- December 3-5, 2018
- Training Workshop on Infectious Diseases Dynamics and Evolution
- Hosted by the National Institute for Communicable Diseases (NICN)
- Johannesburg, South Africa
- Registration (Closed) and more information here
Register here (Closed)
Fogarty International Center, NIH – National Institute for Communicable Diseases
Training Workshop on Infectious Diseases Dynamics and Evolution
December 3-5, 2018
Johannesburg, South Africa
A better understanding of the epidemiology and evolutionary dynamics of infectious diseases is particularly useful to guide intervention strategies, optimize surveillance, and vaccine design, but detailed studies remain scare in low- and middle-income settings.
The objective of this 3-day FIC-NICD workshop is to train epidemiologists, microbiologists, virologists and public health professionals, on the use of the computational methods in infectious diseases. Participants will learn how to use computational methods to characterize seasonality, disease burden, transmission dynamics, molecular analysis and phylodynamics of viral infections, with key focus on influenza and HIV.
Participants will be invited to work with their own data and with publicly available sample datasets. The workshop will include 2 parallel tracks on epidemiology and phylogenetics.
Participants to the epidemiology module will be taught how to use different R packages for statistical and mathematical analyses of epidemiological data, and other tools (such as EpiPoi) to visualize and define influenza seasonality and epidemic periods, estimate excess mortality or excess morbidity, infer time trends, estimate the reproduction number of epidemics, and fit simple mechanistic transmission models to data.
The phylodynamics/phylogeographic module will train participants in the use of the BEAST platform, to perform advanced phylogenetic analyses aimed at deciphering the spatial and evolutionary dynamics of viruses; influenza and HIV will be used as case studies. BEAST is a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo (MCMC) algorithms. Outputs include rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
Participants will be provided a sample FASTA sequence datasets and walked through an example of BEAST analysis. An overview of the possible uses of BEAST will be discussed. If time allows, a few hours will be devoted to the analysis of the participants’ own data.
Philippe Lemey, University of Leuven, Belgium
Martha Nelson, Fogarty International Center, NIH
Amanda Perofsky, Fogarty International Center, NIH
Juliet Pulliam, SACEMA, South Africa
Andrew Rambaut, University of Edinburgh, Scotland
Nidia Trovao, Fogarty International Center, NIH
David Spiro, Fogarty International Center, NIH
Kaiyuan Sun, Fogarty International Center, NIH
Cecile Viboud, Fogarty International Center, NIH
Draft Agenda overview
Monday, December 3
Morning. Introductions and Research highlights (plenary; will include examples from influenza, HIV, animal-human interface and emerging infectious)
Afternoon: Break into phylogenetics and epidemiology groups
Start of 101 talks on principles of phylogenetics and disease modeling
Late afternoon: Software installation checks.
Tuesday December 4: 101 talks and software demonstrations
** For those who need more than a refresher in R, additional examples (and time) are available to become more familiar with R, in break-out groups.
Tuesday evening: Maria Giovani, NIAID programmes
Wednesday December 5: Presentations and hands-on practice with own data
Morning: Short presentations by participants (plenary or break-out groups, depending on size)
Remaining analytical topics to be covered
Afternoon: Work with your own data in small groups, facilitated by instructors.
Congratulations to our 2018 Summer Interns Class!
Five college students joined DIEPS this summer to work on MISMS projects.
Allison Randy-Cofie, Amherst College ’19
Project: Bioinformatics. Generating sub-sampled data sets of influenza A viruses from human, swine, equine, avian and canine hosts for all segments of the viral genome
Anne Lheem, Harvard University ’21
Project: Epidemiology. Identifying associations between influenza virus activity and antibiotic use on a global scale.
Felix Wu, Amherst College ’22
Project: Bibliometrics. Conducting a review of the publications produced by the MISMS and RAPIDD programs to assess their scientific impact and geographical diversity of co-authorship (published in Epidemics).
Garret Kern, Brown University ’22
Project: Bioinformatics. Creating a tool in Python to facilitate the downsampling of large genetic data sets by specified criteria (host, location, time, etc.). Creating R code to visualize pathogen data collected in humans and animal hosts (published in the Journal of Infectious Diseases).
Josh Grubs, Duke University ’18
Project: Biosafety. Creating protocols for chemical safety for use in Pakistan and other developing countries.
MISMS researchers Martha Nelson and Nidia Trovao (Fogarty International Center) conducted an analysis of genetic sequence data obtained from dogs in Guangxi, China, published in mBio in June 2018. The study was conducted as part of NIAID’s Centers for Excellence in Influenza Research and Surveillance (CEIRS), in collaboration with Adolfo García-Sastre, who heads the Center for Research on Influenza Pathogenesis (CRIP) at the Icahn School of Medicine at Mount Sinai, New York City.
Washington, DC – June 5, 2018 – Dogs are a potential reservoir for a future influenza pandemic, according to a study published in the journal mBio. The study demonstrated that influenza virus can jump from pigs into canines and that influenza is becoming increasingly diverse in canines.
“The majority of pandemics have been associated with pigs as an intermediate host between avian viruses and human hosts. In this study, we identified influenza viruses jumping from pigs into dogs,” said study investigator Adolfo García-Sastre, PhD, director of the Global Health and Emerging Pathogens Institute and principal investigator, Center for Research on Influenza Pathogenesis (CRIP), Icahn School of Medicine at Mount Sinai, New York City.
Influenza can jump among animal reservoirs where many different strains are located; these reservoirs serve as mixing bowls for the genetic diversity of strains. Pandemic influenza occurs when viruses jump from animal reservoirs to humans; with no prior exposure to the virus, most people do not have immunity to these viruses. The main animal hosts for influenza are wild birds, poultry and other domestic birds in a species pack; swine; and horses. Some of the viral genes from the 2009 pandemic H1N1 virus originated in birds, from an avian virus that jumped to pigs, exchanged some of its genes with previously circulating swine viruses and then jumped from pigs into humans. Birds and swine are major reservoirs of viral genetic diversity, whereas equines and canines have historically been restricted to one or two stable influenza A viruses lineages with no or very limited transmission to humans.
Fifteen years ago, researchers documented an influenza virus in a horse jumping into a dog, and this created the first circulating canine influenza viruses. Five years ago, researchers identified an avian-origin H3N2 canine influenza virus circulating in farmed dogs in Guangdong, China.
“In our study, what we have found is another set of viruses that come from swine that are originally avian in origin, and now they are jumping into dogs and have been reassorted with other viruses in dogs. We now have H1N1, H3N2, and H3N8 in dogs. They are starting to interact with each other. This is very reminiscent of what happened in swine ten years before the H1N1 pandemic.”
Specifically, in the new study, the researchers sequenced the complete genomes of 16 influenza viruses obtained from canines in Southern China (Guangxi autonomous region) during 2013-2015. Other key study collaborators included Martha Nelson, PhD, a specialist in phylogenetic analysis and transmission reconstruction at CRIP, and Ying Chen, PhD, an influenza surveillance specialist who brought the samples from China. The researchers found that the genomes contained segments from three lineages that circulate in swine in China: North American triple reassortant H3N2, Eurasian avian-like H1N1, and pandemic H1N1. In addition, the swine-origin H1N1 viruses were transmitted onward in canines and reassorted with the CIV-H3N2 viruses that circulate endemically in Asian dogs, producing three novel reassortant CIV genotypes (H1N1r, /H1N2r, and H3N2r).
The viruses in the study were collected primarily from pet dogs presenting with respiratory symptoms at veterinary clinics. Dogs in certain regions of China, including Guangxi, are also raised for meat and street dogs roam freely, creating a more complex ecosystem for canine influenza virus transmission. “The new virus we have identified in our study is H1N1, but it comes from swine and is of avian origin, so it is different antigenically from the new H1N1s that were seen in the pandemic and a different origin as the previous H1N1 seen in humans,” said Dr. García-Sastre.
Future studies will focus on characterizing the virus further and assessing, using human sera, whether humans have existing immunity against canine H1N1 or not. “If there is a lot of immunity against these viruses, they will represent less of a risk, but we now have one more host in which influenza virus is starting to have a diverse genotypic and phenotypic characteristics, creating diversity in a host which is in very close contact to humans,” said Dr. García-Sastre. “The diversity in dogs has increased so much now that the type of combinations of viruses that can be created in dogs represent potential risk for a virus to jump to a dog into a human.”
The researchers say it is time to think about ways to restrict the circulation of the influenza virus in dogs. The United States is free of avian influenza because every time avian influenza has been detected in poultry in this country, the chickens or turkeys are culled and eliminated from circulation,” said Dr. García-Sastre. “There are attempts to restrict influenza virus in pigs through vaccination and one could consider vaccination for dogs.”
CRIP is one of five Centers of Excellence for Influenza Research and Surveillance funded by the National Institute of Allergy and Infectious Diseases.
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The American Society for Microbiology is the largest single life science society, composed of more than 30,000 scientists and health professionals. ASM’s mission is to promote and advance the microbial sciences.
ASM advances the microbial sciences through conferences, publications, certifications and educational opportunities. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.
Post-doctoral fellowships in infectious disease modeling at the Fogarty International Center, NIH
The Division of International Epidemiology and Population Studies (DIEPS) of the Fogarty International Center (FIC), NIH, is seeking a post-doctoral fellow to work with Dr Cécile Viboud on a variety of infectious disease modeling projects. The projects fall under the auspices of two global computational modeling programs to control emerging and re-emerging infectious disease threats. The RAPIDD (Research and Policy for Infectious Disease Dynamics) program has established a global network of infectious disease modelers working at the research-policy interface, and provides evidence-based recommendations for disease control during outbreaks. The MISMS program leads research and training activities on the epidemiology and evolutionary dynamics of influenza viruses in humans and animal reservoirs. DIEPS has a long history of running computational projects and field studies, developing data-rich models, managing international collaborations and training programs, and translating research findings to policy.
The post-doc position would be supported with core FIC funds, allowing for independent, self-initiated research within broadly-defined areas of established DIEPS interests, including the transmission dynamics of respiratory infections, the impact of new vaccines, and anti-microbial resistance. The candidate would also have the opportunity to collaborate with other DIEPS researchers studying infectious diseases, including Dr Martha Nelson‘s work on pathogen evolution at the human-animal interface. The candidate will also have the opportunity to be an instructor at international training workshops. Successful candidates will work in the historic Stone House on the NIH Bethesda campus (3 mi. from DC) and enjoy fruitful interactions with the dynamic community of NIH intramural scientists.
The successful candidate will have a doctoral degree (PhD or equivalent) in computational or evolutionary biology, applied statistics or physics, biostatistics, or related quantitative fields, with at least 1 year of research experience in computational modeling. Strong quantitative and communications skills as well as proficiency in analytical and dynamic modeling, and/or phylogenetic analysis is required. The ability to critically evaluate data, publish scientific papers, work in interdisciplinary environments, and present at conferences is essential.
Interested candidates should contact Cécile Viboud (email@example.com). Applications should include a cover letter, a CV, a brief statement of research interests, and the names (and contact info) of three references. Salary will be commensurate with experience and NIH guidelines.
From February 5-9, 2018, MISMS staff taught a hands-on workshop in Dubai, UAE for participants coming from multiple countries in South Asia, including India, Pakistan, Nepal, and Bangladesh. The course included time-series analysis, R, disease modeling, phylogenetic analysis, and opportunities for participants to study their own data.
Many of the participants were part of the FIC-led MAL-ED study (including sites in India, Nepal, and Bangladesh) and Pakistan-based BEP study.
MISMS researchers identify the cause of sloth bear deaths at the Smithsonian National Zoo in Washington, DC: human-to-bear transmission of the 2009 H1N1 pandemic influenza A virus. Full article.
MISMS researchers analyzed fine-grain insurance claims data on influenza-like-illnesses over eight seasons in ~300 locations throughout the United States. Using statistical methods, they found that seven of eight epidemics likely originated in the Southern US, that influenza spatial transmission is dominated by local traffic between cities, and that seasons marked by novel influenza virus circulation had a particularly radial, localized spatial structure. The findings are in stark contrast to prevailing theories of influenza spatial transmission that suggest that transmission is favored in low humidity environments and that spread is a dominated by air traffic between populous hubs. The findings are published in PLoS Computational Biology.
6th ANISE (African Network for Influenza Surveillance and Epidemiology) Meeting
November 13 to 17, 2017
at Hotel Carlton
Please register and submit your abstract on-line (due August 15) to the meeting website: www.anise-network.org
The agenda is in progress, but we plan to hold plenary sessions from November 13- 15 and training workshops November 16-17.