Dr. Vincent Racaniello: Virologist, Creator of TWIV, Educator Written May 21, 2018 by Imanis Life Sciences, Rochester MN

In 1979, when Dr. Vincent Racaniello became the first scientist to clone an animal RNA virus, he did not foresee how his achievement would enable immense advancements in the therapeutic world. Forty years later, vectors based on the technology Racaniello contributed to are widely used in CAR T-cell therapy, gene therapy, and oncolytic virotherapy. In fact, Racaniello exclaims, “I think almost every cancer is going to be treated with some form of virotherapy in the future.”

In addition to contributing sizably to the way therapeutics have been developed in the last four decades, Racaniello has also played a role in changing the way scientific data is shared. When he was a Ph.D. and post-doctoral student, secrecy was paramount. Data was only shared at conferences or in publications. Now, as an educator himself, he is an advocate for open access data. Perhaps more importantly, he seeks to engage the public in these once secret scientific discussions through his blog, youtube videos, and popular podcasts. He reflects, “Towards the end of my career I view myself more as an educator. We do research, but I want to tell the world about it.”

In this episode of A Vision for the Future, Dr. Racaniello reviews his groundbreaking work at MIT, how oncolytic virotherapy is powering the future of cancer treatment, the largest challenges facing the field of virology, and what inspired him to start his blog and podcast.¹⁾

Vincent Racaniello: Earth's Virology Professor P&S professor offers free virology course via Internet - July 26, 2013

For most of his 30-plus years at Columbia University College of Physicians & Surgeons, Vincent Racaniello taught virology in the same way: He stood up in front of a small number of graduate students in a lecture room and talked.

But five years ago (2008) Racaniello—tired of misinformation about viruses spread by mass and social media—decided to offer his expertise to a wider audience. The weekly podcast This Week in Virology(link is external and opens in a new window) was born in 2008 and soon began reaching thousands of listeners.

Now Racaniello has his sights on reaching an even wider audience: the world.

Anyone with an Internet connection can sign up for Racaniello’s new introductory virology course, Virology I: How Viruses Work(link is external and opens in a new window), through the Coursera(link is external and opens in a new window) platform. The 11-week course starts August 1, and more than 20,000 people have already signed up. (Virology II will be offered in the autumn.)

We recently spoke with Professor Racaniello (via email) about the upcoming Coursera course, one of the first offered by a Columbia instructor.

Why did you decide to offer a virology course on Coursera? ²⁾

Moving beyond metagenomics to find the next pandemic virus

Vincent Racaniello Article information Proc Natl Acad Sci U S A. 2016 Mar 15; 113(11): 2812–2814.

Published online 2016 Mar 14. doi: 10.1073/pnas.1601512113 PMCID: PMC4801287 - PMID: 26976606 - Microbiology

Vincent Racanielloa, Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY, 10032 - Email: ude.aibmuloc@1rrv.

Movements of viruses from animals to humans underlie outbreaks of diseases, such as Ebola hemorrhagic fever, influenza, and Middle East respiratory syndrome. The severe acute respiratory syndrome (SARS) virus pandemic of 2003 was caused by a novel coronavirus (CoV) that originated in Chinese horseshoe bats (1). Results of sequence analyses have shown that viruses related to SARS-CoV continue to circulate in bats, but their potential for infecting humans is not known. Gazing at viral sequences has its limits; experiments need to be done. In PNAS, Menachery et al. (2) develop a framework for deriving viruses from these genome sequences and examining their potential to cause the next SARS pandemic (Fig. 1).

Experimental platform for moving beyond metagenomics to identify viruses with pandemic potential. Samples from animals are subjected to deep, high-throughput sequencing to identify viral genomes. Sequence data are subjected to phylogenetic analyses to …

Entry of SARS-CoV into human cells begins with binding of the viral spike glycoprotein to the cell surface receptor human angiotensin converting enzyme 2 (ACE2) (3). Most of the presumed ancestors of SARS-CoV found in bats are unable to bind this receptor (4). Several years ago in China, a bat CoV, WIV1-CoV, was found to bind to human ACE2 and replicate in human cells (1).

To determine if WIV1-CoV has the potential to infect humans, Menachery et al. (2) synthesized a DNA copy of the genome and introduced it into cells to recover infectious virus. The virus replicated as well as SARS-CoV in differentiated primary human airway epithelial cell cultures, the closest model to the human lung. These findings demonstrate that WIV1-CoV does not require adaptation for efficient replication in human cells.

An important question is whether WIV1-CoV causes disease in an animal model of infection. SARS-CoV does not cause disease in mice, but multiple passages of the virus in this host produced a mouse-adapted virus called SARS-CoV MA15. This virus induces rapid weight loss and lethality by 4 d after intranasal infection (5). When Menachery et al. (2) substituted the spike glycoprotein gene from SARS-CoV MA15 with the corresponding gene from WIV1-CoV, the resulting virus replicated poorly in mice, and did not cause weight loss or lethality.

When wild-type viruses (e.g., not mouse-adapted) were inoculated into mice, neither SARS-CoV nor WIV1-CoV caused weight loss or lethality. However, the two viruses differed markedly in their ability to replicate in mice: SARS-CoV replicated to higher titers in the lung and brain compared with WIV1-CoV. These observations show that although the spike glycoprotein of WIV1-CoV can mediate entry of the virus into human cells, the virus does not cause disease in mice.

A very different outcome was observed when transgenic mice that produce the human ACE2 receptor were used by Menachery et al. (2). In contrast to wild-type mice, intranasal infection of these mice with SARS-CoV did result in weight loss and death. However, WIV1-CoV replicated to lower titers in ACE2 transgenic mice, and caused weight loss in fewer animals. Nevertheless, titers of WIV1-CoV in the lungs and brain were 100-fold higher than in wild-type mice, a likely consequence of the presence of human ACE2 receptor. These results underscore the limitations in using wild-type mice to study SARS-CoV pathogenesis.

The experimental findings suggest that WIV1-CoV is a potential threat to humans. If this virus emerged as a human pathogen, would we be prepared to prevent or treat infections? To answer this question, Menachery et al. (2) identified monoclonal antibodies against SARS-CoV that block infection of cells in culture by WIV1-CoV.

To determine if these antibodies could prevent infection in an animal, human ACE2 transgenic mice were injected with antibody, and 1 d later infected intranasally with SARS-CoV or WIV1-CoV. One antibody blocked replication of both viruses in the lung, and protected mice from weight loss and lethality.

An important conclusion of Menachery et al. (2) is that a mixture of antibodies that block SARS-CoV infection might be used to protect humans if WIV1-CoV entered the population. Identification of a panel of antibodies that can block infection with ACE2-binding CoVs in bats should be an immediate research goal. Neutralizing antibodies are already used to treat human viral infections (e.g., rabies virus), and ZMapp, a mix of antibodies that block Ebolavirus infection, was used experimentally during the 2014–2015 outbreak in West Africa.

It would also be useful to have a vaccine ready in the event that WIV1-CoV or a similar virus enters the human population. A previously developed formalin and UV light-inactivated, whole virus preparation of SARS-CoV protected against infection in young mice. However, aged mice were not completely protected and showed evidence of increased immune pathology (6). When these immunized mice were challenged with WIV1-CoV, no weight loss or lethality was observed, but viral replication was not reduced compared with unimmunized animals, and was accompanied by eosinophilia. The antibodies induced by immunization with the inactivated SARS-CoV also failed to block infection by WIV1-CoV in cells. If WIV1-CoV or a similar virus were to spread in humans, vaccination with inactivated SARS-CoV would not protect against infection.

Previously, Menachery et al. used similar approaches to determine the pathogenic potential of another SARS-like bat virus called SHC014 (7). A recombinant virus was created in which the gene encoding the spike glycoprotein of mouse-adapted SARS-CoV virus was swapped with the gene from SHC014. The recombinant virus, called SHC014-MA15, replicated well in a human epithelial airway cell line and in primary human airway epithelial cell cultures. This virus was attenuated in mice.

However, anti–SARS-CoV monoclonal antibodies did not protect from infection with SCH014-MA15, nor did immunization with inactivated SARS-CoV. SCH014 virus was recovered from an infectious DNA clone made from the genome sequence. This virus infected primary human airway epithelial cell cultures, but not as well as SARS-CoV. In mice, SCH014 did not cause weight loss and it replicated to lower titers than SARS-CoV.

The emergence of pandemic SARS-CoV in 2003, MERS-CoV in the Middle East, and influenza viruses and Ebolaviruses from animal sources emphasize the need to develop approaches for identifying viruses that could potentially initiate new outbreaks. The platform described by Menachery et al. (2) in PNAS, comprising metagenomics data, synthetic virology, transgenic mouse models, and monoclonal antibody therapy is an important advance in allowing assessment of the ability of SARS-CoV–like viruses to infect human cells and cause disease in mouse models.

The results indicate that a bar SARS-like virus, WIV1-CoV, can infect human cells but is attenuated in mice. Additional changes in the WIV1-CoV genome are likely required to increase the pathogenesis of the virus for mice. The same experimental approaches used in the Menachery et al. paper could be used to examine the potential to infect humans of other animal viruses identified by metagenomics surveys.

It is essential to determine which genome changes could increase the pathogenicity of WIV1-CoV in mice. Adaptation of WIV1-CoV to mice would reveal sequences needed for virulence and for moving from a bat to another host. This information could

An important conclusion of Menachery et al. is that a mixture of antibodies that block SARS-CoV infection might be used to protect humans if WIV1-CoV entered the population.

not only be used to identify mutations of potential concern in bat viruses, but would also provide fundamental mechanistic information on how bat CoVs become more pathogenic. A variety of experimental approaches could be used to create such viruses, including animal passage and mutagenesis. However, it is likely that such experiments would not be permitted under the current moratorium on gain-of-function studies involving influenza virus and coronaviruses (https://www.whitehouse.gov/blog/2014/10/17/doing-diligence-assess-risks-and-benefits-life-sciences-gain-function-research).

The current government pause on these gain-of-function experiments was brought about in part by several vocal critics who feel that the risks of this work outweigh potential benefits. On multiple occasions these individuals have indicated that some of the SARS-CoV work discussed in the Menachery et al. (2) article is of no merit. Such conclusions are inaccurate representations of the substantial advances provided by this work.

As a consequence of these experiments with bat CoVs, we know that at least two of these circulating viruses can infect human airway cells, that vaccines do not prevent infection, and that monoclonal antibodies might be used to treat infection with at least one of these viruses should it enter the human population. These findings provide clear experimental paths for developing monoclonal antibodies and vaccines that could be used should another CoV begin to infect humans.

The critics of gain-of-function experiments frequently cite apocalyptic scenarios involving the release of altered viruses and subsequent catastrophic effects on humans (8). Such statements represent personal opinions that are simply meant to scare the public and push us toward unneeded regulation. Virologists have been manipulating viruses for years—this author was the first to produce, 35 y ago, an infectious DNA clone of an animal virus (9)—and no altered virus has gone on to cause an epidemic in humans.

Although there have been recent lapses in high-containment biological facilities, none have resulted in harm, and work has gone on for years in many other facilities without incident (10). I understand that none of these arguments tell us what will happen in the future, but these are the data that we have to calculate risk, and it appears to be very low. As shown by Menacherry et al. (2) in PNAS, the benefits are considerable.

A major goal of life science research is to improve human health, and prohibiting experiments because they may have some risk is contrary to this goal. Being overly cautious is not without its own risks, as we may not develop the advances needed to not only identify future pandemic viruses and develop methods to prevent and control disease, but to develop a basic understanding of pathogenesis that guides prevention. These are just some of the beneficial outcomes that we can predict. There are many examples of how science has progressed in areas that were never anticipated, the so-called serendipity of science. Examples abound, including the discovery of restriction enzymes that helped fuel the biotechnology revolution, and the development of the powerful CRISPR/Cas9 gene-editing technology from its obscure origins as a bacterial defense system.

Banning certain types of potentially risky experiments is short sighted and impedes the potential of science to improve human health. Rather than banning experiments, such as those described by Menachery et al. (2), measures should be put in place to allow their safe conduct. In this way science’s full benefits for society can be realized, unfettered by artificial boundaries. ³⁾

The author declares no conflict of interest. See companion article on page 3048.

Author contributions: V.R. wrote the paper. Copyright notice See the article “SARS-like WIV1-CoV poised for human emergence” in volume 113 on page 3048.

This article has been cited by other articles in PMC. Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences References 1. Ge XY, et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503(7477):535–538. [PMC free article] [PubMed] [Google Scholar] 2. Menachery VD, et al. SARS-like WIV1-CoV poised for human emergence. Proc Natl Acad Sci USA. 2016;113:3048–3053. [PMC free article] [PubMed] [Google Scholar] 3. Li W, et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature. 2003;426(6965):450–454. [PMC free article] [PubMed] [Google Scholar] 4. Graham RL, Ralph Baric RS. Recombination, reservoirs, and the modular spike: Mechanisms of coronavirus cross-species transmission. J Virol. 2010;84(7):3134–3146. [PMC free article] [PubMed] [Google Scholar]⁴⁾

Vineet D. Menachery, Boyd L. Yount, Jr., […], and Ralph S. Baric

The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV highlights the continued risk of cross-species transmission leading to epidemic disease.

This manuscript describes efforts to extend surveillance beyond sequence analysis, constructing chimeric and full-length zoonotic coronaviruses to evaluate emergence potential. Focusing on SARS-like virus sequences isolated from Chinese horseshoe bats, the results indicate a significant threat posed by WIV1-CoV. Both full-length and chimeric WIV1-CoV readily replicated efficiently in human airway cultures and in vivo, suggesting capability of direct transmission to humans.

In addition, while monoclonal antibody treatments prove effective, the SARS-based vaccine approach failed to confer protection. Together, the study indicates an ongoing threat posed by WIV1-related viruses and the need for continued study and surveillance. Keywords: SARS, CoV, emergence, Spike, WIV1 Abstract

Outbreaks from zoonotic sources represent a threat to both human disease as well as the global economy. Despite a wealth of metagenomics studies, methods to leverage these datasets to identify future threats are underdeveloped. ⁵⁾

Guest Essay - Worry About Human Behavior, Not Covid Variants New York Times - June 27, 2021 By Amy B. Rosenfeld and Vincent R. Racaniello

Dr. Rosenfeld and Dr. Racaniello are virology professors at Columbia University Vagelos College of Physicians and Surgeons.

Changes in people’s activities contribute to the rise of infections — such as travel, failure to mask and to adhere to physical distancing policies, and most important right now, insufficient vaccination — and these are often not considered in public discussion of variants.

The huge infection numbers in India, Nigeria and other places are not necessarily because of a particular variant, but in large part because of breached containment measures and crowded populations with poor public health infrastructures. If people are in situations in which they can be infected with the coronavirus, it’s highly likely they will be infected with the fittest variant in the area. Right now, in many places, that’s Delta.

What’s important to understand is that people infected with the variants do not necessarily develop more severe disease or die more frequently from the coronavirus, and it is essential to get vaccinated.

The coronavirus vaccines that have been developed are very effective in preventing severe disease and death caused by all variants, including Delta. Vaccines might not always prevent infections, but they make a substantial impact in reducing virus spread and risk for serious health problems. People who are unvaccinated are at a great risk for infection and harm from any variant of the coronavirus.

During a pandemic, a time of unknowns, people want immediate answers to the question, what does this mutation mean? Providing the correct answers may require years of research. For now, there’s little evidence that the virus is on an endless trajectory of increased transmission and virulence. Today’s vaccines can still end this pandemic.

Amy B. Rosenfeld and Vincent R. Racaniello are virologists in the Department of Microbiology and Immunology at Columbia University Vagelos College of Physicians and Surgeons. Dr. Rosenfeld has studied viruses in the laboratory for two decades. Dr. Racaniello is a co-author of the textbook “Principles of Virology” and the host of the podcast “This Week in Virology” (“TWiV”).

The Times is committed to publishing a diversity of letters to the editor. We’d like to hear what you think about this or any of our articles. Here are some tips. And here’s our email: letters@nytimes.com. ⁶⁾

“The narrative is screwed up in a way,” says Vincent Racaniello, a professor of microbiology and immunology at the College of Physicians and Surgeons of Columbia University. For one, he says, there is only one known strain of the novel coronavirus – the original one, SARS-CoV-2, first discovered in Wuhan. And, two, there's no evidence so far of a variant that can meaningfully evade vaccines, though there are several variants out there.

“People don’t really know what they are talking about,” says the researcher. “I understand, because you talk to doctors and scientists and you figure they would know what they are talking about, but they don’t always.”

Racaniello believes people have been too narrowly focused on how antibodies respond against the coronavirus’ spike protein – and how some variants have appeared to limit the effectiveness of these antibodies in blocking infection. But that’s not the whole story, he says.

Who is Racaniello to say? He wrote the book on viruses. Literally.

A coauthor of the text, “Principles of Virology,” Racaniello has been researching viruses like polio since the 1970s, and started his own lab in the early 1980s. Becoming intrigued with virology after reading the old book, “Fever! The Hunt for a New Killer Virus,” Racaniello began studying at Mt. Sinai School of Medicine and then at MIT alongside greats like David Baltimore, who had just won the Nobel Prize for his role in discovering an enzyme called reverse transcriptase.

TheStreet: Now, fast forward to today, and we have three vaccines that look highly effective. But, we have fears that a new strain could emerge that could evade them…

Racaniello: I am not worried at all that this virus is going to out-evolve vaccines. People have been looking at it the wrong way. People have been looking at antibodies. People say, “ah, the variants are less susceptible to antibodies. But, you know what? They are ignoring T cells. It turns out, none of the variants have changes that would impact the ability of the T-cells to kill an infected cell.

The Johnson & Johnson (JNJ) - Get Report vaccine turns out to be 100% effective at preventing hospitalizations and deaths in South Africa…. I just saw an article today that showed that the U.K. variant … made no difference in the outbreak in the U.K. It made no difference. The people who know, they are not worrying that the vaccines are going to be compromised by a variant. That’s what I can say with certainty.

TheStreet: And for there to be an actual new strain, as opposed to just these variants, it would have to be significantly different, right?

Racaniello: That’s right. It would have to have some substantial biological difference. Just think, there is still just one strain of H.I.V, despite infecting tens of millions of people for 40 years. So this has been a really bad dialogue.

Racaniello: The way vaccines work is that when you get infected after you’re vaccinated you have a memory response and it takes two or three days to kick in. In those two or three days, you are going to be infected, but the infection will be kept down, you won’t get sick and you probably won’t transmit it.

A study was publish that says that the Pfizer (PFE) - Get Report vaccine prevents infection in (most) people. I think that’s a red herring, because it’s too soon after the vaccine, when you have really high antibody levels. Try that study again in a year, and I’m sure people will be infected, although they will be protected against disease, and that’s what we care about.

TheStreet: What do you think of some of this technology coming down the line, and let’s start with progress on these micro-needle patches to replace needle shots…

Racaniello: We have to get away from needles. They are expensive. People have to be trained in how to use them. And, people are scared. I think a lot of anti-vaccine sentiment comes from the fact that parents are scared to put a needle in their kid. So, I think getting away from needles would have a lot of benefits, and micro-needle patches look really good. … I would say at some point we’re not going to need needles anymore (for vaccines). Skin is a really good place to put vaccines.

TheStreet: What about thermo-stabilization for vaccines so they don’t have to be kept in freezers?

Racaniello: The idea that you have to keep vaccines frozen is not good, because not everyone can do that. So, stabilizing vaccines with sugar, or sugar-like compounds, is going to make a big difference. These mRNA vaccines have to be kept at such a low temperature and maybe this could help us get around that.

TheStreet: And what about the future use of messenger RNA technology?

Racaniello: I think the mRNA technology is amazing. We’ve been working on it for years, but decided to try it and it works. The possibilities now – you could imagine making flu vaccines with mRNA, all kinds of other vaccines, and even therapeutics. If you wanted to deliver a protein therapeutically for a short period of time to a patient, maybe this is the way to go. I’m very bullish on mRNA vaccines.

TheStreet: Then there are the broad-spectrum antivirals. Do they hold promise – and, do we need to be careful, as we saw what happened to antibiotics for bacterial infections and the risks there?

Racaniello: We already have antivirals that will inhibit a lot of RNA viruses and others that inhibit a lot of DNA viruses. So, it would be no problem to make an antiviral that would inhibit all coronaviruses, for example. If we would have already had that at the beginning of all this, we could have stopped it altogether in China. But the problem with these broad-spectrum antivirals is … they have to get better before they can be licensed.

But then what happens? You’re going to always have resistance to any antiviral. So, you need more than one. We learned that from the HIV antivirals. We need to treat people with three, and then, you really minimize resistance. The same thing with hepatitis C virus. You use combinations of two and then you eliminate infection without resistance. I think we learned a lot from those two viruses. We can’t just use one. So, we have this molnupiravir (from Merck (MRK) - Get Report). It looks good for SARS-CoV-2, as an oral antiviral. It looks great in patients in phase two studies. But if you just license that one and use it, within months you’re going to have resistance, and it’s going to be useless, so we need to have more than one, especially at the start.

TheStreet: Jumping off that point, as these drugs and vaccines come out, the big pharma names get a lot of attention, and deservedly so – Pfizer, Moderna (MRNA) - Get Report, Johnson & Johnson, AstraZeneca (AZN) - Get Report. But isn’t it university research that lays a lot of the ground work for what we know about viruses?

Racaniello: Sure, in the U.S., anyway, it’s a combination of the National Institutes of Health and then to a lesser extent the National Science Foundation, the Department of Defense and the Department of Agriculture, and then the universities kick in some, but I think they should do more….

But NIH’s budget is about $37 billion a year, and that’s just pathetic. If you think about the return on investment for things like (gene-editing tool) CRISPR, recombinant DNA, polymerase chain reaction – PCR – it’s huge. This pandemic has cost a trillion and a fraction of that could have been used beforehand to make antivirals that could have stopped the pandemic. They don’t invest enough in science research in this country. India and China are starting to outpace us. They get it. Science can save the population.

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