TWiV 435: Two virus particles walk into a cell

The TWiVome discuss the blood virome of 8,420 humans, and thoroughly geek out on a paper about the number of parental viruses in a plaque.

You can find TWiV #435 at, or listen below.

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The purity of plaques

dose-response-plaque-assayThe plaque assay – my favorite assay in the world – is a time-honored procedure to determine the number of viruses in a sample, and to establish clonal virus stocks. The  linear relationship between the number of infectious particles and the plaque count (illustrated; image credit) shows that one infectious particle is sufficient to initiate infection. Despite the one-hit kinetics of plaque formation, could more than one virus contribute to a plaque?

To answer this question, ten genetically marked polioviruses were mixed and subjected to plaque assay. Of 123 plaques, 6 (4.9%) contained more than one virus. Similar results were found when polioviruses with phenotypic markers were studied.

Examination of poliovirus stocks by electron microscopy revealed both single particles and aggregates of 2 to 10 particles. Increasing particle aggregation by treatment of viruses with low pH increased co-infection frequency, indicating that aggregation of particles leads to multiply infected cells.

When these experiments were repeated with mutagenized polioviruses, the co-infection frequency increased – probably because recombination and complementation between two defective genomes leads to rescue of the defects.

Do these findings indicate that poliovirus plaque formation does not follow one-hit kinetics? The results do not prove that, in unmutagenized virus stocks, more than one poliovirus is needed to form a plaque. They only show that a small percentage of plaques contain more than one poliovirus. The presence of more than one poliovirus in 5-7% of plaques is likely a consequence of virion aggregation. It would be informative to prepare poliovirus stocks with no aggregates, and determine if co-infected plaques are still observed.

Some viruses of plants and fungi follow two-hit kinetics: two virus particles, with two different genomes, are needed for infection (illustrated). Assuming that 4-7% of poliovirus plaques are initiated by multiple viruses, the resulting plots deviate only slightly from a straight line, and do not resemble the curves of two-hit kinetics.

What are the implications of these findings for the use of plaque assays to produce clonal virus stocks? Even though the frequence of multiply infected plaques is low, the possibility of producing a mixed population is still possible, if only one plaque purification is done. In our laboratory we have always repeated the plaque purification three times, which should ensure that no multiply infected plaques are isolated.

Update 3/31/17: I would like to see similar experiments done with other viruses, to see how often multiple viruses can be found in a plaque. Examples included hepatitis A virus, which is released from cells in membranous vesicles containing multiple virus particles; and enveloped viruses, which might aggregate more frequently than naked viruses.

I looked back at the 1953 publication in which Dulbecco and Vogt first described the plaque assay for poliovirus, and demonstrated one hit kinetics. The dose-response curve clearly shows one-hit kinetics with little deviation of the individual data points from a straight line.

plaque dose response

Linear relationship between the number of plaques and the virus concentration. Image credit.


Viral RNA is not infectious virus!

Zika RNA and virusA study of sexual transmission of Zika virus among mice (link to paper) demonstrates beautifully that viral nucleic acid detected by polymerase chain reaction (PCR) is not the same as infectious virus.

Male mice were infected with Zika virus and then mated with female mice. Efficient sexual transmission of the virus from males to females was observed. This observation in itself is very interesting but is not the focus of  my comments.

To understand the dynamics of sexual transmission, the authors measured Zika virus shedding in seminal fluid – by both PCR, to detect viral RNA, and by plaque assay, to detect infectious virus. The results are surprising (see figure – drawn in my hotel room).

Zika virus RNA persisted in semen for up to 60 days – far longer than did infectious virus, which could not be detected after about three weeks.

Many laboratories choose to assay the presence of viral genomes by PCR. This is an acceptable technique as long as the limitations are understood – it detects nucleic acids, not infectious virus.

Despite the presence of Zika virus RNA in seminal fluid for at least 60 days after infection, these mice are not likely to transmit virus after a few weeks. There is a lower limit of detection of the plaque assay – approximately 10 plaque forming units/ml – whether that would be sufficient to transmit infection is a good question.

Why Zika viral RNA and not infectious virus would persist for so long is an important and unanswered question that should definitely be studied.

Recently many papers have been published which demonstrate that Zika virus and Ebolavirus can persist in a variety of human fluids for extended periods of time. These results have been interpreted with alarm, both by scientists and by science writers. However, in most cases the assays were done by PCR, not by plaque assay, and therefore we do not know if infectious virus is present. Viral RNA would not constitute a threat to transmission, while infectious virus would.

The lesson from this study is very clear – in novel experimental or epidemiological  studies it is important to prove that any viral nucleic acid detected by PCR is actually infectious virus. Failing to do so clouds the conclusions of the study.

There are few excuses for failing to measure viral infectivity by plaque assays. Please don’t tell me it’s too much work – that’s a poor excuse on which to base selection of an assay. Even if your virus doesn’t form plaques there are alternatives for measuring infectious virus.

If you are wondering how a plaque assay is done, check out my short video below.

Virus Watch: Counting Viruses

In this episode of Virus Watch, I show how to do my favorite assay in all of virology – the plaque assay.

The Wall of Polio, version 3.0

Wall of Polio 3.0Back in 2013 I built a Wall of Polio in my laboratory – a large stack of six-well cell culture plates that have been used to measure the concentration of polioviruses in various samples by plaque assay. It became a focal point of the lab at which many guests came to have their photographs taken. Sadly, the Wall fell twice. Now a new Wall – version 3.0 – has been completed.

The new Wall of Polio is in my office at Columbia University Medical Center, where it will not annoy the Fire Inspector (the former Wall partially blocked an aisle). Furthemore, the new Wall is glued together, so it will not come apart. Its construction is documented in the photographs below. The Wall of Polio 3.0 is built with 1,464 six-well plates of HeLa cells that were used to determine the titer of poliovirus. We have also already had a number of visitors to Wall 3.0.

Because the Wall is impressive, it attracts attention, which can then be used to explain the plaque assay and determining virus titer. Therefore it is simply another tool that I used to teach the world about virology.

When you visit, expect that I will ask to photograph you before the Wall. Only a few have refused.


TWiV 312: She sells B cells

On episode #312 of the science show This Week in Virology, the TWiVbolans discuss the finding that human noroviruses, major causes of gastroenteritis, can for the first time be propagated in B cell cultures, with the help of enteric bacteria.

You can find TWiV #312 at

A saga of HeLa cells

HeLa spinnerWe have been using HeLa cells in my laboratory since 1982, when I arrived at Columbia University Medical Center fresh from postdoctoral work with David Baltimore at MIT. I brought with me a line of HeLa cells and used them for 30 years for our research on viruses. Here is a story of how we lost the cells and then found them ten months later.

As everyone knows, the continuous HeLa cell line was derived from a cervical tumor taken from Henrietta Lacks in 1951 (if you don’t know the story, you should read Rebecca Skloot’s The Immortal Life of Henrietta Lacks, or my shorter summary). When I arrived at the Baltimore lab in 1979, they were using cells derived from the S3 clone of HeLa cells that had been produced by Philip Marcus in the 1950s. I write ‘derived from’ because someone at MIT had further  cloned the S3 line and selected one that was particularly susceptible and permissive to poliovirus infection. This was the cell line that I took with me to Columbia in 1982.

Because we use so many HeLa cells each week, we grow them in spinner cultures (pictured). The cells are suspended in a glass bottle in nutrient medium and continuously stirred by a magnetic bar. The spinner bottle is placed on top of a stir plate, which contains a motor that drives a rotating magnet that in turn spins the bar in the bottle. When we need to produce monolayers of cells for experiments, we remove cells from suspension and plate them on plastic dishes. The HeLa S3 clone that we use grows very well in suspension and also forms excellent monolayers on plastic dishes.

Over the years we used the HeLa S3 subclone to conduct experiments with poliovirus, echoviruses, Coxsackieviruses, enteroviruses, rhinoviruses, and encephalomyocarditis virus. The cells could be infected with all these viruses, develop cytopathic effects, and form plaques, allowing titration of virus titers. They have been an essential part of my laboratory. The Wall of Polio is just one example of how important these cells have been for our work.

In December 2012, the spinner went down. The drive belt that turns the magnet in the spinner platform broke overnight; the cells settled out and died. Normally we would simply go to our stock of cells frozen in liquid nitrogen, thaw them out, and be up and working again within a week. Unfortunately, our liquid nitrogen tank had run dry one week in the summer of 2012, and all the cells had died. We tried recovering some of the HeLa cells that were frozen, but what grew out were not the same as our S3 subclone.

In the course of the next 9 months we tried HeLa cells from many different sources – laboratories here at Columbia, the American Type Culture Collection, and our colleagues elsewhere. None of the HeLa cells performed like our S3 subclone. Some HeLa lines did not grow well in spinner; others did, but formed poor monolayers. Still others did not support replication or plaque formation when infected with viruses we work on now – poliovirus, rhinoviruses, and encephalomyocarditis virus. I located former members of the Baltimore laboratory, hoping that they had taken the special HeLa cells with them, but I came up empty handed.

A few weeks ago I received an email from a former student who had heard my pleas for HeLa cell help on This Week in Virology. She remembered bringing some of our HeLa cells to her postdoctoral laboratory in Canada, and freezing them down when she left. I contacted the laboratory and found to my delight that our HeLa cells were indeed frozen there; a kind member of the laboratory grew up a stock of the cells, froze them, and shipped them off to us. I received them a week ago and put them into culture. They were the HeLa cells that I used to know: I recognized their morphology immediately. They grew beautifully as monolayers, and just today I set up a spinner culture. We are all looking forward to using the cells in our virology experiments.

Meanwhile, I have a large stock of belts for the magnetic spinner plate (I had to buy seventeen of them, to meet the $50 minimum order); I have placed 6 vials of the cells in our liquid nitrogen tank; and I plan to freeze additional vials in my colleagues’ freezers in case ours goes down again.

There are several lessons to be learned from this saga. First, because virologists are completely dependent on cells, they must take care that they have a reliable stock. This means having someone in the lab checking the level of liquid nitrogen every day, and ordering a new tank when the level is low. Second, it’s important to keep stocks of cells frozen elsewhere. We were very lucky to find them in Canada. Third, HeLa cell lines are very different. Finally, HeLa cells are special. I don’t know of any other cell line that grows well in spinner, makes beautiful monolayers, and allows us to work with so many different viruses. Thank you, Henrietta Lacks.

The wall of polio

Polio wall of fameThe Polio Wall of Fame (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 the 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 is one of the most important procedures in virology for measuring the virus titer – the concentration of viruses in a sample. This technique was first developed to calculate the titers of bacteriophage stocks. Renato Dulbecco 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: 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 to Brenda Raud for the sign, construction and design, and some plates too!

Renato Dulbecco, 1914-2012

wee plaques 1952For the second time in a week I note the passing of an important virologist. Renato Dulbecco, together with David Baltimore and Howard Temin, received the 1975 Nobel Prize in Physiology or Medicine for discoveries about how tumor viruses interact with the genetic material of the cell. Dulbecco also devised my favorite virological method, the plaque assay, for determining the virus titer, the number of animal viruses in a sample.

Since the early 1920s bacteriologists had used the plaque assay to quantify the number of infectious bacteriophages (viruses that infect bacteria). Dulbecco noted in 1952 that “research on the growth characteristics and genetic properties of animal viruses has stood greatly in need of improved quantitative techniques, such as those used in the related field of bacteriophage studies.” One limiting factor was the development of suitable animal cell cultures that could be used to determine viral titer. By the 1950s the techniques for reliably producing and propagating human cell cultures were developed, and in 1951 the first immortal human cell line, HeLa, was isolated. Dulbecco took advantage of these advances and showed in 1952 that western equine encephalitis virus formed plaques on monolayers of chicken embryo fibroblasts (figure). Dulbecco also made the important observation that one virus particle is sufficient to produce one plaque. He drew this conclusion from his observation of a linear dependence of the number of plaques on virus concentration. This seminal advance made possible the application of genetic techniques to the study of animal viruses.

Dulbecco’s work on tumor viruses was focused on polyomaviruses – small DNA-containing viruses such as murine polyomavirus and SV40. He found that cells from the natural host of the virus – mice for polyomavirus and monkeys for SV40 – were killed as the viruses replicated and produced new viral progeny. However, these viruses did not replicate in or kill cells from other animals. For example, when hamster cells were infected with murine polyomavirus, no viral replication took place, the cells survived, and a few rare cell were transformed  – their growth properties in culture were altered and they induced tumors when injected into hamsters. Dulbecco later found that the polyomaviral DNA is a circular, double-stranded molecule; and that in non-permissive cells (in which the virus does not replicate) the viral DNA became integrated into the host cell chromosome. He also suspected that a viral protein called T (for tumor) antigen was a key to cell transformation.

Today we understand why polyomaviruses transform cells in which they do not replicate: infection does not kill these cells, and the rare transformed cells contain only viral DNA encoding T antigen. This protein is needed for viral replication in permissive cells because it drives cell proliferation, activating cellular DNA replication systems that are required for producing more viral DNA. In a non-permissive cell, T antigen drives the cell to divide endlessly, immortalizing it and allowing the accumulation of mutations in the cell genome that make the cells tumorigenic.

While the details of how DNA tumor viruses transform cells were being elucidated, other investigators were attempting to understand how another class of viruses – with RNA genomes – had similar effects on cells. In 1951 a young scientist named Howard Temin joined Dulbecco’s laboratory to study how Rous sarcoma virus (RSV) caused tumors. This virus had been discovered by Peyton Rous in 1911, but would only cause tumors in chickens, limiting progress. In Dulbecco’s laboratory, Temin found that RSV induced transformation of cultured chicken embryo fibroblasts – the same types of cells that were being used to develop the plaque assay for animal viruses. Temin took this transformation assay to his own laboratory, where he reasoned that a DNA copy of the RSV viral genome must be integrated into the chromosome of transformed cells. This led him to discover the enzyme reverse transcriptase in RSV particles, which produces a DNA copy of the viral RNA.

By embracing a new technology for the study of animal viruses – cell culture – Dulbecco set the study of both DNA and RNA tumor viruses on a path that would lead to understanding viral transformation, an achievement recognized by the 1975 Nobel Prize.

Dulbecco, R. (1952). Production of Plaques in Monolayer Tissue Cultures by Single Particles of an Animal Virus Proceedings of the National Academy of Sciences, 38 (8), 747-752 DOI: 10.1073/pnas.38.8.747

The Lazarus virus

infected cellThere is an excellent question in the comments to “Are all virus particles infectious?“: if the particle-to-PFU ratio for a virus stock is 10,000:1, and I infect 1,000,000 cells with 10,000 particles, how many plaques would I expect to observe? Answering this question provides insight into the particle-to-PFU ratio of viruses.

If we take 10,000 particles of our virus stock and infect 1,000,000 cells, we are adding just one infectious particle. Therefore a correct answer to the question is one plaque. But would you be wrong if you answered 100 plaques? That would depend on how you justified your answer.

To understand why 100 plaques could be correct, we need to do some math, and calculate the number of virus particles that each cell receives. If we add 10,000 particles to 1,000,000 cells, the MOI is 0.01. At that MOI, 0.01% of the cells will receive more than one virus particle. In a culture of 1 million cells, 100 cells will receive at least two virus particles and could, in theory, become productively infected. Let’s explore why.

The linear nature of the dose-response curve indicates that a single virion is capable of initiating an infection. However, the high particle-to-pfu ratio of many viruses shows that not all virions are successful. A high particle-to-pfu ratio is sometimes caused by the presence of noninfectious particles with genomes that harbor lethal mutations.

To simplify this problem, let’s assume that among the 10,000 noninfectious particles in our sample, half of them have a mutation in gene A and half have a mutation in gene B. This scenario is illustrated in the figure, which shows a cell infected with two viruses (only the viral genomes are shown). Both mutations are lethal – cells infected with either viral mutant do not produce new virus particles. However, when a cell is infected with both virus mutant A and virus mutant B, complementation of the defects might occur. The virus with mutant gene A produces a fully functional gene B product; and the virus with mutant gene B produces a fully functional gene A product. The result is that the infected cell contains functional versions of proteins A and B, and viral replication can occur. It’s also possible that the two viral genomes might undergo recombination, producing a new genome that does not contain any lethal mutations. Either mechanism could explain why we might expect to observe up to 100 plaques in this experiment.

The reality is that the 10,000 noninfectious virus particles in our stock likely have mutations in many genes, not just two. Therefore the probability that complementation or recombination can correct the defects is remote. This is the reason why we are likely to observe just one plaque in our experiment.