolution shapes the diversity of life's genomes. Most commonly, we study these "fingerprints" of natural selection using statistical models of sequence evolution. In the context of of protein-coding sequence evolution, two popular complementary models have emerged: dN/dS-based models, which measure the relative rate of nonsynonymous to synonymous substitutions, and mutation—selection models, which measure site-specific amino acid propensities (or "fitness") using population genetics principles. Importantly, these models have been constructed and studied independently from one another. As a consequence, it has been entirely unknown whether different models reveal similar or incompatible information about the strength and direction of natural selection, in turn hindering our ability to draw robust conclusions about evolutionary pressures. In this talk, I will discuss how we can bridge this gap by deriving a precise relationship between dN/dS-based and mutation—selection models. I use this relationship to identity previously unappreciated limitations and behaviors of these models. For example, this work reveals that dN/dS inferences in the popular software PAML (codeml) are strongly biased, and further that standard metrics of model selection (AIC and BIC) may be positively misleading. I offer specific recommendations for how to most reliably apply models of protein-coding sequence evolution and interpret their results.

Download flyer: [pdf]
Streaming video: [link]

   (Note: live video link will only be available once seminar has begun. A recording will be posted that may be viewed at a later date.)

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CIDID Seminar: Kathryn Holt
Jul
15
10:30am10:30am

CIDID Seminar: Kathryn Holt

Population Genomics of Bacterial Pathogens

Speaker: Kathryn Holt, PhD

NHMRC Career Development Fellow and Associate Professor
Centre for Systems Genomics, University of Melbourne

Abstract:

 Over the last decade, high throughput genome sequencing has revolutionised our ability to investigate and understand bacterial pathogen populations. I have been involved in establishing and applying population genomic frameworks and associated tools to the study of several important pathogens, including typhoid, dysentery and the emerging hospital superbugs Klebsiella pneumoniae and Acinetobacter baumannii . The insights and implications offered by population genomics vary substantially between organisms, but understanding the evolution and spread of antimicrobial resistance is a common and important goal. Here I will highlight some recent insights into the evolution and spread of two highly drug-resistant bacterial pathogens that have very different population structures – SalmonellaTyphi (typhoid) and Klebsiella pneumoniae.

Download flyer: [pdf]

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Jul
11
to Jul 27

8th Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID).

  • University of Washington (map)
  • Google Calendar ICS

The 8th Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID 2016) will be held July 11-27, 2016 at the University of Washington in Seattle, Washington USA.

The Institute consists of a series of two-and-a-half day workshops designed to introduce infectious disease researchers to modern methods of statistical analysis and mathematical modeling and to introduce statisticians and mathematical modelers to the statistical and dynamic problems posed by modern infectious disease data. Prerequisites are minimal, and the modular nature of the Institute enables participants to design a program best suited to their backgrounds and interests. Most participants will likely take two or three modules.

Individuals attending the Institute will receive certificates of course completion in recognition of their participation.

For more details and registration information click here

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CIDID Seminar: Pinky Langat
May
13
10:30am10:30am

CIDID Seminar: Pinky Langat

  • Fred Hutch, Room E3-200/201 (Eastlake) (map)
  • Google Calendar ICS

Exploring the dynamics of influenza virus evolution, selection, and host adaptive immunity

Speaker: Pinky Langat, PhD candidate

Sanger Institute, University of Cambridge, UK

Abstract

 Advances in high-throughput sequencing and phylogenetic approaches have improved our ability to investigate genetic and antigenic variation of influenza viruses and adaptability of host immunity. I will describe studies characterising the genotypic diversity of swine influenza A viruses circulating in Europe, and the global antigenic diversity of swine influenza A viruses using advances in antigenic cartographic models. In addition, to better understand the molecular evolution and epidemiology of influenza B virus on a global scale, we analysed the most comprehensive dataset of whole influenza B virus genomes to date, identifying distinct patterns of antigenic evolution and genome-wide diversity between the two lineages and in different parts of the world. Finally, as part of on-going work to explore how antigenically-variable pathogens shape B cell selection, we isolated naïve and germinal center (GC) B cells from mice challenged with distinct influenza B viruses. By sequencing and analysing B cell receptor repertoires of the GC response to influenza exposure, we can investigate characteristics of B cell selection and affinity maturation to different strains, furthering our potential to study immune adaptability in more detail.

Download flyer: [pdf]

 

 

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CIDID Seminar: Tim Tsang
Apr
11
2:30pm 2:30pm

CIDID Seminar: Tim Tsang

Household transmission of influenza viruses

Speaker: Tim Tsang, PhD

University of Hong Kong, School of Public Health

ABSTRACT

Human influenza viruses cause regular epidemics and occasional pandemics with a substantial public health burden. Household studies have been used to study influenza epidemiology for decades, with the Tecumseh Study being one of the most famous. A recent development is the use of household transmission (case-ascertained) studies with short-term follow-up rather than follow-up over an entire influenza season in household cohort studies. In this talk, I will first describe this study design and review results from previous household transmission studies. I will then present analyses of a household transmission study conducted in Hong Kong. I studied the role of two biological variables on transmission, specifically antibody titers measured by hemagglutination-inhibiting (HAI) assays and viral shedding measured by reverse-transcription polymerase chain reaction (PCR) test. The association between an HAI titer of 1:40 and protection was substantially less than 50% in households, perhaps due to the intense and frequent contacts among household members. Viral shedding was at most weakly correlated with infectivity in households, and other correlates of infectivity should be examined in future studies. I will also talk about potential uses of this study design to obtain information and insights on influenza epidemiology.

Download flyer: [pdf]

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CIDID Seminar: Thomas Friedrich
Feb
26
10:30am10:30am

CIDID Seminar: Thomas Friedrich

Passing through: the role of transmission bottlenecks in influenza virus host adaptation

SPEAKER: Thomas Friedrich, PhD

Associate Professor, Dept. of Pathobiological Sciences
University of Wisconsin-Madison School of Veterinary Medicine
Head of Virology Services Unit, Wisconsin National Primate Research Center

ABSTRACT

Novel influenza viruses emerge unpredictably from avian reservoirs, causing occasional human pandemics. A handful of recent studies in ferrets have shown that surprisingly few molecular changes may be required for airborne transmission of avian influenza viruses between mammalian hosts. We used deep sequencing to trace the evolutionary pathways of 2 such avian viruses as they replicated and were transmitted in ferrets. Airborne transmission involved genetic bottlenecks that were most often driven by strong selection on the gene encoding the viral attachment protein, hemagglutinin (HA). Bottleneck stringency varied among transmission events, and no single viral genotype was consistently transmitted in each event we observed. The strength and nature of transmission bottlenecks could play an important role in determining the ability of a given avian virus to successfully emerge in humans. All work with infected ferrets was performed prior to the current pause on “gain-of-function” research. 

Download flyer [pdf]

Recorded video [link]  

 

 

 

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Feb
11
to Feb 15

AAAS 2016 Annual Meeting

  • Washington Marriott Wardman Park (map)
  • Google Calendar ICS

Betz Halloran has organized two symposia at the AAAS 2016 Annual Meeting under the auspices of the Section on Statistics (U): 
One was co-organized with Matt Ferrari, Penn State, on "Measles Vaccination: Global Challenges". The other is "Lessons from the Ebola Outbreak: Designing Vaccine Trials for Emerging Diseases".  Ira Longini is one of the speakers for this symposium on Ebola. 

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CIDID Seminar: Sergei L. Kosakovsky Pond
Dec
11
10:30am10:30am

CIDID Seminar: Sergei L. Kosakovsky Pond

Scalable and biologically realistic methods for inferring selective pressures from molecular sequence data

 

Speaker: Sergei L. Kosakovsky Pond, PhD

Associate Professor of Medicine
Department of Medicine
University of California, San Diego

 

 

Download flyer: [pdf]

Streaming: Watch the seminar live by clicking here when the seminar begins. You can also use this link to watch the seminar after the event.

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CIDID Seminar: Richard Neher
Nov
6
10:30am10:30am

CIDID Seminar: Richard Neher

How predictable is RNA virus evolution?

Speaker: Richard Neher, PhD

Research Group Leader
Max Planck Institute for Developmental Biology

 

ABSTRACT

To quantitatively monitor diversity and dynamics of entire virus populations, we performed whole genome deep sequencing of HIV-1 populations in 9 untreated patients with 6-12 longitudinal samples spanning 5-8 years of infection. Using this data set, we show that a universal landscape of fitness costs controls minor intrapatient variation and the rate of reversion towards the global HIV-1 consensus. These reproducible patterns of diversity and reversion at single sites are possible only because frequent recombination limits coupling between different parts of the genome. In contrast, segments of influenza viruses don’t recombine. Nevertheless, the shape of phylogenetic trees predicts which of the currently circulating virus variants are most likely to dominate future seasons. Predictive models have the potential to improve strain selection for seasonal influenza vaccines. 

 

Download flyer [pdf]

Streaming: Watch the seminar live by clicking here when the seminar begins. You can also use this link to watch the seminar after the event.

 

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CIDID Seminar: Jennifer Gardy
Oct
2
10:30am10:30am

CIDID Seminar: Jennifer Gardy

The story of an outbreak: Tracking infectious disease transmission with DNA sequencing


Speaker: Jennifer Gardy, PhD

Canada Research Chair in Public Health Genomics
Senior Scientist, BC Centre for Disease Control
Assistant Professor, School of Population and Public Health, UBC
Associate Member, Microbiology & Immunology, UBC


Abstract

With the advent of next-generation DNA sequencing methods, sequencing the complete genome of every pathogen isolate from an outbreak has become possible. With this new, high-resolution molecular epidemiology data, we are able to reconstruct outbreaks of disease with a degree of accuracy that has previously been unattainable, revealing important aspects of transmission dynamics and providing insight into pathogen evolution and population structure. This emerging field of genomic epidemiology still faces challenges, however, including dealing with biological issues such as within-host genetic diversity, technical hurdles related to sample preparation and sequencing, and questions around clinical implementation, validation, and reporting. In this talk, I’ll discuss a multi-year genomic investigation of a tuberculosis outbreak amongst BC’s homeless population, including both the insights gained into the outbreak and the larger questions about genomic epidemiology that the work raised, which we are now addressing in follow-up projects. 

Download flyer [pdf]

Streaming: View seminar live by clicking here when the seminar begins. You can also use this link to watch the seminar after the event.

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7th Summer Institute in Statistics and Modeling in Infectious Diseases
Jul
6
to Jul 22

7th Summer Institute in Statistics and Modeling in Infectious Diseases

  • University of Washington (map)
  • Google Calendar ICS

The 7th Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID 2015) will be held July 6-22, 2015 at the University of Washington in Seattle, Washington USA.

The Institute consists of a series of two-and-a-half day workshops designed to introduce infectious disease researchers to modern methods of statistical analysis and mathematical modeling and to introduce statisticians and mathematical modelers to the statistical and dynamic problems posed by modern infectious disease data. Prerequisites are minimal, and the modular nature of the Institute enables participants to design a program best suited to their backgrounds and interests. Most participants will likely take two or three modules.

Individuals attending the Institute will receive certificates of course completion in recognition of their participation.

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Workshop on Analyzing the Polio Eradication Endgame
Jul
1
to Jul 2

Workshop on Analyzing the Polio Eradication Endgame

Agenda  |   Registration  |  Venue  |  Contact  |  Participants  |  Materials

View maps of venue and hotel 

View map of Fred Hutch campus →

The MIDAS Center for Inference and Dynamics of Infectious Diseases (CIDID) is sponsoring a workshop on July 1 and half of 2, 2015, in Seattle, Washington, USA that will include major groups modeling polio transmission and others involved with the polio eradication endgame.  The workshop will focus on how the complete eradication of wild poliovirus (WPV) and of circulating vaccine derived poliovirus (cVDPV) can be adequately assured when oral polio vaccine (OPV) use is stopped.  In particular, the workshop will focus on the issue of silent circulation (i.e., viral transmission in the absence of detected paralytic cases), which can involve a high number of asymptomatic infections, even in the context of high coverage with inactivated polio vaccine (IPV), as demonstrated in 2013-4 in Israel.  

The detection of WPV or cVDPV silent circulation is possible with environmental surveillance at some expense.  The high cost makes it currently infeasible to ensure a low probability of silent circulation using just data from worldwide sampling.  The sampling will likely need to be focused on those areas with the highest probability of silent circulation.  As the time since the last paralytic poliomyelitis case increases, the probability of silent circulation decreases.  But model analyses show that different conformations of poliovirus transmission systems can have markedly different rates of decrease.  Some theoretically possible systems could sustain silent circulation for many years even when the level of OPV vaccination that achieved elimination of polio cases is sustained.  More theoretical and empirical work on silent circulation is needed to identify the characteristics of transmission systems that make silent circulation possible.  That work will be advanced by better estimates of polio transmission system parameters affecting the possibility of silent circulation.  This workshop will focus on identifying the theoretical modeling work, field studies, data collection, and the data analysis methods most likely to improve the choice of locations and methods for detecting silent circulation.

The four existing active polio modeling groups take different approaches to polio modeling and making inferences about programmatic choices.  This diversity should provide strength.  To ensure that it does, each group could help strengthen the work of the other groups.  That will require the open dialogue and a potential for collaborative modeling and data analysis research that this workshop seeks to promote.  Each modeling group will present what their approach can say about the potential for silent circulation and what data or theory development might best help focus silent circulation detection efforts on the methods and places with the highest chances for detecting silent circulation.  Individuals involved in global polio eradication initiative laboratory or fieldwork efforts or policy formation related to silent circulation participating in this workshop will provide input in guiding the policy issues on which modelers can most productively focus. This interaction between modelers and policy makers is essential for modelers to make the most informative data analyses and policy choice projections.

Agenda

This agenda is meant to promote discussion and can be made flexible to pursue the discussion directions that seem most important. It takes a diverse community of scientists, modelers, and people who can influence policy to understand any complex system in medicine or public health. We hope the discussions in this workshop will be a step in community building that will help insure polio eradication is achieved soon and solidly. Because the polio transmission system is so complex and because the consequences of failing to understand the phase transitions that must be passed through to achieve eradication are so severe, our dialogue could make an essential contribution to understanding what could happen during the endgame and how we should be prepared for whatever might come.

July 1: morning

8:00-8:05  |  Welcome : Betz Halloran

8:05-8:20  |  Introductions

What are the most important endgame issues to be modeled, the most important parameters or relationships to be estimated, and the most important policy guidance to be provided?  (Online material including the presentation and things that might come up in discussion to be provided one week before the workshop.)

8:20-8:25  |   WHO research unit perspective

8:25-8:30  |   Environmental surveillance perspective

8:30-8:35  |   Global Polio Laboratory Network perspective

8:35-8:40  |   Gates Foundation perspective

8:40-8:45  |   Imperial college perspective

8:45-8:50  |   Kid Risk perspective

8:50-8:55  |   Institute for Disease Modeling perspective

8:55-9:00  |   CIDID perspective

9:00-9:50  |    Discussion

9:50-10:20  |   Break

What are the implications of work by each modeling group with regard to how silent circulation could affect the polio eradication endgame?  

10:20-12:00  |  10 minute Presentations by each of the four modeling groups with 15 minute discussions.  (Online material including the presentation and things that might come up in discussion to be provided one week before the workshop.)


July 1: afternoon

Approaches to modeling, parameter estimation, and policy guidance during the endgame: This afternoon focuses on the logic of how models inform policy decisions and the methodology for constructing and analyzing models that inform policy.  Each group is to  illustrate their approach to making inferences that can guide endgame policy with a discussion of the overall philosophy of modeling used by the group and its advantages and disadvantages.

1:00-2:20  |  20 minute presentations with 20 minutes of discussion for two groups

2:20-2:50  |  Break

2:50-4:10  |  20 minute presentations with 20 minutes of discussion for two groups

4:10-5:00  |  Open discussion on how the different approaches taken could be made more complementary and informative

6:00  |   Group Dinner (off-campus)


July 2: morning

Data availability, data collection priorities, data analysis methods and inference processes: Any presentations on any of these topics that any group wishes to make will be woven into the discussion format.  Material for presentation and discussion should be supplied one week before the workshop.

8:00–9:40  |  Discussion of what data the different groups have, the value that could be extracted from the data if it were more widely available to the scientific community, and what it would take to make this data more available.  

9:40-10:10  |  Break

10:10-12:00  |  Discussion of modeling priorities, data collection priorities, and coordination between modeling groups and policy people to insure good decisions during the endgame.
 

Registration

Registration has closed.

Venue

Sze Conference rooms, Thomas Building, Fred Hutchinson Cancer Research Center campus.

Contact

Other modeling groups who would like to participate in this workshop should contact Jim Koopman at jkoopman@umich.edu.

Participants

Workshop Organizing Committee

  • Jim Koopman, U Michigan 
  • David Hutton, U Michigan 
  • Marisa Eisenberg, U Michigan 
  • Katia Koelle, Duke U  (did not attend)

Bill and Melinda Gates Foundation/Seattle

  • Ananda Bandyopadhyay
  • Jay Wenger

CDC/Atlanta

  • Ben Lopman
  • Steve Wassilak

CIDID Policy Studies/U Michigan

  • Chris Henry
  • Ed Ionides
  • Joonha Park

CIDID/Emory University

  • Rustom Antia

CIDID/Fred Hutch

  • Rebecca Allen, CIDID Project Coordinator
  • Charles Cheung
  • Stephanie Shadbolt, CIDID Associate Director
  • Jonathon Sugimoto

Fred Hutch

  • Alvason Zenhua Li

Imperial College/UK

  • Isobel Blake
  • Kathleen O'Reilly
     

Workshop Facilitator

  • M. Elizabeth Halloran/CIDID Director, Fred Hutch and U Washington

 

Institute for Disease Modeling Bellevue 

  • Mike Famulare
  • Hil Lyons
  • Kevin McCarthy

Kid Risk, Inc./Orlando

  • Kimberly Thompson
  • Radboud Duintjer Tebbens

MathEcology

  • Colleen Burgess

University of Maryland

  • Philip Johnson

University of Michigan

  • Joe Eisenberg (did not attend)

University of Minnesota

  • Nicole Basta

Tel Aviv University/Israel

  • Lester Shulman

W.H.O./Geneva

  • Ondrej Mach

 

Materials

General materials can be viewed here.

Participant materials can be viewed here. (password required)

 
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