The phyloepidemic tracing of COVID-19 in Alaska using Nanopore next-generation sequencing
(March 2020 - July 2022)
This project is a multi-institutional collaboration with the University of Alaska Fairbanks and the Alaska State Virology Lab to sequence biobanked clinical COVID patient samples using Nanopore next-generation sequencing. The premise of this study is to sequence SARS-CoV-2 genomes from patient samples throughout the state of Alaska based on temporal and geographic parameters to pinpoint the introduction and spread of viral variants among the various communities throughout the state.
As the lead scientist of the Alaska Pathogenomics group, my responsibilities include developing and implementing a sample processing pipeline to streamline the sequencing process, as well as performing and overseeing all wet-laboratory techniques, quality control, and data acquisition as it pertains to these clinical samples. As of October 2021, close to 100 novel SARS-CoV-2 sequences have been submitted to GISAID with additional samples being processed daily. A manuscript which details the process and findings generated from this study is currently being written and served as a chapter in my Master’s thesis.
Using a mobile sanitation trailer (MST) to heat-treat N95 masks for reuse in industrial and healthcare applications
(May 2020 - Dec 2022)
This study arose during the height of the COVID-19 pandemic as the supply of usable N95 masks became severely restricted worldwide. The Alaska Native Tribal Health Consortium (ANTHC) reached out to the Bortz research laboratory to collaborate and test the efficacy of their custom-built mobile sanitation trailer (MST).
My responsibilities for the project include providing consultation advice to the rest of the MST team, developing a pipeline which uses live influenza virus as a model organism, consolidating and interpreting the results for reporting, and directing and overseeing the work of all undergraduate students and research technicians involved in the project. I have also assisted in writing sections of the manuscript as it pertains to the virology aspect of the study, and the results of this study have been published in the International Journal of Circumpolar Health.
The phyloepidemic tracing of COVID-19 in Alaska using Nanopore next-generation sequencing
(March 2020 - July 2022)
This project is a multi-institutional collaboration with the University of Alaska Fairbanks and the Alaska State Virology Lab to sequence biobanked clinical COVID patient samples using Nanopore next-generation sequencing. The premise of this study is to sequence SARS-CoV-2 genomes from patient samples throughout the state of Alaska based on temporal and geographic parameters to pinpoint the introduction and spread of viral variants among the various communities throughout the state.
As the lead scientist of the Alaska Pathogenomics group, my responsibilities include developing and implementing a sample processing pipeline to streamline the sequencing process, as well as performing and overseeing all wet-laboratory techniques, quality control, and data acquisition as it pertains to these clinical samples. As of October 2021, close to 100 novel SARS-CoV-2 sequences have been submitted to GISAID with additional samples being processed daily. A manuscript which details the process and findings generated from this study is currently being written and served as a chapter in my Master’s thesis.
Alpha/beta testing of virus genome annotation tool developed by JCVI
(May 2019)
The premise of this project was to perform alpha/beta testing of the VIGOR4 genome annotation tool developed by the K Craig Venter Institute prior to its official public release. This involved assessing the user-friendliness of the software in terms of installation and instructional clarity, as well as its effectiveness in annotating a set of viral genomes given a FASTA file. The feedback provided was used to improve the accessibility of the program prior to its official publication.
The Commander complex and their potential as novel antiviral genes
(August 2018 - July 2022)
As a significant component of my Master’s thesis, this project aims to observe a family of genes known as the Commander Complex for their potential antiviral effects. What originally started as a set of one-off experiments during my work as a research technician, it was discovered that select COMMD genes were upregulated during mock and authentic viral infections when measured though qRT-PCR in vitro. Further testing was done by treating human lung adenocarcinomas with various immunostimulants and observing any potential changes in gene expression though qRT-PCR and Western blotting. Immunofluorescent imaging was also performed to identify protein-protein interactions between viral and Commander proteins. The results of this project served as a chapter of my Master’s thesis.
Using next-generation sequencing to trace the spread of African Swine Fever Virus in Ukraine
(August 2018 - October 2019)
In this project, I was contracted by the Department of Defense: Defense Threat Reduction Agency (DoD:DTRA) to assist in developing a portable sequencing workflow to phylogenetically trace the spread of African Swine Fever (ASF) throughout the country of Ukraine. Because there was a lack of sequencing capacity within the country, it was imperative that the project was both cost-effective and deployable in locations that lack access to the traditional laboratory settings found in the West. To achieve this, Nanopore-based sequencing was combined with PCR-based detection methods, and I was tasked with performing these wet lab techniques on-site in Kyiv, Ukraine to both collect data, as well as to train my fellow Ukrainian, Polish, and Georgian colleagues in a series of workshops to increase the sequencing and bioinformatic capacity throughout Eastern Europe.
The project was successfully completed in 2019 and resulted in the publication of both the sequenced genomes and a journal article, and the work performed was used as a basis for expansion into the Odessa and Kharkiv oblasts to trace the spread of several other animal pathogens of concern such as highly-pathogenic avian influenza and porcine circovirus 2.
Influenza data management for NIAID CEIRR
(August 2018 - October 2019)
As part of the NIH initiative to consolidate and standardize influenza data collected throughout the Center of Excellence for Influenza Research Response (CEIRR) network, my role in this project was to manage and curate data from various laboratories within the CEIRR network, including those from the Mount Sinai Hospital, Erasmus University, and the Johns Hopkins Hospital. This involved collecting antibody, plasmid, and virus reagent data and manually performing quality control for each submission to ensure that data are properly formatted in the Data Processing and Coordinating Center (DPCC) standard.
This work requires intimate familiarity with the influenza virus and virology techniques such as hemagglutinin inhibition assays and the development of recombinant viruses to effectively assess the data for accurate reporting.
Detection and sequencing of influenza A virus from Canadian geese (Branta Canadensis)
(October 2017 - May 2018)
As part of my work as a research technician, my role in this project was to develop and test a PCR-based method of detection for influenza A from fecal matter opportunistically collected from Canadian geese throughout the city of Anchorage, Alaska. Using a previously-tested FAM-based probe which is sensitive to the influenza M1 gene, I was able to successfully extract and enrich for viral RNA from avian fecal matter using a modified column-based extraction. The methods developed in this study would serve as the basis for developing swab and tissue-based detection assays for influenza using samples collected during avian necropsies.
Influenza nucleoprotein antagonism of interferon pathways
(August 2016 - May 2018)
Serving as my first undergraduate project, the aim of this research was to study the influenza nucleoprotein (NP) and its potential antagonistic effect on innate immune responses: specifically, the induction of the type I interferon pathway. NPs from various strains of mammalian and avian (both high and low-pathogenicity) influenza were expressed using plasmids transfected into human lung adenocarcinoma in vitro before subsequently treating the cells with poly-I:C a TLR-3 agonist which induces the desired interferon response. A panel of various IFN-dependent and antiviral genes were observed for up/downregulation, using an influenza NS1 plasmid and an empty expression vector as positive and negative controls, respectively.