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.

This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London.

SORMAS (Surveillance, Outbreak Response Management and Analysis System) is an early warning and management system to fight the spread of infectious diseases.

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.

Mathematical Modeling of Infectious Disease Dynamics

Reed-Solomon forward error correcting library

Infectiously simple dependency injection for any JavaScript project

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Infectious Disease Sequencing Platform

Simulation, visualization, and inference of individual level infectious disease models with Julia

Accompanying code for: Kucharski AJ, Russell TW et al. Early dynamics of transmission and control of COVID-19: a mathematical modelling study. Lancet Infectious Diseases, 2020

COVID-19 infectious forecasting using SEIR model and R0 estimation

No description available

A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment

Code and Data for Advancing real-time infectious disease forecasting using large language models

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It was first identified in December 2019 in Wuhan, China, and has since spread globally, resulting in an ongoing pandemic. Long Short Term Memories(LSTMs) can solve numerous tasks not solvable by previous learning algorithms for recurrent neural networks (RNNs). LSTM is applicable to tasks such as unsegmented, connected handwriting recognition, speech recognition and anomaly detection in network traffic or IDS's (intrusion detection systems). LSTMs can also be efficiently applied for time-series predictions. In this project, its shows a four stacked LSTM network for early prediction new Coronavirus dissease infections in some of the mentioned affected countries (India, USA, Czech Republic and Russia) , which is based on real world data sets which are analyzed using various perspectives like day-wise number of confirmed cases, number of Cured cases, death cases. This attempt has been done to help the concerned authorities to get some early insights into the probable devastation likely to be effected by the deadly pandemic.

⛔️ DEPRECATED Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

Repository for Global.health: a data science initiative to enable rapid sharing of trusted and open public health data to advance the response to infectious diseases.

COVID-19 is an infectious disease. The current outbreak was officially recognized as a pandemic by the World Health Organization (WHO) on 11 March 2020. X-ray machines are widely available and provide images for diagnosis quickly so chest X-ray images can be very useful in early diagnosis of COVID-19. In this classification project, there are three classes: COVID19, PNEUMONIA, and NORMAL

Video lectures, slides and code for "The Mathematics and Statistics of Infectious Disease Outbreaks" course at Stockholm University

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

Fast prototyping of infectious-disease models based on reaction equations. Analyze the ODEs analytically or numerically, or run stochastic simulations on networks/well-mixed systems.

An R package with Dynamic Models of infectious diseases

A privacy preserving contact tracing design to battle infectious diseases

R Package - Dynamical Systems Approach to Infectious Disease Epidemiology

Teaching materials for MCMC I module in the Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID)

The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.

Course on nowcasting and forecasting of infectious disease dynamics

International Infectious Disease Data Archive