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About viruses and viral disease

Richard R Ernst Lecture 2022 – Vincent Racaniello

27 May 2022 Leave a Comment

It was my great honor to be selected as the Richard R Ernst Lecturer for 2022.

Following is the text of the email that I received on 25 September 2020 informing me that I had received this award. Note that the committee had already made its decision in December 2019!

The aim of the Richard R. Ernst Lecture is to strengthen the relationship and understanding between the sciences, society, and politics and to raise awareness for the questions and challenges our global society is facing today and will face in the future. The RRE Lecture is a public lecture for a scientifically interested general audience. As part of the event the lecturer will be awarded the Richard R. Ernst Gold Medal. Richard R. Ernst is the 1991 recipient of the Chemistry Nobel prize. Previous recipients of the Gold Medal are:

2009 Prof. Dr. Gottfried Schatz (Biozentrum Basel)
2010 Kofi Annan (Former UN Secretary-General)
2011 Prof. Dr. Ernst Ludwig Winnacker (Secretary General of the Human Frontier Science Program Organization)
2012 Prof. Dr. Sir Roger Penrose (University of Oxford)
2013 Prof. Dr. Ahmed Zewail (Caltech)
2014 Prof. Dr. Kamil Ugurbil (University of Minnesota)
2015 Prof. Dr. Steven Chu (Universities of Berkeley and Stanford)
2017 Prof. Dr. Felicitas Pauss (ETH Zurich und CERN)
2019 Prof. Dr. Emmanuelle Charpentier (MPI for the Science of Pathogens, Berlin)

The ongoing Covid-19 pandemic and the accompanying public discourse have shown more than ever how important the education of the general public about scientific topics and the process of research is. With your series of podcasts, where current research in virology, immunology, microbiology, etc. is discussed with experts in an accessible manner, you provide an invaluable service to the general public and the scientific community.

Watch a recording of the ceremony and my lecture below.

TWiV Special: Monkeypox clinical update with Dr. Daniel Griffin

27 May 2022 Leave a Comment

In this special episode, Dr. Griffin answers questions about the recent cases of monkeypox including their origin, clinical presentation, diagnosis, treatment, and overall risk.

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Show notes at microbe.tv/twiv

Trial By Error: An Innumerate Response from Chalder to Hughes-Tuller Comments on Bogus Data Analysis

26 May 2022 6 Comments

By David Tuller, DrPH

Last year, King College London’s professor of cognitive behaviour therapy, Trudie Chalder, published another one of her extremely incompetent papers. This one is so statistically challenged as to be truly mind-boggling, even by Professor Chalder’s extremely low standards. A team of purportedly expert researchers has mangled descriptions of their own  data so badly that the paper is rendered literally incomprehensible. When it was published, Mark Vink and Keith Geraghty tweeted about it, respectively, here and here.

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Trial By Error: Speaker at CDC Event Promotes CBT and “Very Gradual” GET

23 May 2022 7 Comments

By David Tuller, DrPH

The US Centers for Disease Control and Prevention has a long history of missteps when it comes to the illness or cluster of illnesses currently called ME/CFS—as anyone who has read Osler’s Web knows. In the more recent past—2017–the agency dropped its unfortunate endorsement of the discredited GET/CBT treatment approach but made no public comment about the move until I asked about it. The agency argued that people misunderstood or were confused about what it meant by the terms GET and CBT. This explanation was laughable. No one misunderstood anything. After all, the agency had been citing the PACE trial.

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TWiV 902: Autoantibodies drive severe COVID-19

22 May 2022 Leave a Comment

TWiV reviews recent cases of monkeypox, presence of SARS-CoV-2 RNA but not infectious virus in feces, and the association of autoantibodies to interferons with severe COVID-19.

Hosts: Vincent Racaniello, Dickson Despommier, Rich Condit, Kathy Spindler, and Brianne Barker

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TWiV 901: COVID-19 clinical update #115 with Dr. Daniel Griffin

21 May 2022 Leave a Comment

In COVID-19 clinical update #115, Dr. Griffin reviews cross-variant immunity without vaccination, EUA for boosters in 5-11 year olds, B.1.1.529 attack rate, scent dogs, Omicron and pets, Paxlovid, Veklury, Fluvoxamine, antigen positivity after isolation, inflammasome activation and severe disease, and GI persistence and fecal shedding.

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TWiV 900: Burning down the mouse

15 May 2022 Leave a Comment

TWiV celebrates 900 episodes, Vincent gives the Richard R. Ernst lecture, and we discuss why inflammasome activation in infected macrophages drives severe COVID-19.

Hosts: Vincent Racaniello, Alan Dove, Rich Condit, Kathy Spindler, and Brianne Barker

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Trial By Error: An Interview With Mt Sinai’s David Putrino About Long Covid, ME/CFS, and Related Issues

12 May 2022 12 Comments

By David Tuller, DrPH

David Putrino is a neuroscientist and physical therapist at Mt. Sinai Hospital in New York. He runs a research lab and a rehabilitation center that quickly became a magnet for patients grappling with what has come to be known as long Covid–what the US National Institutes of Health calls post-acute sequelae of SARS-CoV-2 (PASC). We spoke today about his background and how he began treating long Covid patients, the symptom of post-exertional malaise, the tendency to psychologize medical conditions like long Covid and ME/CFS, etc.

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Fighting Viruses with Viruses

5 May 2022 2 Comments

by Gertrud U. Rey

Errors during viral replication can give rise to shortened and/or rearranged genomic sequences known as “defective viral genomes” (DVGs). Because DVGs often lack critical elements needed for replication and formation of new viral particles, virions containing DVGs can only complete a replication cycle if they co-infect a cell together with respective full-length (i.e., wild type) viruses. To replicate their genomes, DVGs often hijack missing proteins from the wild type viruses, a phenomenon that can result in suppression of wild type virus replication. There is increasing evidence to suggest that this suppression can be exploited for the development of antiviral agents.

Marco Vignuzzi at the Institut Pasteur has been exploring this idea by investigating the antiviral potential of DVGs produced during infection of cells with various viruses. In an effort to capture DVGs as they were formed in cell culture, Vignuzzi and colleagues infected mammalian and mosquito cells with Chikungunya virus, a mosquito-borne virus that causes symptoms similar to those caused by dengue virus. They then isolated newly emerging virions from the cells and used those particles to infect new cells – a cycle that was carried out 10 times in a technique known as serial passaging. Sequencing and quantification of viral genomes isolated from the last passage revealed that the number of DVGs increased by about 100,000 between the first and last passage. The most prevalent DVGs were sorted into four groups, with DVGs within each group having deletions of similar sizes and at similar genomic locations. Three of the groups included mostly DVGs derived from mammalian cells and the fourth group included mostly DVGs derived from mosquito cells.

To determine whether DVGs are also generated in an infected arthropod, the authors infected Aedes aegypti mosquitoes with Chikungunya virus by allowing them to feed on virus-infected blood. Ten days after infection, the mosquitoes were dissected, total RNA was isolated, and DVGs were identified by sequencing the RNA using DVG-specific primers. This analysis revealed that the DVGs produced in mosquitoes had similar deletion patterns and profiles as those produced in cell culture, suggesting that DVGs are generated both in cell culture and mosquitoes.

All subsequent studies were done using 20 mammalian- and mosquito-derived DVGs that occurred most frequently and persisted through all passages. To confirm that the DVGs were indeed defective and unable to replicate inside a cell in the absence of full-length virus, the authors introduced (i.e., “transfected”) RNA molecules encoding each DVG into mammalian cells and extracted total RNA from the cells at 8, 20, 28, and 44 hours post-transfection. DVG RNA was then quantified by PCR using primers specific for the respective DVGs. The authors observed that in contrast to wild type virus levels observed in control cells, which increased steadily over time, DVG levels decreased across all time points. This finding confirmed that in the absence of wild type virus DVG RNA was not replicated, but degraded over time.

To see whether the 20 DVGs actually interfered with replication of wild type virus, the authors transfected mammalian cells with a 1:1 ratio of an RNA encoding a DVG and an RNA encoding a full-length fluorescently-tagged wild type Chikungunya virus, so they could monitor the presence of the wild type virus by fluorescence microscopy at various timepoints. Wild type Chikungunya viruses transfected together with most DVG-encoding RNAs continued fluorescing strongly at 48 hours post-transfection, suggesting that most DVGs did not inhibit or reduce the replication of wild type virus when transfected at a 1:1 ratio. However, when the DVG/full-length virus ratio was increased to 10:1, fluorescence of full-length Chikungunya viruses decreased by 10 – 1,000-fold in the presence of almost all DVGs, suggesting that a higher ratio of most DVG RNAs increased the likelihood of these genomes to confiscate needed replication elements from wild type viruses and thus interfere with their reproduction. Interestingly, the smallest DVG with the biggest deletions did not seem to interfere with wild type virus replication, probably because this genome was missing too many elements and could not be adequately compensated by the presence of full-length virus. Overall, these results suggested that both mammalian- and mosquito cell-derived DVGs can interfere with wild type virus replication in mammalian cells. Remarkably, when this experiment was repeated in mosquito cells, most of the mosquito cell-derived DVGs that could inhibit wild type virus replication in mammalian cells were unable to do so in mosquito cells. Although the exact reason for this effect is unclear, it is possible that the prevalence of arthropod-borne viruses in mosquitoes has led these viruses to evolve some resistance to the effects of DVGs during viral replication in mosquitoes.

The authors also found that although most DVGs only inhibited Chikungunya virus strains that were closely related to the strain they were derived from, a small number of DVGs also inhibited more distantly related viruses like Sindbis virus, suggesting that DVGs may be capable of inhibiting a broad range of viruses.

In a final set of experiments aimed to evaluate the ability of the DVGs to prevent viral spread within mosquito hosts, the authors injected mosquitoes with DVG-encoding RNAs, and two days later they infected them with a fluorescently-tagged wild type Chikungunya virus. A control group of mosquitoes was only infected with Chikungunya virus but did not receive any DVGs. Five days after infection, the mosquitoes were killed and analyzed for infection and viral spread by looking for the presence of virus in the midgut and the rest of the body, respectively. All mosquitoes had similar levels of virus in the midgut, whether they had received DVGs or not, suggesting that DVGs had no significant impact on infection. However, mosquitoes that had received DVGs had significantly lower levels of virus in the rest of the body compared to control mosquitoes, suggesting that DVGs can reduce replication and spread of virus in mosquitoes.   

Because all experiments involved delivery of DVGs before or concurrently with wild type virus infection, it is unclear whether DVGs would have any therapeutic effect if they were applied after infection. Presently, the most feasible use for DVGs would be as a vector control strategy by engineering and releasing mosquitoes that are unable to transmit virus. However, considering that DVGs have immunostimulatory potential and their presence in humans correlates with milder disease and better outcome after influenza virus, respiratory syncytial virus, hepatitis C virus, and dengue virus infections, it would be interesting to see if they could be applied as direct therapeutics in humans. Using a combination of lab experiments and computational approaches, Vignuzzi and colleagues identified DVGs with optimal interference activity in a follow-up study. Based on these results, the French biotechnology company Meletios Therapeutics is currently developing a new class of antivirals against Zika virus and Chikungunya virus. This is exciting news, because there are currently no effective antiviral treatments for these two viral infections, and I look forward to following up on these new developments in a future post.  

TWiV 896: Memory B cells, the way we were

1 May 2022 2 Comments

TWiV explains a study of how climate change is predicted to increase cross-species viral transmission risk, and increased memory B cell potency and breadth after a SARS-CoV-2 mRNA vaccine boost.

Hosts: Vincent Racaniello, Dickson Despommier, and Amy Rosenfeld

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by Vincent Racaniello

Earth’s virology Professor
Questions? virology@virology.ws

With David Tuller and
Gertrud U. Rey

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Contents

Table of Contents
ME/CFS
Inside a BSL-4
The Wall of Polio
Microbe Art
Interviews With Virologists

Earth’s Virology Course

Virology Live
Columbia U
Virologia en Español
Virology 101
Influenza 101

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