Open Source Ebola Research: Bitcoin Community Comes Together
Copyright law is preventing information about Ebolavirus from being widely dessiminated. Some of these “pay wall” manuscripts describe Ebolavirus resistance genes like Niemann-Pick Type C. An ideal funding mechanism would promote the public release of manuscripts describing Ebolavirus concurrently with public release of genomic sequencing data of the resistance genes in the population. We describe a bitcoin fund drive or a “BitDrive” that can encourage more open source publishing and provide DNA sequencing for both victims genomes and viral genomes to better understand the resistance genes and mutation rate of the Ebolavirus.
Courtagen Life Sciences sequences the NPC1 gene responsible for 95% of Niemann-Pick Type C as the basis of a clinical sequencing test designed to inform seizure management. With the Ebolavirus outbreak of 2014 and recent communication with the Hempel family we have become aware that mice Niemann-Pick Type C carriers are likely resistant to Ebolavirus infection.
Work performed at the Whitehead Institute implies even heterozygous knock out mice for the NPC1 gene are resistant to infection. This reminds us of malaria and sickle cell anemia where carriers of a disease have a selective advantage via resistance to malaria. A similar discovery was recently made in regards to the APOL1 gene mutations and Trypanosoma brucei infection. These data challenge the recent emergence hypothesis of Ebolavirus and perhaps suggests a more adaptive history than that presented by modern media. If one considers there is positive selection for NPC1 as it is selective for filovirus resistance and simultaneously associated with diabetes the Ebolavirus outbreak may present a very different propagation than models currently forecast.
Since Ebolavirus requires the NPC1 gene for entry to the cell, we believe it is vital to understand the genomic variation in the human NPC1 gene throughout the population. To complement and underscore this point Steve Bellan et al. demonstrate that there are asymptomatic seropositive patients found in Liberia. These people contracted the virus but did not get symptoms. Numbers vary from 46%-71% of seropositive asymptomatic patients. This dramatically alters the pandemic picture if we can predict this.
NPC1 genetic variants are only one immunity candidate known to date and its unlikely they can account for 46-71% of immunity. The Leroy paper implies these asymptomatic patients are getting an attenuated immune response suggesting successful filovirus entry into the cell.
Rasmussen et al. also demonstrate host genetics in mice that impact the pathogenesiss of the Ebolavirus. There is a noticed change in expression of genes (TEK and Tie1) in the coagulation pathway when comparing resistant and vulnerable mice. Some common variants in the promoters of these genes exist. There are several targets to consider and its unlikely one target will exclusively explain resistance but NPC1 is one of the best studied to date. Hypothetically, common variants in NPC1 should be reconsidered as potential delayed entry genotypes. We need to underscore how little we really understand about this pathway. Variants in this gene DO NOT confer any guarantee of resistance and this project is speculative but we believe a solid understanding of the best target we know today is a very important starting point.
As a result Courtagen queried our clinical sequencing database for all variants we have seen in this NPC1 gene (1000s of mitochondrial and Epilepsy patients sequenced to date). There are 90 with NPC1 variants published at the bottom of this thread. To comply with HIPAA and patient confidentiality, we stripped all names and other variants or phenotypes from this list. This is simply a list of variants we have seen which augments what is known about this gene in 1000G. Below is a growing list of excel sheets provided by labs that have generously contributed variants to the public domain.
If these are damaging to the protein these variants may suggest resistance to infection. We encourage others to bring these data forward. Only with a good understanding of population risk can a viral outbreak be properly addressed.
How you can help:
There are many articles related to Ebolavirus that are behind paywalls due to copyright. Many of these Ebolavirus manuscripts are tax funded but are not public. To be fair to journals, several papers have been put public already as a result of Ebolavirus spread. Here is a particularly interesting paper that does not cost $35 to download but describes a promising filovirus drug that we believe may offer a productive strategy. The sequence data from The Broad Institute implies a very vulnerable polymerase in this strain. Hypothetically, we should be able to target this with terminating nucleotides likes BCX4430. While vaccines are the ultimate goal, its unlikely they can be manufactured for global populations in a short time frame and its unlikely they will adapt with the mutagenesis of the virus. Small molecules like nucleotides or NPC1 inhibitors can be made in vast quantities and in short time frames. These are more pertinent for patients already exposed to the virus.
To address the paywalled Ebola manuscripts and their poor use of copyright law we have put forward a Bitcoin address as a survey tool to collect the publics interest in putting these papers public. Any gift amount provides an address to the blockchain we can consider as a vote. If you are feeling more generous you can even donate more sizable bitcoins and these proceeds will be put to the below uses.
We will use the blockchain to ensure all proceeds go to The Broad Institute or Albert Einsteins College of Medicine to sequence the mitochondrial genomes and NPC1 genes (perhaps whole exomes) of the victims and survivors. Given the pace of science today, The Broad Institute or AECM may choose to alter the experimental design with whats known at the time of funding and adequate review protocols will be utilized to ensure effectiveness. We have no financial connection to either group but for full disclosure Courtagen’s CSO (Kevin McKernan) used to work closely with some of the Broad scientist on the human genome project (1996-2000 @ Whitehead Institute/MIT). The above groups have access to victim & survivor DNA based on their recent work. This project is described below and Courtagen has already published public open-source methods to enable this type of mitochondrial sequencing and NPC1 sequencing. The method used to sequence human mitochondria are similar to the published Broad method to the sequence the Ebolavirus itself (nextera library prep).
Albert Einsteins College of Medicine work highlighted the NPC1 connection to Ebola and hopefully they can sequence the NPC1 gene in all of the victims. The Broad just published this paper sequencing 99 strains from different victims.
As in every EVD outbreak, the 2014 EBOV variant carries a number of genetic changes distinct to this lineage; our data do not address whether these differences are related to the severity of the outbreak. However, the catalog of 395 mutations, including 50 fixed nonsynonymous changes with 8 at positions with high levels of conservation across ebolaviruses, provides a starting point for such studies (table S4).
They found 395 variants and 50 amino acid changing variants in the strains. This is a very high mutation rate across 99 strains but may be the achilles heel of the virus. Polymerases with such low fidelity are vulnerable to incorporating terminating nucleotides like AZT or BCX4430. Human DNA polymerases don’t tolerate these nucleotides and thus modified nucleotides are strong candidates for Ebolavirus treatment.
Why sequence Mitochondrial genomes of the victims or the survivors?
Any disease that induces a fever needs to “redline” the mitochondria to make this happen. Given the Mitochondrias’ intimate coordination with the Niemann-Pick Type C gene (NPC1), its very likely that certain human mitochondrial haplogroups will have different reactions to the virus. The genetics of both the NPC1 gene and the mitochondria is important logistical information for any pandemic management as it may predict a differential R0 (R nought or Replicative ratio) and assist algorithmic calculation of the spread.
Knowing Niemann-Pick Type C individuals are potentially resistant to Ebolavirus, the survivors and victims should be sequenced to understand the prevalence of variation in this gene. Funds are also required to sequence this gene in 10,000+ other ethnically diverse individuals so the background mutation rate is known in under sampled ethnicities in minority, middle east and Indian populations. The ESP6500 and 1000 Genomes databases are valuable but are just a small ethnic selection not representative of global population structure.
We will put in place transparent blockchain means to get all of this funding to the Researcher. Please note there is an option to reward the Journals for their generosity. The choice is yours but we welcome ideas on how to best distribute funds to many Journals fairly. All research published with these funds will be published in open source journals as a stipulation of the receipt of funds.
Please note, we are in the process of implementing Multi-Sig Bitcoin. We have Cold Wallets stored in multiple locations and are working to implement multiple signatories with Empowered Law. Once complete, the most vulnerable hack is this website. For this reason if you see these addresses change after 10/25/2014 (multi-sigs will begin with a 3), confirm the addresses do not look suspicious with a taint analysis on the block chain. The below addresses are new addresses that were generated off the grid with a bootable USB Ubuntu OS and an offline printer making off grid cold wallets. These keys have never seen the internet. This is to prevent a hack of our web server and a reposting of new addresses. This same pair of addresses can be found at various social media outlets regarding this project. When multi-sig is implemented, addresses at both this website and the above sites will both change.
Donate to this bitcoin address for all coins to go to the Research at the Broad & Albert Einsteins:
Donate to this bitcoin address for proceeds to assist the Journals in defraying these costs.
WHY USE DIGITAL CURRENCY TO FUND OUTBREAK RESEARCH?
There are an estimated 3000 microbes on every US dollar. Ironically, this publication is behind a paywall but it does measure the differences between plastic and cotton money all of which have some microbes on them. Bitcoins don’t have any and thus can’t be a vector for disease!
We have one Paypal address for donations and at the moment cannot itemize the use of those funds. All funds in this bucket will go to Research. Paypal operates on credit cards technology developed in the 1950s. Its is a notoriously leaky financial instrument with Millions of credit card numbers getting stolen every month. We are open to ideas on how to make this process as transparent as the block chain but encourage blockchain usage as its a public and cryptographically secure ledger that enables public scrutiny of any charity.
If you are new to Bitcoin, Blockchain.info and Coinbase are good places to start. Coinbase has two factor authentication and is safer with your information than a credit card.
Courtagen and Medicinal Genomics are doing their part by putting every Niemann-Pick Type C variant we have found in our clinical cohorts public below.
Below are variants we have found in the NPC1 gene through the course of sequencing patients.
- NPC-1 missense variants 1 – Ensemble collection of variants in the public domain
- Illumina’s Collection of Variants – ILMN has generously offered to release all of their NPC1 variants
- Courtagen’s NPC-1 Variants- Variants discovered in Courtagen’s Epilepsy sequencing pipeline. Variants in red are Viral binding domains. Some common variants exist in this region! Amino Acids 381-611 is the minimal viral binding domain.
- The Broad Institutes exAC database- An Excellent resource for over 60,000 exomes sequenced to date.
Ted Foss, PhD for Mongo Database brilliance
Doug Smith & Rick Boles for comments
Illumina- For generously placing all NPC1 variants in their database public.
Chris & Hugh Hempel for tenacity, patience, and perseverance
Principal Investigators that we are intending to fund are:
- Kartik Chandran, Associate Professor of Microbiology and Immunology, Harold and Muriel Block Faculty Scholar in Virology, Albert Einstein College of Medicine
- Stephen Gire, Harvard &The Broad Institute- http://sabetilab.org/people/research-scientists/stephen-gire
- Steve E Bellan for underscoring the importance of Leroy et al.
- Jonathan Eisen for showcasing the history of paywall release.
- Caleb for making we watch Contagion Oct. 11th and motivate a deep dive this.
We had an anonymous but “well respected” expert in immunology weigh in on this and they suggested we underscore the speculative nature of the hypothesis that NPC1 variants in human are resistant. This “reviewer” was not comfortable having the exact comments represented here even under an anonymous submission.
Pardis Sabeti’s Tribute to the 5 authors of the Gire paper that did not survive this outbreak.