brianzelip
Co-maintainer of @archivesspace, former tech manager and emerging technologies librarian.
@archivesspaceBaltimore, MD
Pinned Repositories
archivesspace
The ArchivesSpace archives management tool
Azellaz
Quality bags built from scratch in Baltimore
clues
Note taking web app for the whodunnit murder mystery game Clue
concats
🔨 Desktop app to output a single-column csv file of rows of concatenated fields from an input csv or tsv file.
github-vscode-themes
npm package wrapper around Primer's (unpublished) github-vscode-theme.
hyper-github-dark-dimmed
GitHub Dark Dimmed theme for Hyper terminal
hyper-github-light
GitHub Light theme for Hyper terminal
intro-to-github
GitHub workshop material
which-baltimore-neighborhood
📍 Geolocation progressive web app that tells you which Baltimore neighborhood you're in
relaymaryland.com
Relay, Maryland's homepage
brianzelip's Repositories
brianzelip/hyper-github-dark-dimmed
GitHub Dark Dimmed theme for Hyper terminal
brianzelip/hyper-github-light
GitHub Light theme for Hyper terminal
brianzelip/intro-to-github
GitHub workshop material
brianzelip/platforms-talk
Talk prepared for Code{4}Lib MDC 2019 meetup
brianzelip/spa-ssg
Single page application (Vue, Svelte, React, etc) static site generator
brianzelip/2020-11-03-umaryland-online
brianzelip/actions-test
brianzelip/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.
brianzelip/awesome-hyper
🖥 Delightful Hyper plugins, themes, and resources
brianzelip/bump
Automate new version releases for node.js projects
brianzelip/calc
Calculator in javascript
brianzelip/clicky-menus
Simple click-triggered navigation submenus. Accessible and progressively enhanced.
brianzelip/covid-19-ppe
3D models for Covid-19 Personal Protective Equipment
brianzelip/daneden.me
🏡 This is my website. There are many like it, but this one is mine.
brianzelip/eleventytwo
Boilerplate 11ty setup
brianzelip/firehouserummy
Family card game
brianzelip/gh-actions-demo
Learning GitHub Actions
brianzelip/github-issue-templates
:symbols: A collection of GitHub issue and pull request templates
brianzelip/github-slideshow
A robot powered training repository :robot:
brianzelip/github-vscode-theme
GitHub's VS Code themes
brianzelip/hyper-site
The official website for the Hyper terminal
brianzelip/lc-git
Library Carpentry: Introduction to Git
brianzelip/lc-test
Test for Library Carpentries PR
brianzelip/ludacris
🎶 Get song lyrics. No BS. https://ludacris.netlify.com
brianzelip/parcel-plugin-bundle-log
Log the Parcel bundle object to your console
brianzelip/parcel-plugin-static-files
Parcel plugin to copy static files to the built output
brianzelip/peruse
A simple framework for publishing online books.
brianzelip/relay
Relay, MD
brianzelip/supercookie
⚠️ Browser fingerprinting via favicon!
brianzelip/wp-dev-course
Example files for my WordPress Development Course on Udemy