IÂ spoke withÂ virologist Ian Goodfellow, whose laboratory works on noroviruses, about why he went to Sierra Leone to establish an Ebolavirus diagnostic and sequencing laboratory. The obstacles he encountered were considerable, but the results were very useful.Â Recorded at the Emerging Infectious Diseases A to Z (EIDA2Z) conference hosted by the National Emerging Infectious Diseases Laboratories (NEIDL).
The Zika Effect
Having worked on viruses for over 40 years, I know a fair number of people in the field, and I am amazed at how many of them have started to work on Zika virus. What exactly is attracting virologists to this emerging virus?
There are probably many reasons why Zika virus would be of interest to a research lab – what I call the Zika Effect -Â but here are what I think areÂ theÂ three main factors.
First, Zika virus has become medically important in the past year, as it has spread globally and is infecting many people each day. There are many unanswered questions about the virus, and for a scientist, there is nothing better than unanswered questions (except maybe getting money to answer the questions – see below). Because the virus is causing human disease, these questions have an immediacy – such as, does the virus cause birth defects; does the virus cross the placenta, and if so, how; how does the virus enter the central nervous system and cause disease, to name just a few. Because of the nature of Zika virus infection, the virus has attracted not only virologists, but neurobiologists, cell biologists, developmental biologists, and structural biologists. In short: scientists love answering questions, and when it comes to Zika virus, they are not in short supply.
Second, Zika virus is not dangerous to work with – a biosafety level 2 laboratory (BSL-2) is all that is needed. Most virologists carry out their work under BSL-2 containment, so if you are working on influenza virus, poliovirus, herpesvirus, and a host of other viruses, you are ready to work with Zika virus. This situation is in contrast to that which took place in 2015 with the ebolavirus outbreak in west Africa. Work on ebolavirus must be conducted under BSL-4 containment – which few virologists have access to (for a look inside a BSL-4 laboratory, check out the documentary Threading the NEIDL). Consequently far fewer laboratories began work on ebolaviruses after that outbreak.
The third reason for the Zika effect is the reward:Â the promise of a publication in a high profile scientific journal, a promotion, a new job, and new grant funding for the laboratory. Not the purest motivation, but a reality: in the United States, government funding of scientific research has been flat for so many years that any new opportunity is seized. Many laboratories are on the brink of extinction and reach out to any funding opportunity. Few will admit that funding or publication drives their interest in Zika virus, but there is no doubt that itÂ is a majorÂ factor. If research money were plentiful, and if luxury journals were not so tightly linked to career success, there would likely be fewer entrants in the Zika race. And a race it is – at least in these early days, when low-hanging fruit is ripe for picking, papers roll out on a weekly basis and it is difficult to compete without a large research group.
The fact that so many laboratories are working on Zika virus is not only impressive but encouraging: it means that the scientific establishment is flexible and nimble. There is no doubt that the more minds engaged on a problem, the greater the chance that important questions will be answered. But working on Zika virus is not for the faint of heartÂ – which I document on a weekly basis inÂ Zika Diaries, a personal account of our foray into this seductive virus.
Scientists, share your Zika virus reagents!
Today I learned that a number of investigators refuse toÂ share theirÂ samples of Zika virus with other laboratories.
There are countlessÂ stories aboutÂ scientists not sharing reagents because they want to be the first to make a discovery. This behavior allows them to publish first, secureÂ more grant funding, garner invitationsÂ to speak at meetings, and generally strokeÂ their egos.
This sort of selfish behavior happens all the time in science, but it is particularly offensive at a time when a new virus is spreading rapidly, and we need information about its biology, pathogenesis, and epidemiology to be able to treat and prevent infections. Not sharing reagents means that advances will come more slowly, orÂ perhaps not at all: how do you know whichÂ laboratory will make the crucial findings?
Science has enough of a public image problem already. Do we need to make it worse by not sharing materials to work on a virus that has rapidly entered the public’s eye, and about which there are so many unanswered questions?
By keeping reagents to their own laboratories, scientists areÂ being short-sighted and narrow-minded. Will you be pleased when you need a reagent and you can’t obtain it from another source?
Dear fellow scientists: scientific researchÂ is not about you and your ego. It is about contributing to human health. Get with the program.
The wall of polio
The Polio Wall of FameÂ (pictured) is a set of fifteen sculptured busts of 17 individuals who made important contributions to understanding and preventing poliomyelitis. The busts are mounted on an exterior wall of Founder’s Hall at theÂ Roosevelt Warm Springs Institute for Rehabilitation in Warm Springs, Georgia, USA.
In my laboratory we have a slightly different wall – we call it The Wall of Polio. It consists of a collection of six-well cell culture plates that have been used to measure the concentration of polioviruses in various samples by plaque assay.
The plaque assay isÂ one of the most important procedures in virology for measuring the virus titer â€“ the concentration of viruses in a sample. This technique was first developed to calculate the titers of bacteriophage stocks.Â Renato DulbeccoÂ modified this procedure in 1952 for use in animal virology, and it has since been used for reliable determination of the titers of many different viruses.
We love the plaque assay so much that we cannot bear to throw away the plates after they have been counted. They reside in various nooks and crannies in the laboratory, but one creative use has been to construct a wall – think of Legos using cell culture plates. When a visitor comes to the lab, I photograph them in front of the Wall of Polio (sign inspired by Pink Floyd). When you visit don’t be surprised when I ask to photograph you in front of the Wall of Polio.
Update from my postdoctoral scientist Rea:Â The wall has >1000 plates, stands over 6 ft tall, and contains data from only one experiment which took me almost 4 months to do. Credit goes toÂ Brenda RaudÂ for the sign, construction and design, and some plates too!
Thirty years in my laboratory at Columbia University
Thirty years ago this month I arrived in the Department of Microbiology at Columbia University’s College of Physicians and Surgeons (P&S) to start my own laboratory. Thirty is not only a multiple of ten (which we tend to celebrate), but also a long time to be at one place. It’s clearly time to reminisce!
After studying influenza viruses with Peter Palese in New York City, in 1979 I headed to David Baltimore‘s laboratory at MIT. It was not long after Baltimore had received the Nobel Prize in Physiology or Medicine for discovering retroviral reverse transcriptase. In his laboratory I first encountered poliovirus, which would hold my interest for many years to come. The moratorium on recombinant DNA research had just been lifted, and it was now possible to clone complete viral DNA genomes. My first project was to make a DNA copy of poliovirus RNA, clone it into a bacterial plasmid, and determine its sequence. The result gave us the first glimpse of the viral genome. I then found that a DNA copy of poliovirus RNA is infectious in mammalian cells, a story that I have documented elsewhere.
The next step in my career was to have my own laboratory. With these two papers in hand I was able to obtain several respectable job offers, including one in the Microbiology Department at P&S. The department chair was Harold S. Ginsberg, an adenovirologist. My decision to accept his offer was influenced by the strong virology component of the department, which included Saul Silverstein and Hamish Young. I moved back to New York City in September 1982 with a DNA copy of the poliovirus genome in hand. In the last few weeks in the Baltimore laboratory, I had cloned a DNA copy of another poliovirus strain – type 2 Lansing – which had the interesting ability to infect mice. I spent the first few years in my new laboratory studying this virus and how it caused paralysis in mice. We found that the type 2 Lansing viral capsid was important for the ability to infect mice. Later, we narrowed this down to 8 amino acids. The type 1 Mahoney strain of poliovirus – which I had studied in the Baltimore laboratory – cannot infect mice. However, if we substituted 8 amino acids of the Mahoney capsid with the corresponding sequence from the Lansing genome, the recombinant virus could infect mice.
Our sequence analysis of poliovirus RNA had revealed an unusually long 5′-noncoding region. We began to carry out experiments to understand how such a viral RNA could be translated, and found that this long sequence enabled translation in the absence of a cap protein. This observation lead to the discovery by others that the poliovirus 5′-noncoding region contains an internal ribosome entry site (IRES). In the ensuing years our interest in translation continued. Examples include our finding that cell proteins bind to the poliovirus 5′-noncoding region, now known to participate in regulation of translation and genome replication, and understanding the inhibition of cell translation by poliovirus. Years later we developed a functional assay for the IRES in yeast, allowing identification of cell proteins needed for internal ribosome binding.
There is one area of research that has received the most attention in my laboratory, and on which we have published most extensively: the interaction of viruses with cell receptors. Towards the end of my stay in the Baltimore laboratory I became interested in how poliovirus attaches to and enters cells. Â I came to Columbia with a strong interest in identifying the cell receptor for poliovirus, which we subsequently achieved.Â This finding lead to a series of studies on virus attachment to cells and virus entry. We produced transgenic mice susceptible to poliovirus, and used them to study aspects of poliovirus replication and pathogenesis, including how the virus attaches to its cellular receptor, regulation of viral tissue tropism, and the basis for attenuation of the Sabin vaccine strains.
The finding that poliovirus tropism is regulated by the interferon response lead to a change in the direction of our research. Beginning in the early 2000s we began studying how poliovirus interacted with the innate immune response. We found that poliovirus is relatively resistant to the antiviral effects of interferon, a property conferred by the viral 2Apro proteinase. How poliovirus is sensed by the innate immune system has also become a focus of our work. With the looming prospect of poliovirus eradication, and subsequent prohibition of work on the virus, we have also turned our attention to rhinoviruses, agents of respiratory illness. One focus has been to establish a mouse model for rhinovirus infection.
This story would not be complete without mentioning my foray into science communication. I have written a virology textbookÂ andÂ a blog about viruses, and began three science podcasts, including This Week in Virology, This Week in Parasitism, and This Week in Microbiology. My use of social media to teach microbiology to the world has been documented in a Social Media and Microbiology Education and in my Peter Wildy Prize Address.
None of this work would have been possible without the participation of 24 Ph.D. students (Nicola La Monica, Cathy Mendelsohn, Eric Moss, Robert O’Neill, Mary Morrison, Ruibao Ren, Elizabeth Colston, Michael Bouchard, Suhua Zhang, Alan Dove, Sa Liao, Yanzhang Dong, Yi Lin, Brian McDermott, Melissa Stewart Kim, Steven Kauder, Julie Harris, Amy Rosenfeld, Juliet Morrison, Angela Rasmussen, Jennifer Drahos, and Esther Francisco), 7 postdoctoral fellows (Gerardo Kaplan, Marion Freistadt, Michael Shepley, Ornella Flore, Juan Salas-Benito, and Scott Hughes), and many technicians and undergraduate students. My laboratory currently consists of postdoctoral scientist Rea Dabelic, and graduate students Ashlee Bennett and Michael Schreiber (pictured above).
Counting my time here, together with my Ph.D. and postdoctoral years, I’ve been working on viruses for 37 years. I do not know how much longer I will be doing the same, but it’s safe to say that it won’t be for another 37 years. But whenever I stop directing virology research, I will continue to write, podcast, and teach – you can expect nothing less fromÂ Earth’s virology professor.
TWiM #18: Escherichia coli K-12, an emerging pathogen?
Hosts:Â Vincent Racaniello, Michael Schmidt,Â Stanley Maloy and Elio Schaechter.
On episode #18 of the podcast This Week in Microbiology,Â Vincent, Michael, Elio, and Stanley explain how to make the human intestinal commensal and benign laboratory bacterium Escherichia coli K-12 into an invasive organism, and theÂ unearthing of century-old spores in New York City.
Click the arrow above to play, or right-click to downloadÂ TWiM #18 (54 MB, .mp3, 74 minutes).
Subscribe to TWiM (free) on iTunes,Â Zune Marketplace, via RSS feed, by email or listen on your mobile device with the Microbeworld app.
Links for this episode:
- Conversion of E. coli K-12 to an invasive form (mBio)
- Pedigree of E. coli K-12 (pdf)
- The facade of E. coli K-12 (Small Things Considered)
- Unearthing of century old bacteria in NYC (ABC News)
- Bacteria in 30,000 year old salt crystals (Geology)
- Old bacteria in ice
- Old, small, cold… (Small Things Considered)
- IP6 mediated autoprocessing of bacterial toxins (PloS Path)
- Letters read on TWiM #18
Send your microbiology questions and comments (email or mp3 file) to firstname.lastname@example.org, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twim.