The group’s research response to COVID-19

This is an update on the group's research response to the COVID-19 pandemic. As an infectious disease group we have been keen to contribute to the international research effort where we could be useful, while recognising the need to continue our research on other important infections where possible.

  • Bugbank. Thanks to a pre-existing collaboration between our group, Public Health England and UK Biobank, we were in a position to help rapidly facilitate COVID-19 research via SARS-CoV-2 PCR-based swab test results. Beginning mid-March, we worked to provide regular (usually weekly) updates of tests results, which were made available to all UK Biobank researchers beginning April 17th. This is one of several resources on COVID-19 linked to UK Biobank. Beginning in May we provided feeds to other cohorts: INTERVAL, COMPARE, Genes & Health and the NIHR BioResource. We provide updates on this work through the project website We have published a paper describing the dynamic data linkage in Microbial Genomics (press release). Key collaborators in this project are Jacob Armstrong (Big Data Institute) Naomi Allen (UK Biobank) and David Wyllie and Anne Marie O'Connell (Public Health England).

  • Epidemiological risk factors for COVID-19. Graduate student Nicolas Arning and I are developing an approach to quantify the effects of lifestyle and medical risk factors for COVID-19 in the UK Biobank that accounts for inherent uncertainty in which risk factors to consider. The new method employs the harmonic mean p-value, a model-averaging approach for big data that we published previously. We are in the process of evaluating the performance of the approach, comparing it to machine learning, and interpreting the results.

  • Antibody testing for the UK Government. Postdoc Justine Rudkin has been working in the lab with Derrick Crook, Sir John Bell and others to measure the efficacy of antibody tests for the UK Government. They have tested many hundreds of kits to establish the sensitivity and specificity of the tests to help evaluate the utility of a national testing programme. This work was crucial in demonstrating the limitations of early blood-spot based tests, and the credibility of subsequent generations of antibody tests. The work has been published in Wellcome Open Research.

Work on other infections that has continued during the lockdown. Postdoc Sarah Earle continues research into pathogen genetic risk factors for diseases including tuberculosis and meningococcal meningitis, while Steven Lin has continued to pursue work on hepatitis C virus genetics and epidemiology. Many of our close collaborators are infection doctors and they have of course been recalled to clinical duties. Laboratory work in the group has been severely disrupted, particularly several of Justine's Staphylococcus aureus projects. We are keen to pick up on those projects where we left off when the chance arrives.

Teaching: Online lectures and practical on Phylogenetics in Practice

On March 16th, we were in the interesting position of running an infectious disease course at the Big Data Institute on the day the national lockdown was announced in response to the COVID-19 pandemic. As a result, we were among the first in the university to do remote teaching, something Katrina Lythgoe and the rest of us had prepared for in anticipation of the lockdown a week earlier that never happened.

These are the two online lectures in the Health Data Sciences CDT that I gave called Phylogenetics in Practice.

The online practical, which applies phylogenetics approaches to understand the Zika virus epidemic, is implemented as a Docker container, and available here.

How experts use disease modeling to help inform policymakers

Harry Stevens and John Muyskens for The Washington Post put you in the spot of an epidemiologist receiving inquiries from policymakers about what might happen:

Imagine you are an epidemiologist, and one day the governor sends you an email about an emerging new disease that has just arrived in your state. To avoid the complexities of a real disease like covid-19, the illness caused by the novel coronavirus, we have created a fake disease called Simulitis. In the article below, we’ll give you the chance to model some scenarios — and see what epidemiologists are up against as they race to understand a new contagion.

Fuzzy numbers, meet real-world decisions.

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PLOS ONE publishes additional Coronavirus-related papers

Today PLOS ONE added to its collection of COVID-19 papers since we started fast-tracking submissions on January 31st. This study was conducted by Constantinos Siettos from the Universita degli Studi di Napoli Federico II, Italy and colleagues.

Johns Hopkins providing course on using epidemiology to understand the Covid-19 numbers

The numbers are fuzzy. You take them at face value, and you end up with fuzzy interpretations. Starting at the end of this month, Johns Hopkins is providing a two-week epidemiology course on understanding these numbers better:

This free Teach-Out is for anyone who has been curious about how we identify and measure outbreaks like the COVID-19 epidemic and wants to understand the epidemiology of these infections.

The COVID-19 epidemic has made many people want to understand the science behind pressing questions like: “How many people have been infected?” “How do we measure who is infected?” “How infectious is the virus?” “What can we do?” Epidemiology has the tools to tell us how to collect and analyze the right data to answer these questions.


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The Humility of Expertise

  Ed note: Today we welcome Junaid Nabi back to the blog. For more about Junaid, please see the bottom of this post. The following is adapted from a speech that was delivered as one of

Research News: The Military And Motor Neuron Disease: Military-related factors affecting survival of veterans with ALS

Military-related factors affecting survival of veterans with ALS By Beth Jones Military veterans may have higher rates of death from the progressive neurodegenerative disease amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, than

Pursuing Preprints, Preventing Pandemics: How pre-peer-review posting can accelerate outbreak science | PLOS Research News

0000-0002-8715-2896 Preprints – scientific papers posted online prior to peer review – offer opportunities to share and discuss research rapidly and openly, and Michael Johansson, infectious disease expert and founder of the nonprofit Outbreak Science,

Responding to Emergencies One Behavior at a Time

A group of Ebola response volunteers in Nigeria.

To improve the health and safety of people in the United States and around the world, we have to influence and change behaviors. It can be difficult to try new things, or stop old things as behaviors range from simple to complex, but one way to consider behavior change is to think of any change as a passive or active choice.

Public health practitioners must think about interventions in terms of the behaviors they are asking people to adopt, stop or continue. What would encourage someone to change what they are currently doing? Before you can influence someone’s behavior or change their choices about a behavior (risky or protective) you need to know how their judgments and decisions are made about that behavior in the first place.

Behaviors are rooted in traditions

During the Ebola response behavior change was critical to prevent people from getting sick and ultimately stop a disease threat. In the wake of the outbreak, communities in West Africa were encouraged to give up or change their traditional burial practices. Some of these longstanding rituals, like washing the body, proved dangerous because the virus can live on the skin of a victim after death. Communicators developed public health messaging to help change social norms and customs for burials. It was important to understand behavioral science and anthropology in order to communicate about safe burial practices in a way that would make people choose to change a behavior that was ingrained in their culture.

Behaviors are rooted in social 7 Things to Consider When Communicating About Health. Trust: Will people trust the information? Who is the best source to put the information out? Information: What information is necessary, and how will people find it? How much is enough, or too much? Motivation: How relevant is the information to the people we’re trying to reach? Environment: What are the conditions that surround and affect the audience? Capacity: What is people’s ability to act on the information? Are there barriers? Perception: What will the audience think about the information? What will inspire them to act on it? Response: How will people respond? What can we do to stay engaged with them and give them support as they take action?norms

The 2016 Zika virus outbreak is the first time in more than 50 years that a virus has been linked to serious birth defects. Due to the impact of Zika virus infection during pregnancy, social norms and perceptions around provider visits had to be addressed to alleviate concerns about the cost of screening. Clinicians were educated about the risks associated with Zika virus, how to prevent infections, and reporting suspected cases to their state, local, or territorial health departments and women were offered free clinical services, education, and access to Zika prevention kits.

Behaviors are rooted in beliefs

The fight to eradicate polio teaches us the importance of beliefs in behavior change during a response to a public health threat. Creating an effective polio vaccine was only the first step in the effort to eradicate polio. Of course an effective vaccine was necessary to prevent polio virus infections, but getting communities to accept the vaccine was equally important. Public health practitioners created messages that build on cognitive, developmental, and social psychology to persuade parents to bring their children into clinics to get vaccinated.

Behaviors inform preparedness and response

Responding to emergencies effectively requires combined expertise in many fields, including behavioral science. Epidemiology, for example, allows us to understand how many people have a disease and characterize the disease, while behavioral science identifies the role of human behavior and psychosocial factors. Behavioral science expertise can identify methods to communicate and design campaigns to change behavior that are culturally and socially acceptable.

It is important that we maintain humility when we try to understand why people do or think what they do. We often assume that we understand human behavior, but we must remain open-minded when working with people from all different backgrounds and cultures. Who’s to say that what our culture considers right and true necessarily translates to the same belief systems elsewhere? Thus public health ethics is also an important consideration when suggesting behavioral change interventions. When we are in situations that are particularly dangerous or stressful, our assumptions about other people’s behavior can lead to recommendations or actions that seem counterintuitive or wrong to them. Careful application of behavioral science is critical to any mission that seeks to improve public health and safety, here and around the world.

The Communication Research and Evaluation blog series highlights innovative research and evaluation methods used at CDC to improve behavior change campaigns.

Day Zero: The impact of Cape Town’s water shortage on public health

0000-0002-8715-2896 A story that’s been making the rounds recently is the impending water shortage in Cape Town. Multiple years of droughts have resulted in lower and lower water levels in the reservoirs that supply the