A vast majority of the newly discovered human pathogens are viruses that have jumped to humans from an animal host ("cross-species transmission"). The majority of these viruses have RNA rather than DNA for genetic material, and this allows their genomes to mutate rapidly and adapt to new environments. Some of these emergent viruses, such as Ebola and Zika, can result in epidemics of human disease. To accurately predict the likelihood and potential consequences of an emergence of a novel viral pathogen into new host species, it is essential to understand the dynamics of virus populations during adaptation to a new host. Next generation sequencing technology enables to process of virus evolution to be defined at unprecedented depth, however, the massive data sets generated by this novel technology require computational expertise to disentangle. This presentation will introduce the attendees to some examples of how biologists and computer scientists have collaborated and used cutting edge ultra-deep sequencing technology to study the dynamics of a 2009 rabies outbreak. This case study, based on a dramatic increase (>350%) in the gray fox population infected with a rabies variant for which striped skunks server as the reservoir hosts, will be used to help illustrate the changes in the viral genome during cross-species viral transmission.

Speaker Bios


Dr. Monica Borucki

Dr. Borucki is a Biomedical Scientist in the Biosciences and Biotechnology Division of LLNL. Her research focuses on the mechanisms of viral evolution and emergence, biosurveillance, and viral forensics. Before coming to LLNL, she served as a Research Geneticist at USDA-ARS and adjunct faculty at Washington State University where she investigated the epidemiology and virulence of food pathogen, Listeria monocytogenes. Her postdoctoral experience involved investigation of the ecology and genetics of South American hantaviruses at the University of Nevada, Reno. She received her Ph. D. from Colorado State University where she studied the evolution of La Crosse virus, a mosquito-borne virus that causes encephalitis. She received her M. S. at California Polytechnic State University San Luis Obispo investigating the revival and characterization of ancient Bacillus spores from bees entombed in amber.



Dr. Jonathan Allen

Dr. Allen is a Research Staff Member in the Pathogen Bioinformatics Group at LLNL. He is working to develop and apply novel algorithms to detect and characterize pathogens using next-generation sequencing. Previously, Dr. Allen was a postdoctoral fellow at LLNL where he worked on creating computational methods to facilitate the detection of engineered biological threats.  Prior to joining LLNL, he worked as a software engineer at The Institute for Genomic Research and University of Maryland’s Institute for Advanced Computer Studies, where he helped develop some of the early software tools used for automated genome annotation in eukaryotic genomes.  Dr. Allen holds a B. S. in Computer Science from UC Santa Cruz, and he received his Ph. D. in Computer Science from Johns Hopkins University in 2006.



Elizabeth Lopez

Elizabeth Lopez has been a biotechnology, biology and biochemistry teacher in the Livermore Valley Joint Unified School District since 2005. Currently, she teaches at Granada High School in Livermore. Prior to this, Liz worked in the biotechnology industry, first at Mendel Biotechnology and later at Illumina, both companies are in the San Francisco Bay area. Elizabeth has her B. A. in Molecular and Cellular Biology from UCSC, and M. A. in Biology from Clemson University. She was awarded the Excellence in teaching award in 2009 from Sandia National Laboratory. Liz has partnered with Lawrence Livermore National Laboratory and Rutgers University working in the Waksman Student Scholars Program and is currently working part-time in the Science Education Program at LLNL.

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