Louise Moncla

Postdoc
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I am currently a post-doc in the Bedford lab who uses genomics to understand virus emergence and transmission. I received my Bachelor’s degree in biology from Penn State University, and my PhD from the University of Wisconsin-Madison under the direction of Thomas Friedrich. During my PhD, I developed protocols for generating and bioinformatically processing deep sequence data from RNA viruses. We used this data to investigate how RNA viruses evolve within individual hosts, and during transmission between them. I am particularly interested in how viruses adapt to new host species, and the role that transmission bottlenecks play in viral evolution.

I started my post-doc in the Bedford lab in 2017 with the goal of using phylogenetics to trace virus evolution and transmission. I’ve worked on combining genomics data across scales to understand how new mutations are generated during infection and propagated between individuals and across communities. I also employ genomic epidemiology methods to investigate drivers of viral outbreaks, which we recently applied to Zika virus in Colombia and mumps in Washington State. Finally, I have a long-term interest in the virologic and evolutionary factors that facilitate avian influenza virus host switching. I maintain the avian flu builds at nextstrain.org/flu/avian and have contributed to past and ongoing work that examines avian influenza evolution at the animal-human interface.

Papers

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

Cryptic transmission of SARS-CoV-2 in Washington State

Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

Comprehensive mapping of avian influenza polymerase adaptation to the human host

Within-host evolution of human influenza virus

Projects

ncov - Nextstrain build for novel coronavirus SARS-CoV-2

fauna - RethinkDB database to support real-time virus analysis

mumps-seq - Protocols for sequencing mumps viruses

mumps-wa-phylodynamics - Public repository for genomic epidemiology investigation of the 2016/2017 mumps outbreak in Washington state

h5n1-cambodia - Within-host diversity in H5N1-infected humans and poultry in Cambodia

sacra - Cleaning scripts for real-time pathogen analysis

Posts

Quantifying within-host evolution of H5N1 influenza in humans and poultry in Cambodia

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

Multiple introductions of mumps virus into Washington State

Characterization of 27 mumps virus genomes from the Washington state outbreak