Calculating Herd Immunity, Other COVID-19 News and Updates

June 26, 2020

June 26, 2020 | Researchers are attempting to trace the emergence of COVID-19 in an effort to understand how pathogens jump from animals to humans. Meanwhile, mathematicians are developing a model estimating herd immunity. These updates, plus more, are featured in this week’s COVID-19 news from the biotech and research industries.

Literature Updates

Refining research about when COVID-19 emerged will assist in understanding how such pathogens jump from animals to humans, Australian evolutionary experts from the University of Sydney and University of Melbourne say in an article published in Science. It complements another piece written by an international group of researchers tackling the controversial question of when measles first emerged, finding it could be linked to the rise of large cities after sequencing the genome of a measles strain from 1912. Although the human COVID-19 SARS-CoV-2 virus split from its closest known relative (another coronavirus from a horseshoe bat) about 30 to 40 years ago, the jump to humans most likely happened more recently. The chance of a virus jumping between species will generally increase with the amount of contact, the authors say, referring to the fact that human civilization is increasingly encroaching into the habitat of wild animals. DOI: 10.1126/science.abc5746

Researchers at the Yerkes National Primate Research Center and the Emory Vaccine Center have shown a new adjuvant (3M-052) helps induce long-lasting immunity against HIV, a finding that has implications for developing a successful vaccine against COVID-19. In the study, involving 90 rhesus monkeys, researchers showed that the new, synthetic small molecule successfully induced vaccine-specific, long-lived bone marrow plasma cells that are critical for durable immunity. In a striking observation, those 3M-052-induced plasma cells were maintained at high numbers for more than one year after vaccination. Study results published in Science Immunology. DOI: 10.1126/sciimmunol.abb1025

Administering the MMR (measles, mumps, rubella) vaccine could serve as a preventive measure to dampen septic inflammation associated with COVID-19 infection, according to an article published in mBio by researchers at Louisiana State and Tulane universities. Vaccination with MMR in immunocompetent individuals has no contraindications and may be especially effective for healthcare workers who can easily be exposed to COVID-19, they say. In their view, a clinical trial with MMR in high-risk populations may provide a low-risk-high-reward preventive measure in saving lives during the pandemic. In the lab, vaccination with a live attenuated fungal strain-induced trained innate protection against lethal polymicrobial sepsis—protection mediated by long-lived myeloid-derived suppressor cells (MDSCs) previously reported inhibiting septic inflammation and mortality in several experimental models. The researchers say that an MMR vaccine should be able to induce MDSCs that can inhibit or reduce the severe lung inflammation/sepsis associated with COVID-19. Supporting their hypothesis are the milder symptoms seen in the 955 sailors on the U.S.S Roosevelt who tested positive for COVID-19 (MMR vaccinations are given to all U.S. Navy recruits) and epidemiological data suggesting a correlation between people in geographical locations who routinely receive the MMR vaccine and reduced COVID-19 death rates. COVID-19 also has not had a big impact on children, possibly due to their more frequent exposures to live attenuated vaccines that can also induce the trained suppressive MDSCs that limit inflammation and sepsis. The efficacy of MMR directly in a nonhuman primate model of COVID-19 infection is being tested in the lab. DOI: 10.1128/mBio.00907-20

A collaborative team of researchers from Japan and the U.S. has found that SARS-CoV-2 isolates replicate efficiently in the lungs of Syrian hamsters and cause severe pathological lesions in the lungs of these animals similar to commonly reported imaging features of COVID-19 patients with pneumonia. SARS-CoV-2−infected hamsters mounted neutralizing antibody responses and were protected against rechallenge with SARS-CoV-2. Moreover, passive transfer of convalescent serum to naïve hamsters inhibited virus replication in their lungs. Syrian hamsters were consequently deemed a useful small animal model for the evaluation of vaccines, immunotherapies, and antiviral drugs. The research published in PNAS. DOI: 10.1073/pnas.2009799117

A group of researchers from Seoul National University in South Korea, University of Cambridge in the U.K. and Lehigh University in the U.S. have worked together to produce the first open-source, all-atom model of a full-length spike protein of COVID-19 that plays a central role in viral entry into cells. Details were published in The Journal of Physical Chemistry B. The model-building program can be found from the home page of CHARMM-GUI, a program that simulates complex biomolecular systems simply, precisely and quickly. Scientists can use the models to conduct innovative and novel simulation research for the prevention and treatment of COVID-19. DOI: 10.1021/acs.jpcb.0c04553

Herd immunity to COVID-19 could be achieved with less people being infected than previously estimated, according to research published in Science. Mathematicians from the University of Nottingham and University of Stockholm devised a simple model categorizing people into groups reflecting age and social activity level, reducing herd immunity from 60% to 43%. The reduction is attributed mainly to activity level rather than age structure. The more socially active individuals are the more likely they are to get infected—and to infect others if they become infected. Consequently, herd immunity level is lower when immunity is caused by disease spreading than when immunity comes from vaccination. DOI: 10.1126/science.abc6810

In Science Advances, an international team of researchers report that T cell and B cell epitope identification using the immunoinformatics approach could direct the experimental study of existing drugs with a higher probability of discovering appropriate vaccine candidates with fewer experiments and higher reliability. The team performed virtual screening of antiviral compounds targeting the spike glycoprotein (S), main protease (Mpro), and the SARS-CoV-2 RBD-ACE2 complex of SARS-CoV-2. PC786, an antiviral polymerase inhibitor, showed improved binding affinity toward all the targets. Additionally, the post-fusion conformation of the trimeric S protein RBD domain with ACE2 revealed conformational changes associated with the PC786 drug binding. DOI: 10.1126/sciadv.abb8097

Updates from Industry

The German Research Foundation, the country’s largest research funding organization, has established an interdisciplinary commission for pandemic research made up of 18 members representing all research disciplines. It complements clinical or application-oriented research already underway and will focus on basic research—looking at not only the medical and epidemiological perspective but also the economic, ethical, legal, social, psychological and historical aspects of the pandemic. Most of the commission members have been named and their first meeting was to be June 15. Press release.

The Department of Energy's Oak Ridge National Laboratory (ORNL) has launched a COVID-19 Rapid Access Licensing Program allowing companies to license select technologies at no cost for one year. In collaboration with researchers, ORNL's Technology Transfer Office is creating a growing portfolio of inventions available to license through the program. The licenses are nonexclusive and interested licensees must demonstrate intent to use ORNL's innovations to address COVID-19 and commit to disseminating resulting products as widely and quickly as possible. Only U.S. entities, companies and universities are eligible. Alternative licenses will be available for companies creating products that require exclusivity to support large development investments, such as for diagnostic platforms, drug delivery systems, therapies and vaccines. Press release.

Researchers at the National Science Foundation (NSF) Spatiotemporal Innovation Center at George Mason University and the Center for Geographical Analysis at Harvard University are building a spatiotemporal platform to support rapid response to COVID-19. The platform will serve as a comprehensive data repository of virus cases and associated information from resources such as authoritative reports, news releases, earth observation and social media. The researchers are sharing their data with research communities through smart data discovery capabilities for easy access using spatiotemporal computing infrastructure previously built to assist with the computing and processing needs of researchers for studying COVID-19 with online collaboration. NSF funding for the project began in June 2020 and will conclude in late May 2021. Press release.

Repertoire Immune Medicines reports that is has received funding from the COVID-19 High Performance Computing Consortium to identify viral epitopes most likely to induce durable immunity to SARS-CoV-2 through induction of long-term memory in T cells. Under this grant, Repertoire will leverage the cloud computing resources of Amazon Web Service (AWS) to simulate and predict the complex immunological interactions across patient populations that lead to clearance of SARS-CoV-2. The research project will combine Repertoire’s state-of-the-art experimental platform, which measures T Cell Receptor (TCR)-antigen interactions at single-cell resolution, and then simulates these interactions on AWS. The work stands in contrast to most current investigations into COVID-19 vaccines that are focused on the B cell derived antibody responses to a handful of viral targets, typically those derived from the spike, membrane and nucleocapsid proteins. Press release.

The University of Kentucky (UK) has announced a research collaboration with Atomwise to explore potential COVID-19 therapies. An associate professor in UK’s college of medicine was granted the project from Atomwise’s Artificial Intelligence (AI) Molecular Screen award program, which seeks to democratize access to AI for drug discovery and enable researchers to accelerate the translation of their research into novel therapies. The project is focused on the papain-like protease (PLpro) essential in the infection process of SARS-CoV-2. Disrupting the function of this protein would not only interrupt the infection process but also give the innate-immune response a chance to detect and respond to infected cells. The quest is on for novel inhibitors of PLpro, as well as examining the use of compounds developed against the coronaviruses MERS and SARS-CoV-1. With Atomwise's AtomNet AI screening technology, more than 10 million small molecules can be virtually bound to PLpro. Top-scoring compounds will then have their specificity and inhibitory activity characterized using more traditional biophysical techniques. The collaboration is one of 15 COVID-19 related efforts at Atomwise. The AI virtual screening and a subset of synthesized compounds for physical testing are being made available to researchers at no cost. Press release.