Your viral past

4 June 2015

virusesDid you ever wonder what different virus infections you have had in your lifetime? Now you can find out with just a drop of your blood and about $25.

Immune defense systems of many hosts produce antibodies in response to virus infections. These large proteins, which are generally virus specific, can block or inhibit virus infection, and persist at low levels for many years after the initial infection. Hence it is possible to determine whether an individual has had a virus infection by looking for anti-viral antibodies in the blood. Up to now the process of identifying such antibodies has been slow and limited to one or a few viruses. A new assay called VirScan allows unbiased searches for all the virus antibodies in your blood, providing a picture of all your past infections.

To identify the human antivirome, DNAs were synthesized encoding proteins from all viruses known to infect humans – 206 species and over 1000 strains. These DNAs were inserted into the genome of a bacteriophage, so that upon infecting bacteria, the viral peptides are displayed on the phage capsid. These ‘display’ phages were then mixed with human serum, and those that were bound by antibodies were isolated. The DNA sequence of the phage genomes were then determined to identify the human virus bound by the antibodies.

This method was used to assay samples from 569 humans. The results show that each person had been exposed to an average of 10 viruses, with a range from a few to over 20 (two individuals had antibodies to 84 different virus species!). The most frequently identified viruses included herpesviruses, rhinoviruses, adenoviruses, influenza viruses, respiratory syncytial virus, and enteroviruses. The overall winner, found in 88% of samples, is Epstein-Barr virus.

These results are not unexpected: all of us are infected with at least a dozen viruses at any time, and the viruses identified in this study known to infect much of the human population. What was surprising is the absence of some common viruses, such as rotaviruses, and the ubiquitous polyomaviruses. According to serological surveys, the most common human viruses are the small, single-stranded DNA containing anelloviruses. Yet the related torque teno virus was only found in 1.7% of samples. These differences are likely due to a combination of technical and biological issues (e.g., failure of antibodies to certain viruses to persist in serum).

This new assay may one day become a routine diagnostic tool that is used along with complete blood counts and chemistries to know if a patient’s signs and symptoms might be attributable to a past virus infection. VirScan technology is not limited to virus infections – it can be used to provide a history of bouts with bacteria, fungi, and parasites.

VirScan might also allow us to determine which virus infections are beneficial, and which contribute to chronic diseases such as autoimmune or neurodevelopmental disorders or cancer. The assay can be used to conduct unbiased population-based studies of the prevalence of virus infections and their possible association with these diseases. Such connections were not previously possible with antibody assays that search for one virus at a time. This approach was not only inefficient, but required guessing the responsible virus.

Some other findings of this study are noteworthy. As expected, children had fewer virus infections than adults. HIV-positive individuals had antibodies to more viruses than HIV-negative individuals, also expected given the damage done by this virus to the immune system. Frequencies of anti-viral antibodies were higher outside of the United States, possible due to differences in genetics, sanitation, or population density. In most samples, there was a single dominant peptide per virus, although there were occasional differences among populations. This information might be useful for improving vaccines, or tailoring them to specific countries or regions.

Update: It would be very informative to use VirScan to search for antibodies against viruses that are not known to infect humans. Other animal viruses, plant viruses, insect viruses: to which do a significant fraction of humans respond? The information might identify other viruses that replicate in humans and which might constitute future threats (or present benefits).


On episode #339 of the science show This Week in Virology, tre TWiV amici present three snippets and a side of sashimi: how herpesvirus inhibits host cell gene expression by disrupting transcription termination.

You can find TWiV #339 at

RudivirusMany microbes live in extreme environments, encountering conditions that are very hot, very cold, highly acidic, or very salty. The viruses that infect such microbes must also be able to retain infectivity in extreme conditions. How do they do it?

Clues come from the observations that the genomes of viruses that infect Archaea in extreme geothermal environments encode proteins that have never been seen before. The idea is that such unusual proteins must endow these viruses with the ability to maintain infectivity under extreme conditions.

The hosts of Rudiviruses (rudi=small rod in Latin), the Archea Sulfobolus islandicus, live at high temperatures (80° C) and low pH (3.0). These non-enveloped viruses consist of double-stranded DNA wrapped in a helical manner with thousands of copies of a 134 amino acid protein (illustrated; image credit). The three-dimensional structure of Sulfobolus islandicus rod-shaped virus 2 (SIRV2) reveals a new type of organization of virus particles, and provides clues about how it retains infectivity in extreme environments.

Resolution of the SIRV2 structure reveals that it consists of dimers of a single protein which forms helices that are tightly wrapped around the DNA genome. The result is a coiled DNA protected by a coat of protein that stabilizes and protects the genome. Without DNA, over half of the capsid protein is unstructured. Only in the presence of DNA does the viral protein form an alpha helix that wraps around the nucleic acid.

The DNA genome of SIRV2 is in the A-form, in contrast to B-form DNA which is found in most other organisms. The two types of DNA differ in their geometry and dimensions. It was previously thought that A-DNA occurs only when the nucleic acid is dehydrated.

These two usual properties of SIRV2 are also found in gram positive bacteria which form desiccation and heat resistant spores when starved of nutrients. Sporulation is accompanied by a change in the bacterial genome from B-DNA to A-DNA, which is caused by the binding of small acid-soluble proteins. Like the SIRV2 capsid protein, small acid-soluble proteins of spore-forming bacteria are unstructured in solution, and become alpha helices when bound to DNA. These observations suggest that binding of the SIRV2 capsid protein changes the viral DNA to the A-form, conferring stability in extreme environments.


mosquito brainAs far as I know, mosquitoes do not eat sushi. But mosquito cells have proteins with sushi repeat domains, and these proteins protect the brain from lethal virus infections.

Mosquitoes are vectors for the transmission of many human viral diseases, including yellow fever, West Nile disease, Japanese encephalitis, and dengue hemorrhagic fever. Many mosquito-borne viruses enter the human central nervous system and cause neurological disease. In contrast, these viruses replicate in many tissues of the mosquito, including the central nervous system, with little pathological effect and no alteration of behavior or lifespan. The defenses that allow such persistent infection of mosquitoes are slowly being unraveled.

A protein called Hikaru genki, or Hig, is crucial for controlling viral infections of the mosquito brain. Originally discovered in the fruit fly Drosophila, Hig is produced mainly in the brain of Aedes aegyptii, the natural vector for dengue and yellow fever viruses. Experimental reduction of Hig mRNA or protein in the mosquito leads to increased replication of dengue virus and Japanese encephalitis virus. This increase in viral replication is accompanied by more cell death in the mosquito brain, and decreased survival.

How does Hig protein impair virus replication? The Hig protein of A. aegyptii binds dengue virus particles via the E membrane glycoprotein. As Hig protein is located on the cell surface, binding to virus particles prevents virus entry into cells. Impairment of endocytosis is limited to insect cells – introduction of Hig into mammalian cells had no effect on virus replication. Clearly other components of insect cells must participate in the Hig-mediated antiviral mechanism.

The antiviral activity of Hig protein depends on the presence of sushi repeat domains, also known as complement control protein (CCP) domains. These consist of 60 amino acid repeats with four conserved cysteines and a tryptophan. The CCP domain is found in many proteins of the complement system, a collection of blood and cell surface proteins that is a major primary defense and a clearance component of innate and adaptive immune responses. The sushi domain mediates protein-protein interactions among complement components. Capturing the dengue and Japanese encephalitis viruses by the A. aegyptii Hig protein is just one example of the virus-binding ability of proteins with CCP domains. An insect scavenger receptor with two CCP domains is a pattern recognition receptor that recognizes dengue virus and recruits mosquito complement to limit viral replication. Some CCP containing proteins are virus receptors (complement receptor 2 binds Epstein-Barr virus, and membrane cofactor protein is a receptor tor measles virus).

Because the Hig antiviral machinery is largely limited to the mosquito brain, it is possible that it prolongs mosquito life to allow virus transmission to other hosts. Transmission of virus to other hosts requires replication in the salivary gland, which cannot take if the mosquito dies of neural infection. I wonder why humans do not have have similar mechanisms to protect their neural tissues from virus infections. Is neuroinvasion a less frequent event in humans, compared with mosquitoes, thereby providing less selective pressure for protective mechanisms to evolve?


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

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

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.


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.


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.


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

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.