TWiV 337: Steamer

17 May 2015

On episode #337 of the science show This Week in Virology, Vincent meets up with Michael and Steve to discuss their finding of a transmissible tumor in soft-shell clams associated with a retrovirus-like element in the clam genome.

You can find TWiV #337 at www.twiv.tv.

On episode #336 of the science show This Week in Virology, the TWiVsters explore mutations in the interferon pathway associated with severe influenza in a child, outbreaks of avian influenza in North American poultry farms, Ebolavirus infection of the eye weeks after recovery, and Ebolavirus stability on surfaces and in fluids.

You can find TWiV #336 at www.twiv.tv.

Rb and E2fA major goal of viral oncotherapy – the use of viruses to destroy tumors –  is to design viruses that kill tumor cells but not normal cells. Two adenoviruses provide perfect examples of how this specificity can be achieved.

Adenovirus CG0070, designed to treat bladder cancer, and adenovirus Oncorine, for head and neck tumors, replicate only in tumor cells. The selectivity is caused by mutations introduced into the viral genomes.

When adenovirus infects a cell, the first event is synthesis of mRNA that encodes the E1 proteins. These proteins are needed to start cellular DNA synthesis. Most cells in our bodies are not dividing, an environment not conducive to viral replication. The adenovirus E1 proteins solve this problem. The E1A protein binds the cellular Rb (retinoblastoma) protein, which is normally bound to members of the E2f family of transcription factors (illustrated, upper left). Binding of E1A to Rb frees E2f which goes on to induce the transcription of cell genes needed for DNA synthesis and cell division.

The genome of CG0070 (illustrated below) has been modified so that the promoter for mRNA synthesis of the E1 proteins is replaced by the viral E2f promoter. This promoter requires E2f transcription factors for activity; hence the promoter does not function in non-dividing cells in which Rb is bound to E2f. However, many tumors lack Rb, and E2f is always available. CG0070 will replicate in such tumor cells.

GC0070 adenovirus

The genome of adenovirus Oncorine lacks the early region protein E1b-55K. The function of this viral protein is to bind the cellular protein p53, which would otherwise halt division and induce death of the infected cell. Binding to p53 leads to its degradation, allowing the virus to execute its 24 hour reproductive cycle. Adenovirus lacking the E1b-55K protein will not replicate in normal cells. However, the virus will replicate in p53 deficient tumors.

E1b-55k

Oncorine has been licensed in China for the treatment of head and neck tumors, while CG0070 is in phase III clinical studies for the treatment of bladder cancer. Both oncolytic adenoviruses were developed by using knowledge of fundamental aspects of viral replication, yet another illustration of how basic research can lead to clinical applications.

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Virology 2015It is the first week in May, which means that the spring semester has just ended at Columbia University, and my annual virology course is over.

Each year I teach an introductory undergraduate virology course that is organized around basic principles, including how virus particles are built, how they replicate, how they cause disease, and how to prevent infections. Some feel that it’s best to teach virology by virus: a lecture on influenza, herpesvirus, HIV, and on and on. But this approach is all wrong: you can’t learn virology by listening to lectures on a dozen different viruses. In the end all you will have is a list of facts but you won’t understand virology.

I record every one of my 26 introductory lectures as a videocast, and these are available on the course website, or on YouTube. If you have listened to my lectures before, you might be wondering what is new. I change about 10% of each lecture every year, updating the information and adding new figures. This year I’ve also added two new lectures, on on Ebolavirus and one on viral gene therapy.

Once you have taken my introductory course, then you will be ready for an advanced course on Viruses. A course in which we go into great detail on the replication, pathogenesis, and control of individual viruses. I am working on such a course and when it’s ready I’ll share it with everyone.

I want to be Earth’s virology professor, and this is my introductory virology course for the planet.

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On episode #335 of the science show This Week in Virology, the TWiVumvirate discusses a whole Ebolavirus vaccine that protects primates, the finding that Ebolavirus is not undergoing rapid evolution, and a proposal to increase the pool of life science researchers by cutting money and time from grants.

You can find TWiV #335 at www.twiv.tv.

rhinovirus receptorsRhinovirus is the most frequent cause of the common cold, and the virus itself is quite common: there are over 160 types, classified into 3 species. The cell receptor has just been identified for the rhinovirus C species, which can cause more severe illness than members of the A or B species: it is cadherin-related family member 3.

Because viruses are obligate intracellular parasites, the genome must enter a cell before new particles can be made. The first step in this process is binding of the virus particle to a receptor on the plasma membrane. Two different membrane proteins serve as receptors for members of rhinovirus A and B species: intracellular adhesion molecule 1, and low-density lipoprotein receptor (illustrated).

It has not been possible to propagate species C rhinoviruses in conventional cell cultures, which has hampered research on how the virus replicates. The lack of a cell culture system required a different approach to identifying a cell receptor for this virus. It was known that the virus replicates in primary organ or cell cultures derived from sinus tissue, but not in a variety of epithelial and transformed cell lines (e.g. HeLa cells). In silico comparison of gene expression profiles revealed 400 genes that are preferentially expressed in virus-susceptible cells. This list was narrowed down to 12 genes that encode plasma membrane proteins. A subset of these genes were introduced into cells and tested for the ability to serve as a rhinovirus C receptor. Introduction of the gene encoding cadherin-related family member 3 (CDHR3) into HeLa cells allowed rhinovirus C binding and infection.

The cadherin family comprises cell surface proteins that are involved in cell-cell communication. The exact cell function of CDHR3 is not known, but the protein is found in human lung, bronchial epithelium, and cultured airway epithelial cells. A mutation in the gene encoding this protein is associated with wheezing illness and asthma in children. This mutation, which causes a change from cysteine to tyrosine at amino acid 529, was found to increase virus binding and virus replication in HeLa cells that synthesize CDHR3. It will be important to determine if this amino acid change increases rhinovirus C replication in humans, thereby leading to more serious respiratory illness.

The CDHR3 gene was used to establish a stable HeLa cell line that produces the receptor and which can be infected with species C rhinoviruses. This cell line will be useful for illuminating the details of viral replication in cells, which has so far been elusive due to lack of a susceptible and permissive cell line. It may also be possible to produce transgenic mice with the human CDHR3 gene, which could serve as a model for studying rhinovirus C pathogenesis. Transgenic mice that produce the receptor for the related polioviruses, CD155, are a model for poliomyelitis.

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TWiV 334: In vino virus

26 April 2015

On episode #334 of the science show This Week in Virology, the TWiVles talk about endogenous viruses in plants, sex and Ebolavirus transmission, an outbreak of canine influenza in the US, Dr. Oz, and doubling the NIH budget.

You can find TWiV #334 at www.twiv.tv.

EmbryogenesisAbout eight percent of human DNA is viral: it consists of retroviral genomes produced by infections that occurred many years ago. These endogenous retroviruses are passed from parent to child in our DNA. Some of these viral genomes are activated for a brief time during human embryogenesis, suggesting that they may play a role in development.

There are over 500,000 endogenous retroviruses in the human genome, about 20 times more than human genes. They were acquired millions of years ago after retroviral infection. In this process, viral RNA is converted to DNA, which then integrates into cell DNA. If the retroviral infection takes place in the germ line, the integrated DNA may be passed on to offspring.

The most recent human retroviral infections leading to germ line integration took place with a subgroup of human endogenous retroviruses called HERVK(HML-2). The human genome contains ~90 copies of these viral genomes, which might have infected human ancestors as recently as 200,000 years ago. HERVs do not produce infectious virus: not only is the viral genome silenced – no mRNAs are produced – but they are littered with lethal mutations that have accumulated over time.

A recent study revealed that HERVK mRNAs are produced during normal human embryogenesis. Viral RNAs were detected beginning at the 8-cell stage, through epiblast cells in preimplantation embryos, until formation of embryonic stem cells (illustrated). At this point the production of HERVK mRNA ceases. Viral capsid protein was detected in blastocysts, and electron microscopy revealed the presence of virus-like particles similar to those found in reconstructed HERVK particles. These results indicate that retroviral proteins and particles are present during human development, up until implantation.

Retroviral particles in blastocysts are accompanied by induction of synthesis of an antiviral protein, IFITM1, that is known to block infection with a variety of viruses, including influenza virus. A HERVK protein known as Rec, produced in blastocysts, binds a variety of cell mRNAs and either increases or decreases their association with ribosomes.

Is there a function for HERVK expression during human embryogenesis? The authors speculate that modulation of the ribosome-binding activities of specific cell mRNAs by the viral Rec protein could influence aspects of early development. As Rec sequences are polymorphic in humans, the effects could even extend to individuals. In addition, HERVK induction of IFITM1 might conceivably protect embryos against infection with other viruses.

The maintenance of open reading frames in HERV genomes, over many years of evolution, suggests a functional role for these elements. Evidence for such function comes from the syncytin proteins, which  are essential for placental development: the genes encoding these proteins originated from HERV glycoproteins. However, not all endogenous retroviruses are beneficial: a number of malignant diseases have been associated with HERV-K expression.

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On episode #333 of the science show This Week in Virology, Vincent returns to Vanderbilt University and meets up with Ben, Megan, Bobak, and Meredith to learn about life in the Medical Scientist Training Program, where students earn both an MD and a Ph.D.

You can find TWiV #333 at www.twiv.tv.

QuasispeciesVirus populations do not consist of a single member with a defined nucleic acid sequence, but are dynamic distributions of nonidentical but related members called a quasispecies (illustrated at left). While next-generation sequencing methods have the capability of describing a quasispecies, the errors associated with this technology have limited progress in our understanding of the genetic structure of virus populations. A new method called CirSeq reduces next-generation sequencing errors to allow an accurate description of viral quasispecies.

The key to eliminating sequencing errors is a clever approach based on the conversion of viral RNAs to circular molecules. When copied with reverse transcriptase, tandemly repeated cDNAs are produced (illustrated below). Mutations in the original viral RNA will be shared by all repeats derived from a circle, but not errors produced during copying or sequencing. The latter can be computationally subtracted, reducing sequencing error to a point that is much lower than the estimated mutation rate of an RNA virus.CirSeq

CirSeq was used to characterize poliovirus populations produced by seven serial passages in HeLa cells. The calculated mutation frequency, 2 X 10-4 mutations per nucleotide, was substantially lower compared with estimates determined by conventional sequence analysis. Over 200,000 sequence reads per nucleotide position were used to detect >16,500 variants per population per passage. This number represents ~74% of all possible alleles. Many mutations were detected at nearly all positions in the viral RNA. Most mutations occur at a frequency between 1 in 1000 to 1 in 100,000. The conclusion is that the virus population produced in HeLa cells consists mainly of genomes with the consensus sequence, and small amounts of many variant genomes. These variants are only those that give rise to viable viruses; lethal mutations are not observed.

CirSeq was also used to calculate the mutation rate of poliovirus. The rates vary according to type: transitions occurred at a rate of 2.5 X 10-5 to 2.6 X 10-4 substitutions per site, while transversions were observed at a rate of 1.2 X 10-6 to 1.5 X 10-5 substitutions per site. Nucleotide-specific differences in mutation rate were also observed: C to U and G to A transitions were 10 times more frequent than U to C and A to G. These rates are consistent with previously determined values using other methods.

This method can also be used to determine the fitness of each base at every position in the genome, according to changes observed during the seven passages in HeLa cells. This analysis allows determination of which bases are neutral, and which are selected, and when combined with analysis of protein structure, can provide new insights into viral functions.

By enabling a sequencing approach that gives an accurate description of virus populations at a single-nucleotide level, CirSeq can be used to provide an unprecedented view of how virus populations change during evolution.

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