Andersen Lab

We are using infectious disease genomics to investigate the interaction between the human host and highly pathogenic viruses such as Zika, Ebola, and Lassa. Our goal is to understand how these viruses evolve in response to selection pressures imposed by the host immune system. Using a combination of computational biology, experimentation, and field work in West Africa our hope is to change the way we develop vaccines and therapeutics for these and other emerging pathogens.


Positions available

Come join us at the beautiful Scripps Research Institute campus in La Jolla, California. We are currently looking to hire wet lab and computational postdocs.


Roots, Not Parachutes - a call for sustainable research collaborations

Rooted_CollaborationsInfectious disease outbreaks continue to pose challenges to global health and security, prompting reactive countermeasures. Recently, severe outbreaks of Ebola and Zika virus were designated by the World Health Organization as “Public Health Emergencies of International Concern.” Other emerging viral pathogens have warranted similar attention, including virus outbreaks from Lassa, Chikungunya, avian influenza, Nipah, SARS, and MERS. Additionally, endemic human pathogens, such as dengue and West Nile virus, have expanded to new regions due to changing demographics and increased urbanization. Recently there has been a lot of focus on “Parachute Research“, where foreign researchers “parachute” into countries affected by infectious disease outbreaks, such as Zika and Ebola. These researchers then conduct research in isolation, and depart without creating sustainable infrastructure or a lasting impact in the affected countries. In a recent commentary in the journal Cell, we instead advocate for the creation of long-term sustainable collaborations in outbreak-prone areas of the world.

International research collaborations are essential in combating major public health emergencies. Failure to collaborate can delay critical findings, hamper outbreak response, and erode trust between institutions and nations. In the commentary, we draw on our experience establishing the Viral Hemorrhagic Fever Consortium and the African Center of Excellence for Genomics of Infectious Disease in West Africa and show how “rooted” collaborations can assist during public health emergencies. Recognizing that many successful infectious disease research collaborations exist, we highlight their critical and often unheralded role in mitigating and preventing infectious disease outbreaks.

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Review on Ebola evolution in Nature

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The 2013-2016 Ebola epidemic in West Africa was of unprecedented size and devastation, but also stands a landmark for infectious disease genomics. By sequencing virus genomes directly from patient samples, scientists are now able to investigate how viruses evolve, transmit between individuals, and spread across country borders during outbreaks, directly informing infection control.


Zika sequences from Miami mosquitoes

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Data here. Protocol here. Three pools of Aedes aegypti mosquitoes collected in Miami Beach on August 22nd and 23rd, 2016, were found to be infected with Zika virus. Through our collaborators, Scott Michael and Sharon Isern from Florida Gulf Coast University, we recently received samples of these mosquitoes for sequencing using our amplicon-based protocol for MiSeq.


Zika sequence from local Florida transmission

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Data here. Protocol here. In collaboration with Dr. Diogo Magnani in the Watkins Laboratory in the Dept. of Pathology at the University of Miami’s Miller School of Medicine, we recently received plasma and saliva from two people with Zika virus infections living in the Miami area. Using our amplicon-based approach previously used to sequence Zika virus from travel-related Zika virus cases in Florida, we sequenced the entire coding sequence from the saliva of one individual believed to have been infected in or near Miami.