Structure of Zika virus

Zika virus reconstructionSix months after Zika virus became a household word, we now know the three-dimensional structure of the virus particle. And it looks like very much like other flaviviruses, such as West Nile and dengue viruses.

In the old days, solving a virus structure was a big deal. A virus is, after all, a very large assembly of many proteins. To solve the structure of a virus – which will tell us the location of the amino acid chains in three dimensional space – was a technical tour de force. It was necessary to purify large amounts of virus particles, and then find the conditions to produce crystals, a hit and miss affair. If you were lucky to grow virus crystals – which could take a year or more – you then crossed your fingers to see if they diffracted in an X-ray beam. When X-rays are aimed at a crystal, the beams bounce off atoms in the crystals, and their reflections provide information on where the atoms are located. Finally you could collect the diffraction data, do a lot of math on a computer, and determine the three dimensional structure.

The first virus structure to be solved by X-ray crystallography was of a plant virus, tomato bushy stunt virus in 1976, followed by poliovirus and rhinovirus in 1985. Many X-ray structures of viruses have been solved, with resolutions less than 2 Angstroms that allow us to see not only the amino acid chain, but all the atoms in the side chains.

The Zika virus structure was not solved by X-ray crystallography. It was done by cryo-electron microscopy (cryo-EM) and image reconstruction. It’s easier and faster than X-ray crystallography, and can achieve comparable resolutions.

It is not necessary to produce crystals to determine structures by cryo-EM. Instead, samples of purified viruses are rapidly frozen and photographed with an electron microscope at very low temperatures. This procedure preserves native structure, and allows visualization of the contrast inherent in the virus particle. Photographs of thousands of virus particles – each in a slightly different orientation – are taken and processing computationally to create the final three-dimensional image.

The cryo-EM structure of Zika virus tells us how the virus particle is put together. It looks very much like other flaviviruses, which consist of a membrane surrounding the capsid, which in turn carries the viral RNA genome. Inserted into the membrane are 180 copies of the viral proteins E and M. Although inserted in a fluid lipid bilayer, they are arranged with a symmetry that reflects their contacts with the underlying icosahedral capsid. In the illustration, which I produced from the freely available cryo-EM data, you can clearly see five copies of the E glycoprotein (red) at one five-fold axis of symmetry.

One structural difference between Zika virus and other flaviviruses is a loop of amino acids exposed on the surface of the particle. This sequence of the E glycoprotein, and a sugar molecule attached to it, might be involved in regulating Zika virus tropism and pathogenesis. The ability of West Nile virus to enter the central nervous system of mice has been linked to glycosylation at a similar position, while cell receptors are thought to attach to sugars on the dengue virus capsid.

The authors of the Zika virus cryp-EM structure have produced an animation which illustrates aspects of the structure (below). Watch my lecture on virus structure for more information how viruses are put together.

Updated 7 April 2016 to provide an explanation of how the sugar attached to the E glycoprotein of Zika virus might regulate tropism and pathogenesis.

TWiV 383: A zillion Zika papers and a Brazilian

TWiVEsper Kallas and the Merry TWiXters analyze the latest data on Zika virus and microcephaly in Brazil, and discuss publications on a mouse model for disease, infection of a fetus, mosquito vector competence, and the cryo-EM structure of the virus particle. All on episode #383 of the science show This Week in Virology.

Audio and full show notes for TWiV #383 at microbe.tv/twiv or listen below.

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A minimal cell operating system

Syn3.0If the DNA sequence of a cell is like the operating system of a computer, then the smallest cellular OS has just been written. Called Syn3.0, it encodes everything needed to make a viable, autonomously replicating cell.

Mycoplasma is a genus of bacteria that are the smallest known free-living organisms. They also have the smallest genomes of any autonomously replicating cell: the DNA of Mycoplasma genitalium is just over one million base pairs in length and encodes 525 genes.

The entire 1,078,809 bp genome of Mycoplasma mycoses was synthesized in 2010 and transplanted into cells of another species, where it replaced the resident genome. In another nod to computer science, the authors refer to ‘installing’ the new genome into a cell, much like a new OS is installed on a hard drive.

This genome engineering tour de force was then followed by the synthesis of a reduced Mycoplasma genome. By combing the literature and carrying out extensive mutagenesis, genes were identified that were nonessential for growth in a rich culture medium. From the design of the new genome, to its installation into a new cell, took only 3 weeks.

The result, Syn3.0, has 438 protein coding genes and 35 RNA genes. Its 531,000 base genome is the smallest of any autonomously replicating cell found in nature. The doubling time of the cell is 180 minutes (compared with 16 hours for M. genitalium). The cells are smaller than the parent organism and are polymorphic in apperance (illustrated; image credit).

What is encoded by this minimal cellular OS?

Most of the genes (41%) are involved in expression of the genome: transcription, regulation, RNA metabolism, translation, protein folding, RNA, ribosome biogenesis, rRNA modification, and tRNA modification.

Seven percent of the synthetic genome is involved in preservation of genome information: DNA replication, DNA repair, DNA toplogy, DNA metabolism, chromosome segregation, and cell division.

Genes involved in cell membrane synthesis constitute 18% of the genome, and genes involved in cytosol metabolism, 17%.

Perhaps the greatest surprise is that 17% of the Syn3.0 genes have no known functions. Some of these genes are also present in other organisms and must have important roles. Their study should be stimulated by the creation of Syn3.0.

I would be very excited to see this technology applied to the study of viral genomes. For most small viral genomes it has already been determined that all of the genes are needed for replication in cell culture. For example, the genome of poliovirus, a 7,500 nucleotide RNA molecule, encodes about a dozen proteins. None of these protein coding sequences can be removed without destroying the ability of the virus to replicate.

However, viruses with larger genomes carry some genes that are dispensable for replication in cell culture. For example, the DNA genomes of adenoviruses, herpesviruses, and poxviruses encode proteins that can be deleted without affecting replication in cell culture. Many of these genes encode antagonists of the immune response, and have a role only during infection of an animal with an immune system.

Undoubtedly the most interesting application of the technology used to produce Syn3.0 would come from analysis of the genomes of giant viruses such as Mimivirus, Pandoravirus, and Pithovirus. The genomes of these viruses range from 600,000  to over 2.4 million base pairs in length. They encode mostly proteins of unknown function, as well as molecules not seen in other viruses, such as components of the protein synthesis apparatus. I hope that we will soon see the synthesis of reduced genomes of these giant viruses to identify the minimal gene set needed for production of infectious viruses in a host cell.

Put another way, what is the smallest operating system needed to run a giant virus?

TWiV 382: Everyone’s a little bit viral

TWiVOn episode #382 of the science show This Week in Virology, Nels Elde and Ed Chuong join the TWiV team to talk about their observation that regulation of the human interferon response depends on regulatory sequences that were co-opted millions of years ago from endogenous retroviruses.

You can find TWiV #382 at microbe.tv/twiv, or listen below.

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Top secret, viruses with RNA genomes!

Top secret!Today it is well known that viruses may contain DNA (poxvirus, mimivirus) or RNA (influenza virus, Zika virus), but for many years it was thought that genomes were only made of DNA. The surprise at finding only RNA in a virus is plainly evident in a 1953 letter from Harriett Ephrussi-Taylor to James D. Watson (pictured, Cold Spring Harbor Archives Repository*).

While DNA was discovered in the late 1800s, its role as genetic material was not proven until the famous experiments of McLeod, Avery, and McCarty, published in 1944. They showed that DNA from a strain of Pnemococcus bacteria that formed smooth colonies, when added to a rough colony former, produced smooth colonies.

By this time many viruses had been identified, and it was assumed that their genetic information was DNA. The ‘kitchen blender’ experiments of Hershey and Chase in 1952 proved that the genetic information of bacteriophage T2 is DNA. Watson and Crick proposed the double-helical structure of DNA in 1953, and a few years later published the Central Dogma, which suggested that information flowed in biological systems from DNA to RNA to protein.

Amidst all these experimental findings, which gave rise to the field of molecular biology,  comes the note in 1953 from Ephrussi-Taylor to Watson. Under the heading TOP SECRET she writes:

Burnet swears, from work in his lab, that flu virus has principally, if not exclusively RNA. Suspects the same for polioviruses. ??

During her career, Dr. Ephrussi-Taylor carried out work on bacterial transformation by DNA and was knowledgeable about its history as genetic material. Frank Macfarlane Burnet was an Australian immunologist who worked on influenza virus early in his career.

By the 1950s many viruses had been isolated which we now know have genomes of DNA (bacteriophage, poxvirus) or RNA (yellow fever virus, poliovirus, influenza virus). But it was the first virus discovered – tobacco mosaic virus, in the 1890s – that lead the way to establishing RNA as genetic material. Wendell Stanley produced crystals of TMV in 1935 and found that they contained 5% RNA. But Stanley and others thought TMV was a protein, and that the RNA was either a contaminant, or played a structural role.

A structural role for RNA was reinforced as late as 1955 when Heinz Fraenkel-Conrat separately purified TMV protein and RNA. When he mixed the two components together, they formed infectious, 300 nm rods. When the RNA was omitted, noninfectious aggregates formed. This finding reinforced the belief that RNA helped form virus particles.

TMVThis view changed when Fraenke-Conrat gave his wife, Beatrice Singer, the task of purifying TMV RNA until it had lost all infectivity. To everyone’s surprise she found that TMV RNA itself was infectious, proving in 1957 that it was the viral genetic material. However, RNA also has a structural role in TMV virus particles, as it organizes the capsid protein (yellow in illustration at left) into regularly repeated subunits.

Demonstration of infectivity of RNA from animal viruses soon followed, for mengovirus, a picornavirus, in 1957 and for poliovirus in 1958 (the latter done at my own institution, the College of Physicians and Surgeons of Columbia University!).

By the early 1950s the idea that RNA could be viral genetic material was clearly in the minds of virologists, hence Ephrussi-Taylor’s amusing letter on influenza virus and poliovirus.

*Thanks to @infectiousdose for finding this amazing letter.

TWiV 381: Add viruses and Zimmer

TWiVOn episode #381 of the science show This Week in Virology, Carl Zimmer joins the TWiV team to talk about his career in science writing, the real meaning of copy-paste, science publishing, the value of Twitter, preprint servers, his thoughts on science outreach, and much more.

You can find TWiV #381 at microbe.tv/twiv, or listen below.

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Understanding viruses

Virology lecturesIf you want to understand life on Earth, you need to know about viruses.

We have reached the halfway point in my 2016 Columbia University undergraduate virology course. So far we have learned the basics of virus replication: how viruses enter cells, how the genome is reproduced, and how proteins are made and assembled into new virus particles. In the second half of the course, we will consider how viruses cause disease, how immune responses prevent infection, vaccines, antivirals, emergence of new viruses, and much more.

All of my lectures are recorded as videos and available freely on YouTube. Below is a list of the first thirteen lectures, with links to the YouTube videos. You can also subscribe to the videos at iTunes University. If you would like copies of the lecture slides and study questions, go to virology.ws/course.

Lecture 1: What is a virus?
Lecture 2: The infectious cycle
Lecture 3: Genomes and genetics
Lecture 4: Structure
Lecture 5: Attachment and entry
Lecture 6: RNA directed RNA synthesis
Lecture 7: Transcription and RNA processing
Lecture 8: DNA replication
Lecture 9: Reverse transcription and integration
Lecture 10: Translation
Lecture 11: Assembly
Lecture 12: Infection basics
Lecture 13: Intrinsic and innate defenses

 

Moving beyond metagenomics to find the next pandemic virus

I was asked to write a commentary for the Proceedings of the National Academy of Sciences to accompany an article entitled SARS-like WIV1-CoV poised for human emergence. I’d like to explain why I wrote it and why I spent the last five paragraphs railing against regulating gain-of-function experiments.

Towards the end of 2014 the US government announced a pause of gain-of-function research involving research on influenza virus, SARS virus, and MERS virus that “may be reasonably anticipated to confer attributes to influenza, MERS, or SARS viruses such that the virus would have enhanced pathogenicity and/or transmissibility in mammals via the respiratory route.”

From the start I have opposed the gain-of-function pause. It’s a bad idea fostered by individuals who continue to believe, among other things, that influenza H5N1 virus adapted to transmit by aerosol among ferrets can also infect humans by the same route. Instead of stopping important research, a debate on the merits and risks of gain-of-function experiments should have been conducted while experiments were allowed to proceed.

Towards the end of last year a paper was published a paper on the potential of SARS-virus-like bat coronaviruses to cause human disease. The paper reawakened the debate on the risks and benefits of engineering viruses. Opponents of gain-of-function research began to make incorrect statements about this work. Richard Ebright said that ‘The only impact of this work is the creation, in a lab, of a new, non-natural risk”. Simon Wain-Hobson wrote that a novel virus was created that “grows remarkably well” in human cells; “if the virus escaped, nobody could predict the trajectory”. I have written extensively about why these are other similar statements ignore the value of the work. In my opinion these critics either did not read the paper, or if they did, did not understand it.

Several months later I was asked to write the commentary on a second paper examining the potential of SARS like viruses in bats to cause human disease. I agreed to write it because the science is excellent, the conclusions are important, and it would provide me with another venue for criticizing the gain-of-function pause.

In the PNAS paper, Menachery et al. describe a platform comprising metagenomics data, synthetic virology, transgenic mouse models, and monoclonal antibody therapy to assess the ability of SARS-CoV–like viruses to infect human cells and cause disease in mouse models. The results indicate that a bat SARS-like virus, WIV1-CoV, can infect human cells but is attenuated in mice. Additional changes in the WIV1-CoV genome are likely required to increase the pathogenesis of the virus for mice. The same experimental approaches could be used to examine the potential to infect humans of other animal viruses identified by metagenomics surveys. Unfortunately my commentary is behind a paywall, so for those who cannot read it, I’d like to quote from my final paragraphs on the gain-of-function issue:

The current government pause on these gain-of-function experiments was brought about in part by several vocal critics who feel that the risks of this work outweigh potential benefits. On multiple occasions these individuals have indicated that some of the SARS-CoV work discussed in the Menachery et al. article is of no merit. … These findings provide clear experimental paths for developing monoclonal antibodies and vaccines that could be used should another CoV begin to infect humans. The critics of gain-of-function experiments frequently cite apocalyptic scenarios involving the release of altered viruses and subsequent catastrophic effects on humans. Such statements represent personal opinions that are simply meant to scare the public and push us toward unneeded regulation. Virologists have been manipulating viruses for years—this author was the first to produce, 35 y ago, an infectious DNA clone of an animal virus—and no altered virus has gone on to cause an epidemic in humans. Although there have been recent lapses in high-containment biological facilities, none have resulted in harm, and work has gone on for years in many other facilities without incident. I understand that none of these arguments tell us what will happen in the future, but these are the data that we have to calculate risk, and it appears to be very low. As shown by Menacherry et al. in PNAS, the benefits are considerable.

A major goal of life science research is to improve human health, and prohibiting experiments because they may have some risk is contrary to this goal. Being overly cautious is not without its own risks, as we may not develop the advances needed to not only identify future pandemic viruses and develop methods to prevent and control disease, but to develop a basic understand- ing of pathogenesis that guides prevention. These are just some of the beneficial outcomes that we can predict. There are many examples of how science has progressed in areas that were never anticipated, the so-called serendipity of science. Examples abound, including the discovery of restriction enzymes that helped fuel the biotechnology revolution, and the development of the powerful CRISPR/Cas9 gene-editing technology from its obscure origins as a bacterial defense system.

Banning certain types of potentially risky experiments is short sighted and impedes the potential of science to improve human health. Rather than banning experiments, such as those described by Menachery et al., measures should be put in place to allow their safe conduct. In this way science’s full benefits for society can be realized, unfettered by artificial boundaries.

TWiV 380: Viruses visible in le microscope photonique

TWiVOn episode #380 of the science show This Week in Virology, the TWiVeroos deliver the weekly Zika Report, then talk about a cryoEM structure of a plant virus that reveals how the RNA genome is packaged in the capsid, and MIMIVIRE, a CRISPR-like defense system in giant eukaryotic viruses.

You can find TWiV at microbe.tv/twiv, or you can listen below.

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Zika virus infection of the nervous system

FlavivirusEvidence is mounting that Zika virus is neurotropic (able to infect cells of the nervous system) and neurovirulent (causes disease of the nervous system) in humans.

The most recent evidence comes from a case report of an 81 year old French man who developed meninogoencephalitis 10 days after returning from a 4 week cruise to New Caledonia, Vanuatu, Solomon Islands, and New Zealand (meningoencephalitis is infection of the meninges – the membranes that cover the brain – and the brain). His symptoms included fever, coma, paralysis, and a transient rash. A PCR test revealed Zika virus genomes in the cerebrospinal fluid, and infectious virus was recovered after applying the CSF to Vero cells in culture.

A second case report concerns a 15 year old girl in Guadeloupe who developed left hemiparesis (weakness of one side of the body), left arm pain, frontal headache, and acute lower back pain. After admission she developed dysuria (difficulty urinating) that required catheterization. PCR revealed the presence of Zika virus genomes in her serum, urine, and cerebrospinal fluid; other bacterial and viral infections were ruled out.

Until very recently Zika virus was believed to cause a benign infection comprising rash, fever, joint pain, red eyes, and headache. There is now strong evidence that the virus can cause congential birth defects, and growing evidence that the virus is neurotropic and neurovirulent. Previously the entire Zika virus genome was recovered from brain tissue of an aborted fetus.

Zika virus is classified in the family Flaviviridae, and other members are known to be neurotropic, including West Nile virus, Japanese encephalitis virus, and tick-borne encephalitis virus. West Nile virus infection may lead to acute flaccid paralysis, meningitis, encephalitis, and ocular manifestations. Examination of additional cases of Zika virus infection will be needed to document the full spectrum of illness caused by this virus.

Update: Neurotropism of Zika virus is also indicated by the findings that the virus infects human cortical neural progenitors.