I am a Bioinformatician at the Massachusetts Department of Public Health. Before that, I worked in the Sabeti Lab at the Broad Institute. I got my PhD at Harvard’s department of Organismic and Evolutionary Biology and I got my bachelor’s and my MEng from MIT, where I majored in Computer Science and Molecular Biology and Math and minored in Writing.
I work on pathogen identification and characterization through metagenomic and amplicon sequencing, which I use to study undercharacterized or novel viral species, interactions between co-occurring infections, and disease outbreaks, especially among vulnerable and underserved populations. Broadly, I am interested in disease surveillance, human and disease evolution and migration, and personal genomics.
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak
December 2021
Summary: An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021—the first large outbreak mostly in vaccinated individuals in the US—prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants
February 2022
Abstract: The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic CARMEN (mCARMEN), that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
SARS-CoV-2 Reinfection in a Liver Transplant Recipient
August 2021
Objective: To distinguish SARS-CoV-2 reinfection from recrudescence in a liver transplant recipient with 2 distinct episodes of COVID-19 using clinical history and viral genomic sequencing.
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
December 2020
Abstract: Analysis of 772 complete SARS-CoV-2 genomes from early in the Boston area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, while other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed significantly in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help understand the link between individual clusters and wider community spread.
Combining genomics and epidemiology to track mumps virus transmission in the United States
February 2020
Abstract: Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. We paired epidemiological data from public health investigations with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing on Massachusetts university communities. Our analysis suggests continuous, undetected circulation of mumps locally and nationally, including multiple independent introductions into Massachusetts and into individual communities. Despite the presence of these multiple mumps virus lineages, the genomic data show that one lineage has dominated in the US since at least 2006. Widespread transmission was surprising given high vaccination rates, but we found no genetic evidence that variants arising during this outbreak contributed to vaccine escape. Viral genomic data allowed us to reconstruct mumps transmission links not evident from epidemiological data or standard single-gene surveillance efforts and also revealed connections between apparently unrelated mumps outbreaks.
| [read article in PLOS Biology] |
| [read about it in Reuters] [read about it in The Harvard Gazette] [read about it in The Harvard Crimson] [read about it in Broad News] |
This MATLAB-to-Julia translator aims to do much of the tedious work of converting source code from MATLAB to Julia, in hopes that a MATLAB user who is curious about Julia could spend most of their first moments with the language exploring its capacity to improve their existing programs rather than wrangling with bugs or a new syntax.
90 scripts and counting for small, recurring biology-related tasks that I have accumulated during my graduate career. Includes scripts for processing fasta files, aligned fasta files, blast output, vcf files, tables, and lists; downloading files; searching files in bulk; inferring sequence lineages; and more.
Volunteering
I mentor an exceptional undergraduate student through Harvard’s Women in STEM Mentorship Program.
This fall and last fall I have been an Educational Counselor for MIT Admissions, which means I interview students from my hometown for admission to MIT undergrad.
This fall, I also mentored high school students at Cambridge Rindge and Latin School (CRLS, confusingly not CLRS) on career planning and college applications.
Last fall and winter (2020) I mentored an exceptional high school student through HPREP (Health Professions Recruitment and Exposure Program) at Harvard Medical School. I also helped judge Harvard’s 2021 National Collegiate Research Conference poster session and MIT’s 2021 Science Olympiad Invitational.
I also do other, less academic volunteering. When the weather is nice, my friends and I pick up trash around town, both in organized clean-up events and on our own. I also like to hunt down secondhand copies of my favorite books to populate previously a particular favorite little library in our old neighborhood and now a little library of our very own, which we built.
I am a member of the Novavax Phase 3 COVID-19 vaccine trial. If you look closely, you can find me as a data point in the Phase 3 publication: Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine. If you haven’t already, get boosted!
More coming soon. 🙂
L. A. K. 