- I should have loved biology
- Bioinformatics Algorithms - an introduction
- Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine
- Genome Sequencing and Covid-19: How Scientists Are Tracking the Virus - The New York Times
- Ψ in RNA Vaccine - Twitter Thread (PT-BR)
- Conheça a Dra. Katalin Karikó, a cientista que desenvolveu a técnica da vacina de RNAm para a COVID-19
- Twitter Thread on Israel Vaccination
- A Vida é um copia e cola
by John Rhodes
Against pandemic infectious disease, nobody wins the race until everyone wins.
By January 7, Chinese scientists had isolated a novel virus from patients in Wuhan and analyzed the genetic material. The sequence they obtained revealed it as a novel coronavirus, distinct from SARS-CoV, the cause of the outbreak 18 years before. In consequence, SARS-CoV was renamed SARS-CoV-1 and the new corona virus dubbed SARS-CoV-2. Using this sequence (the order in which the four chemical building blocks of RNA are arranged), scientists constructed diagnostic tests for detecting the virus. The scientists provided full genome sequence information to the WHO and shared their data on the Global Initiative for Sharing All Influenza Data platform. Of the initial 41 people hospitalized with pneumonia and officially identified as having SARS-CoV-2 infection, two-thirds were exposed in the Huanan Seafood Wholesale Market.
Let’s rerun, for a moment, the alarming calendar of events at the start of the COVID-19 pandemic. On December 30, 2019, Chinese health officials report a cluster of pneumonia cases in the city of Wuhan in Central China to the National Health Commission. Chinese authorities set in motion an investigation to understand and contain the disease. By January 7, Chinese scientists have isolated a mystery virus and analyzed the genetic material, naming the deadly pathogen SARS-CoV-2. On January 11, we learn of the first recorded death, and on January 23, the local government in Wuhan locks down the city. By January 24, China reports 835 cases, while in Korea and Japan, cases are on the rise. A little over six weeks later, on March 11, with 116,558 cases worldwide and more than 4,000 dead, the WHO declares the SARS-CoV-2 outbreak a global emergency. The pandemical disease caused by the virus is named COVID-19. By this date, the United States has confirmed more than 1,000 cases across 38 states, the United Kingdom has reported six deaths, and Italy, the worst hit country in Europe, reports 631 people have died of the disease.
The SARS-CoV-2 virus was then grown in Vero cells in large (50 liter) culture vessels and subjected to further investigations. These showed that the virus, including the gene for the spike protein (the part of the coronavirus that binds ACE2) was stable in this cellular environment, allowing researchers to proceed. The next step was to kill the virus. In the history of vaccines, the conventional way to kill vaccine viruses has been with formaldehyde, which “pickles” the virus, retaining its native shape, helping to ensure that the immune system can identify it. In this case the scientists used a chemical called β-propiolactone, which is more targeted than formaldehyde. It has been used to kill influenza viruses, and although scientists do not completely understand how it kills viruses, they believe it poisons the proteins whose function is to get the virus inside human cells. After killing the virus, the researchers checked to make sure its shape wasn’t damaged. Happily, using an electron microscope, the team of scientists saw discrete, intact, oval shapes “embellished with crown-like spikes,” confirming that the virus’s shape was unaltered.
In the early 20th century, Gaston Ramon, the French veterinarian who pioneered the chemical inactivation of bacterial toxins, was trying to improve the yield of horse antibodies used to treat children with diphtheria. Henoticed that if an abscess happened to develop at an injection site, the horse produced a lot more antibodies. This prompted him to inject the horses with toxin combined with starch, breadcrumbs, and tapioca. This ingenious use of these otherwise innocuous agents produced sufficient irritation to provoke sterile abscesses, which increased the antibody yield.
(…) these vaccines consist of a harmless carrier virus containing an inserted gene encoding a key antigen from the pathogenic virus.
Nonreplicating vectors do not grow in the body, but they do infect cells, and the pathogenic antigens they carry present the full range of their danger signals to the innate immune system. This is key to the success of these vaccines.
This vaccine was one of the very first to reach clinical trials, just 10 short weeks after the sequencing of the SARS-CoV-2 virus. By the end of March 2020, the live vaccine was in phase I clinical trials in two approved hospitals in Wuhan—the Wuhan Rest Center of the Chinese People’s Armed Police Force and Tongji Hospital, part of Tongji Medical College at the Huazhong University of Science and Technology. The trial included 180 healthy people between 18 and 60 years of age. Like all phase I trials, no placebo or mock vaccine was included for comparison, and the trial was not “blinded”—both doctors and recipients knew what was being administered. The study began by giving the lowest vaccine dose to 36 individuals. Once this was shown to be safe (seven days later), a second group of 36 volunteers received a higher dose. Researchers then repeated the process with the third group, who received the highest dose of all—this being the dose predicted to be effective with similar vaccines in previous studies. Not surprisingly, the volunteers had to pass certain tests. They had to be negative for antibodies to coronavirus, meaning they hadn’t already been exposed to the disease and developed an immunity. They had to have no previous exposure to the related virus, SARS-CoV-1. And they needed healthy lungs. The primary purpose of this study was to establish safety, but the exciting part for the scientists running the trial was measuring neutralizing antibodies made against the virus. They made this measurement 14 days, 28 days, 3 months, and 6 months after the injection.
The Tianjin adenovirus used in the COVID-19 vaccine race is adenovirus serotype 5 (Ad5).
(…) the gene encoded the SARS-CoV-2 spike protein was incorporated into the Oxford vector known as ChAdOx1. These studies were led by Sarah Gilbert, whom we met in chapter 3—a vaccinologist well used to challenging diseases such as malaria and, more recently, influenza. Preclinical studies with the Oxford candidate in mice showed good antibody and T-cell responses to the vaccine, known as ChAdOx1 nCoV-19. And in a protection study in rhesus macaques, ChAdOx1 nCoV-19 successfully prevented pneumonia in animals challenged with SARS-CoV-2.
On August 11, 2020, Russia announced that it had successfully developed a COVID-19 vaccine at the Gamaleya Research Institute of Epidemiology and Microbiology in Moscow. A surprise aspect of this news was that Russian authorities had already approved the vaccine for general use, an aspect provoking international criticism because no one had yet conducted large-scale phase III safety and efficacy testing. Commentators suggested that vaccinated human subjects were deliberately exposed to virus in a clinical setting in order to demonstrate the vaccine’s effectiveness. Reports indicated that the vaccine employed nonreplicating adenovirus vectors delivering the gene encoding SARS-CoV-2 spike protein—the same approach taken by the Belgian COVID-19 vaccine group and Chinese scientists based in Tianjin.
These differ from the previous class in that once they are injected and have entered human cells, they undergo several rounds of replication, infecting more cells and providing sustained stimulation of the immune system.
One principal example of an established vaccine exploiting this technology is the HPV vaccine protecting against cervical cancer and genital warts.
Investigators have examined many ingenious delivery techniques for DNA vaccines. A US biotech company in Philadelphia has produced an optimized DNA vaccine encoding the SARS-CoV-2 spike protein designed to be injected into the protective middle layer of the skin known as the dermis. A proprietary handheld electrical device is then used to deliver electrical pulses at the site of injection which briefly open small pores in cell membranes, allowing the plasmids to enter dermal cells before the pores close again. The company initiated their phase I clinical trials in healthy volunteers in Kansas City and Philadelphia in 2020.
This is the category delivering vaccines in the form of RNA. On March 16, 2020, the same day that Chinese scientists in Tianjin launched their clinical trial of a COVID-19 viral vector vaccine, scientists based in Boston commenced the first clinical trial of their RNA vaccine.
RNA has several theoretical advantages over the live vector and the nonliving protein-based vaccines. The first is safety: mRNA or messenger RNA, is noninfectious, eliminating the risk of unwanted invasiveness, and it does not integrate with the genetic material of the human cell. The second is that mRNA, unlike DNA, interacts directly with the machinery of cells without requiring intermediate steps. The third is that once it has done its job, vaccine mRNA is naturally broken down by “housekeeping” enzymes that maintain the normal functioning of cells.
The mother of nucleic acid vaccination is Margaret Liu.
Things suddenly began to look brighter for RNA vaccines in 2005 with the publication of a paper by medical researcher Drew Weissman and colleagues at the University of Pennsylvania. This provided a promising way around the difficulties for mRNA vaccines in humans. Success hinged on chemically modifying the building blocks of mRNA in relatively subtle ways.
The way around these problems, insightfully suggested in Drew Weissman’s publication in 2005, was to add small chemical groups to the building blocks of vaccine RNA. Without these groups, three kinds of Toll-like receptors could sense the RNA. But with the groups added, no Toll-like sensors could sense the modified RNA, allowing RNA vaccines to be effective. Comparing RNA from infectious pathogens and RNA from the human cellular machinery further explained what was going on: chemical modifications were converting the appearance of vaccine RNA from a pathogen-associated profile to a profile resembling normal human RNA. This put control back in the hands of the vaccine designers. Because vaccine RNA is manufactured from DNA by a cell-free biochemical procedure, this makes it easy to use modified building blocks in the synthetic process, allowing scientists to avoid unwanted effects on the immune system. The vaccine designers can then choose whether or not to add defined adjuvants to their modified RNA vaccines.
On July 14, 2020, the company behind this leading RNA vaccine published their phase I results in The New England Journal of Medicine. Given as two doses, 28 days apart, their vaccine, mRNA-1273, produced good neutralizing antibodies to SARS-CoV-2 in all subjects, equivalent to antibody levels seen in patients recovering from natural infection. Helper T-cell responses also occurred. And with no concerns about adverse effects, the vaccine progressed to phase III studies and approval in December 2020.
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