David Kennedy

Assistant Professor of Biology

David Kennedy

Research Summary

Ecology and evolution of infectious diseases, with particular interest in how disease dynamics influence pathogen emergence, virulence evolution, and drug or vaccine resistance.

Huck Graduate Students

Huck Affiliations

Links

Publication Tags

Vaccines Pathogens Viruses Poultry Drug Resistance Vaccination Principal Component Analysis Virulence Aquaculture Resistance Pathogen Farms Caenorhabditis Industry Clinical Trials Strain Markov Chain Monte Carlo Host Range Efficacy Genetic Drift Economics Pharmaceutical Preparations Severe Acute Respiratory Syndrome Parallel Computing Marek Disease

Most Recent Publications

Developing an empirical model for spillover and emergence: Orsay virus host range in Caenorhabditis

Clara L. Shaw, David A. Kennedy, 2022, Proceedings of the Royal Society B: Biological Sciences

Pathogen evolution during vaccination campaigns

Troy Day, David A. Kennedy, Andrew F. Read, Sylvain Gandon, 2022, PLoS Biology on p. e3001804

The economics of managing evolution

Troy Day, David A. Kennedy, Andrew F. Read, David McAdams, 2021, PLoS Biology

What the reproductive number R<sub>0</sub> can and cannot tell us about COVID-19 dynamics

Clara L. Shaw, David A. Kennedy, 2021, Theoretical Population Biology on p. 2-9

What you need to know about the new COVID-19 variants

David Kennedy, 2021,

The evolutionary epidemiology of pathogens during vaccination campaigns

Troy Day, David Kennedy, A Read, Sylvain Gandon, 2021, arXiv preprint arXiv:2109.13680

Developing an empirical model for spillover and emergence: Orsay virus host range in Caenorhabditis

Clara Shaw, David Kennedy, 2021, bioRxiv

Exceptions to the rule: Why does resistance evolution not undermine antibiotic therapy in all bacterial infections?

Amrita Bhattacharya, Anton Aluquin, David Kennedy, 2021, bioRxiv

Detection, not mortality, constrains the evolution of virulence

David Kennedy, 2021, bioRxiv

Why it matters that the coronavirus is changing -- and what this means for vaccine effectiveness

David Kennedy, 2020,

Most-Cited Papers

Imperfect vaccination can enhance the transmission of highly virulent pathogens

Andrew F. Read, Susan J. Baigent, Claire Powers, Lydia B. Kgosana, Luke Blackwell, Lorraine P. Smith, David A. Kennedy, Stephen W. Walkden-Brown, Venugopal K. Nair, 2015, PLoS Biology on p. e1002198

Why does drug resistance readily evolve but vaccine resistance does not?

David A. Kennedy, Andrew F. Read, 2017, Proceedings of the Royal Society B: Biological Sciences

Potential drivers of virulence evolution in aquaculture

David A. Kennedy, Gael Kurath, Ilana L. Brito, Maureen K. Purcell, Andrew F. Read, James R. Winton, Andrew R. Wargo, 2016, Evolutionary Applications on p. 344-354

Why the evolution of vaccine resistance is less of a concern than the evolution of drug resistance

David A. Kennedy, Andrew F. Read, 2018, Proceedings of the National Academy of Sciences of the United States of America on p. 12878-12886

Monitor for COVID-19 vaccine resistance evolution during clinical trials

David A. Kennedy, Andrew F. Read, David A. Kennedy, 2020, PLoS Biology

Industry-Wide Surveillance of Marek's Disease Virus on Commercial Poultry Farms

David A. Kennedy, Christopher Cairns, Matthew J. Jones, Andrew S. Bell, Rahel M. Salathé, Susan J. Baigent, Venugopal K. Nair, Patricia A. Dunn, Andrew F. Read, 2017, Avian Diseases on p. 153-164

Using quantitative disease dynamics as a tool for guiding response to avian influenza in poultry in the United States of America

K. M. Pepin, E. Spackman, J. D. Brown, K. L. Pabilonia, L. P. Garber, J. T. Weaver, D. A. Kennedy, K. A. Patyk, K. P. Huyvaert, R. S. Miller, A. B. Franklin, K. Pedersen, T. L. Bogich, P. Rohani, S. A. Shriner, C. T. Webb, S. Riley, 2014, Preventive Veterinary Medicine on p. 376-397

Pathogen growth in insect hosts: Inferring the importance of different mechanisms using stochastic models and response-time data

David A. Kennedy, Vanja Dukic, Greg Dwyer, 2014, American Naturalist on p. 407-423

Effects of multiple sources of genetic drift on pathogen variation within hosts

David A. Kennedy, Greg Dwyer, 2018, PLoS Biology

Combining principal component analysis with parameter line-searches to improve the efficacy of Metropolis–Hastings MCMC

David A. Kennedy, Vanja Dukic, Greg Dwyer, 2015, Environmental and Ecological Statistics on p. 247-274

News Articles Featuring David Kennedy

Sep 30, 2022

Disease outcomes differ by new host species in virus spillover experiments

Why has the SARS-CoV-2 virus ravaged the global human population, but many other animal viruses haven't? Using nematode worms as a model, researchers at Penn State conducted a set of experiments to investigate the factors influencing the disease outcomes of virus spillover events.

Full Article

Nov 29, 2021

Vaccine Makers Already Testing Their Shots Against Omicron Variant

As concerns about the new Omicron variant grow, vaccine makers say they're already working on ways to protect people against the potential new threat.

Full Article

Nov 26, 2021

Will Covid variant omicron need a new vaccine? Time and data will tell

The discovery of another coronavirus variant has raised new concerns about the ability of existing vaccines to protect against the mutating virus — and whether they’ll need to be updated.

Full Article

Nov 16, 2021

New tool weighs costs and benefits of managing evolution of pathogens and pests

Spend money now on antibiotic stewardship practices or save the money but run the risk of potentially deadly antibiotic-resistant bacteria emerging later? A new economic tool can help physicians, farmers and other people whose activities may influence the evolution of biological organisms, such as pathogens and insects, decide when they should invest in evolution management strategies.

Full Article

Apr 28, 2021

Are the vaccines effective against mutant Covid variants?

India is undergoing a massive vaccination effort in the midst of a devastating rise in reported daily cases and deaths. While the main cause of the rise in cases is yet to be determined, epidemiological and virological data point to the rise of new variants of concern being a major contributing factor.

Full Article

Mar 17, 2021

How Much Should We Really Worry About the Coronavirus Variants?

Even as things look promising for summer, the coronavirus is still finding new ways to threaten our creep back to normal and our general sense of health and safety.

Full Article

Jan 15, 2021

How devastating could Brazil's 'super-covid' be? Study finds coronavirus overwhelmed the country, killing nearly 40% of hospitalized patients as fears grow its variant could ALREADY be in America

Nearly 40 percent of hospitalized COVID-19 patients in Brazil died of the virus as the nation's health care system was inundated with coronavirus cases last year, a new study estimates.

Full Article

Dec 22, 2020

Why it matters that the coronavirus is changing — and what this means for vaccine effectiveness (Philadelphia Inquirer)

If this new version of the virus is here to stay, as it appears to be, what does that mean? Will this new version of the virus replace the old one? Will it be easier to catch? And, most important, will the current vaccines still be effective?

Full Article

Dec 22, 2020

Why it matters that the coronavirus is changing — and what this means for vaccine effectiveness (The Conversation)

A new variant of SARS-CoV-2 is spreading rapidly in the United Kingdom, with over 1,400 cases since September. SARS-CoV-2, the virus that causes COVID-19, generally accumulates mutations slowly over time, but this new variant had accumulated many mutations quickly.

Full Article

Dec 14, 2020

What happens if you skip the second dose of the COVID-19 vaccine?

As Pfizer’s COVID-19 vaccine begins circulating, there is another big logistical challenge ahead: reminding people to get the second dose.

Full Article