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NAalytics / Assemblies Of Putative SARS CoV2 Spike Encoding MRNA Sequences For Vaccines BNT 162b2 And MRNA 1273RNA 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.
AmElmo / ProofshotGive AI coding agents eyes. Records browser sessions, captures screenshots, collects errors, and bundles proof artifacts — so humans can verify what the agent built.
J-Rios / TLG JoinCaptchaBotTelegram Bot to verify if users joining a group are human. The Bot sends a captcha challenge to each new user and removes those who fail to solve it within a specified time.
prosopo / CaptchaOpen-source, frictionless CAPTCHA and bot defense. A privacy-focused alternative to reCAPTCHA and hCaptcha.
claw-eval / Claw EvalClaw-Eval is an evaluation harness for evaluating LLM as agents. All tasks verified by humans.
lechmazur / ConfabulationsHallucinations (Confabulations) Document-Based Benchmark for RAG. Includes human-verified questions and answers.
CyborgTests / Playwright Manual Step Automation🤖🇺🇦 Cyborg Test adds manual verification steps to Playwright tests, letting testers confirm actions during execution. Combine automation with human checks in one flow.
swghosh / DeepFaceKeras implementation of the renowned publication "DeepFace: Closing the Gap to Human-Level Performance in Face Verification" by Taigman et al. Pre-trained weights on VGGFace2 dataset.
fossifer / Telegram CAPTCHA BotA bot running on Telegram which will send CAPTCHA to verify if the new member is a human.
CleanTalk / Anti Ddos LiteAnti-DDoS-Lite (Anti-Crawler app) is a small PHP app to protect your site against DDoS attack.
Harry-zklcdc / Go Bingai PassPass BingAI Human machine Verification
worldcoin / World Id LensARCHIVED. Human verification for Lens Protocol with World ID.
ywatanabe1989 / Scitex PythonPython toolkit for reproducible science. CLI commands, 371+ MCP tools, built-in skills. From raw data to manuscript — with reproducibility verification. For AI and human researchers.
alexdevassy / AI Powered Vulnerability Impact AnalyzerVulnerability impact analyzer that reduces false positives in SCA tools by performing intelligent code analysis. Uses agentic AI with open source models to understand CVEs and verify actual vulnerability impact in your codebase. Keeps your code secure with on-premises execution and human-in-the-loop verification.
doraemonkeys / Claude Code Debug ModeCursor-style Debug Mode skill for coding agents. Hypothesis-driven debugging with runtime log instrumentation and human-in-the-loop verification.
presidio-oss / Factif AIAI-powered computer control for automated testing. Factifai uses vision models (Claude, GPT-4o, Gemini) to interact with applications naturally - clicking, typing, and verifying results just like a human would.
Haohao-end / Ctrip Style AI Travel AssistantA stateful multi-agent travel service system built on LangChain & LangGraph. Features intelligent task delegation, permission control, and human-in-the-loop verification for flight booking, hotel reservations, car rentals, and tour planning.
sfw / LoomLoom is an AI harness, that can be used with local or cloud LLMs, for complex tasks. It decomposes work, drives execution through a verification harness, and keeps models on track with structured state instead of history. It can route between thinking and acting models, verifies outputs, and exposes an APP/TUI/API/CLI/MCP for both humans & agents.
AFP-Medialab / Verification PluginA verification “Swiss army knife” helping journalists, fact-checkers, and human rights defenders to save time and be more efficient in their fact-checking and debunking tasks on social networks especially when verifying videos and images
TelechaBot / Kitan🌟 Kitan: A Telegram bot guardian ensuring friendly interactions by authenticating users as real humans with cutting-edge verification methods.
