Lydia A. Krasilnikova
A5045166828- SARS-CoV-2 and COVID-19 Research
- Virology and Viral Diseases
- SARS-CoV-2 detection and testing
- COVID-19 epidemiological studies
- Zoonotic diseases and public health
- Biosensors and Analytical Detection
- Animal Disease Management and Epidemiology
- Animal Virus Infections Studies
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Viral Infections and Outbreaks Research
- COVID-19 Clinical Research Studies
- Microbial infections and disease research
- Viral gastroenteritis research and epidemiology
- Viral Infections and Vectors
- Cancer Genomics and Diagnostics
- Paranormal Experiences and Beliefs
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Identity, Memory, and Therapy
- American and British Literature Analysis
- Innovative Microfluidic and Catalytic Techniques Innovation
Broad Institute
2018-2025
Harvard University
2018-2024
Howard Hughes Medical Institute
2023-2024
Center for Systems Biology
2018-2020
Phylogenetics of superspreading One important characteristic coronavirus epidemiology is the occurrence events. These are marked by a disproportionate number cases originating from often-times asymptomatic individuals. Using rich sequence dataset early stages Boston outbreak, Lemieux et al. identified events in specific settings and analyzed them phylogenetically (see Perspective Alizon). ancestral trait inference, authors several importation events, further investigated context contribution...
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays detecting severe acute respiratory syndrome 2 (SARS-CoV-2) other viruses their emerging variants. Here, we present cost-effective virus variant detection platform, called microfluidic Combinatorial Arrayed Reactions Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics microfluidics with streamlined workflow clinical use. We...
An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), July 2021-the first large mostly vaccinated individuals the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection transmission among individuals. To address these questions, we combined viral genomic epidemiological data from 467 individuals, including 40% outbreak-associated cases. The Delta variant accounted for 99% this...
Abstract SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as August 1, 2020. To investigate the introduction, spread, epidemiology Boston area, we sequenced analyzed 772 complete genomes from region, including nearly all within first week epidemic hundreds major outbreaks at conference, nursing facility, among homeless shelter guests staff. The data reveal over 80 introductions into predominantly elsewhere United...
Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about extent circulation relationship between these prior outbreaks. We paired epidemiological data from public health investigations with analysis virus whole genome sequences 201 infected individuals, focusing on Massachusetts university communities. Our suggests continuous, undetected locally nationally, including multiple independent introductions into individual Despite presence lineages,...
Transmission reconstruction--the inference of who infects whom in disease outbreaks--offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We developed JUNIPER (Joint Underlying Network Inference Phylogenetic Epidemiological Reconstructions), a highly-scalable pathogen outbreak reconstruction tool that incorporates intrahost variation, incomplete sampling, algorithmic parallelization. Central to is statistical model within-host variant...
<title>Abstract</title> Transmission reconstruction––the inference of who infects whom in disease outbreaks––offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We developed JUNIPER (Joint Underlying Network Inference Phylogenetic Epidemiological Reconstructions), a highly-scalable pathogen outbreak reconstruction tool that incorporates intrahost variation, incomplete sampling, algorithmic parallelization. Central to is statistical...
ABSTRACT Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most were fully vaccinated, many whom also symptomatic, prompting a comprehensive public health response, motivating changes national masking recommendations, raising questions about infection transmission vaccinated individuals. To characterize the viral population underlying it, we...
Abstract Despite widespread vaccination, eleven thousand mumps cases were reported in the United States (US) 2016–17, including hundreds Massachusetts, primarily college settings. We generated 203 whole genome virus (MuV) sequences from Massachusetts and 15 other states to understand dynamics of spread locally nationally, as well search for variants potentially related vaccination. observed multiple MuV lineages circulating within during evidence introductions state, extensive geographic...
A postdoc explains how being medicated for bipolar changed her life and the way she conducts research.
Abstract Summary In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, detection superinfections recombination events. While sample barcoding methods exist to track contamination, they are not always used only detect in the experimental pipeline from point added. The underlying information a sample, however, carries about occurring at any stage. Here, we present Polyphonia, tool for...
Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop robust model for reconstruction that tracks the composition within-host populations over time lineages transmitted between hosts. We confirm our reliably describes variant frequencies dataset 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts,...