Virus researchers of Vilnius University (VU) Life Sciences Center Dr. Gytis Dudas and Dr. Allison Black from the USA have published a book The Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health. The book is intended for public health professionals who are interested in genomic epidemiology or who want to start applying it in their work. The authors introduce the readers to the essential principles of genomic epidemiology, tools and the implementation and application of genomic monitoring systems in practice.
What is genomic epidemiology? According to one of the authors Dr. Gytis Dudas, combining genomics and epidemiology in practice refers to the branch of science that seeks to trace the spread of various infectious diseases based on the genomes of the agents of those diseases.
"Epidemiology, as a field of science, is probably perceived by many as an attempt to understand diseases, their prevalence in populations and the factors responsible for those diseases. Genomes - the entire genetic material of one or another organism - is perhaps a less heard, but understandable term. Genomic epidemiology would not exist without the ever-improving and expanding technology of sequence reading (sometimes called sequencing), which nowadays allows scanning the genome of any disease-causing virus, bacterium or fungus", says Dr. G. Dudas.
The benefits of genomic epidemiology
Speaking about genomic epidemiology, a researcher from the VU Life Sciences Center suggests imagining the situation as if there was a sharp increase in tick-borne encephalitis cases one summer. "From the larger number of cases, we can only raise the question: what happened? Has a more aggressive strain of tick-borne encephalitis arrived? Perhaps the health care systems have started to use newer diagnostic methods and are able to detect cases that would have been missed before? Genomic epidemiology is one source of information that can significantly limit the number of possibilities," he describes.
During the West African Ebola virus epidemic of 2013–2016, when sequencing technologies were already quite advanced, genomic epidemiology contributed at various stages to the response of the three most affected countries in the region (Guinea, Sierra Leone, and Liberia) by this hemorrhagic fever. Just answering the question of whether the strain of Ebola virus that caused this epidemic had always been circulating in the region undetected, or whether it came from somewhere else, revealed that this particular strain of Ebola virus entered the region from Central Africa (a much more common range for Ebola) sometime within a decade from about 2004 to 2013–2016.
In the middle of the epidemic, precisely thanks to genomic epidemiology, it was already possible to say that travelers infected with the Ebola virus contributed much more to the spread of the disease among settlements than, for example, the urbanization of the entire region, which was unique to this West African epidemic. Until then, the Ebola virus had normally circulated in hard-to-reach small villages in the rainforests of Central Africa. In later stages, the World Health Organization (WHO) in West Africa used genomic epidemiology to isolate the last chains of transmission of the still-circulating Ebola virus, allowing the detection of a new case to determine whether it belonged to a chain of infection that WHO was already aware of and following, or a new one that has so far been overlooked and should be tracked down with additional resources.
Will help health professionals learn
Genomic epidemiology developed as an offshoot of the academic fields of population genetics and phylogenetics, so much of genomic epidemiology research is still conducted by scientists rather than public health professionals, who lack the necessary expertise. During the COVID-19 pandemic, the benefits of genomic epidemiology became more than obvious, and even countries that previously did not have similar programs began to develop their sequencing capabilities and contributed available resources to the sequencing of the SARS-CoV-2, the causative agent of COVID-19.
The ensuing tsunami of sequencing data (over 16 million SARS-CoV-2 genomes have now been scanned worldwide) has been both an unprecedented opportunity to learn more about the virus and a challenge to the existing methods. Genomic epidemiology will sooner or later become a routine part of the work of every public health worker but learning it from academic publications alone is not a sustainable solution, and it is this key gap that this book seeks to fill.
More about the book:
Dr. A. Black and Dr. G. Dudas's book The Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health was published by Chapman & Hall in the United Kingdom.
Although the book is aimed at public health professionals interested in (or perhaps considering implementing) genomic epidemiology, the information is presented in plain language that is understandable to the general public. In the book, you will find a discussion of the fundamental theoretical ideas of genomic epidemiology, for example, how quickly mutations appear in the genomes of microorganisms under certain circumstances, when epidemiological links between two cases of a disease can be ruled out. Genomic monitoring systems, representative sampling, etc. are also discussed. After acquiring this knowledge, the book reviews several practical examples of the application of genomic epidemiology (including the history of the discovery of the SARS-CoV-2 line B.1.620 discovered in Lithuania). The book concludes with an overview of the tools currently widely used in genomic epidemiology and the discussion on problems that the intricacies of real biological data can pose for analyses.
More about the authors of the book:
Dr. Allison Black currently leads the molecular epidemiology activities of the Washington State Department of Health. The researcher received her PhD at the University of Washington, Seattle, in Trevor Bedford's laboratory. During his doctoral studies, Dr. A. Black sought to better understand the Zika virus epidemic in the Americas and the Ebola virus epidemic in the province of North Kivu (Democratic Republic of Congo), and also devoted a lot of time to the development of genomic epidemiology in the United States. You can find more of her work here.
Dr. Gytis Dudas works at VU Life Sciences Center. The researcher defended his thesis at the University of Edinburgh, in Andrew Rambaut's laboratory. During his doctoral studies, Dr. G. Dudas has mainly studied the West African Ebola virus epidemic and MERS-CoV outbreaks in the Arabian Peninsula. You can find more of his work here.