Research
RNA Virus Genomic Epidemiology
Like many of our colleagues, we have spent the last ~18 months responding to the COVID-19 pandemic and have spent much of our time working on the genomic epidemiology of SARS-CoV-2. While a part of the Grubaugh Lab, we were able to identify the first locally acquired cases of COVID-19 in Connecticut as being imported from other states opposed to other countries, aid local and state health departments in outbreak investigations, and establish the SARS-CoV-2 Genomic Surveillance Initiative. Our routine sequencing initiatives have provided ample data to answer important questions regarding SARS-CoV-2 introductions, variants, and viral dynamics.
Looking forward, we will continue to work closely with local and state health departments, as well as our partners in professional sports leagues, to conduct "real-time" genomic epidemiology of SARS-CoV-2. As well, we will look to apply these tools and techniques to other locally relevant pathogens, such as West Nile virus.
Relevant Publications:
Genomics of Disease Control/Elimination
Helminth infections are diseases of poverty and are a massive cause of human morbidity around the world. For many parasitic nematodes there are active large-scale disease control and/or elimination programs in place. We are interested in incorporating genomic epidemiology approaches to better understand parasite transmission in light of control/elimination programs. Specifically, we are focused on filarial worms and hook worms.
The Global Program to Eliminate Lymphatic Filariasis (LF) was established by the W.H.O. in the 1990's to eliminate LF transmission as a public health concern, largely through the use of mass drug administration (MDA). While this program has been remarkably successful at disrupting the human/mosquito transmission cycle in some areas, there are numerous countries where LF transmission persists after decades of MDA. Persistent transmission could be due to a number of factors such as drug resistance, parasite reintroductions, or simply sub-optimal MDA participation. We are interested in developing genomic epidemiology approaches for Wuchereria bancrofti, the most common species of worm causing LF, to better understand, and ultimately alleviate, persistent LF transmission.
As well, we are partnering with Michael Cappello's group at the Yale School of Medicine to develop genomic tools for Necator americanus, the human hookworm, with a particular emphasis on understanding transmission dynamics in Ghana.
Relevant Publications:
Training and Methods Development
Public health and global health must be a collaborative endeavor, therefore It is a core function of our lab to be able to train our colleagues in all aspect of work. Whether it is teaching folks how to key out mosquitoes, do library preparation, or build a custom Nextstrain pipeline, we pride ourselves on knowing our systems well enough to teach them to others. If we can be anything, we want to be good collaborators!
We deal with large variety of organisms in the lab, from RNA viruses with tiny 10Kb genomes to eukaryotic worms with actual chromosomes, so we have a number of different sequencing approaches available to us. We are always tinkering with different library preparation and sequencing strategies to make the process as simple and straightforward as possible. Our goal is to be able to go from sample collection through to a finished analysis entirely in-house, while making our approaches transferable across a range of different laboratory infrastructures.
Relevant publications:
Check out the latest publications on my Google Scholar to get full picture of the work I have done previously and the work the Fauver lab will be doing in the future.