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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A promising Ebolavirus antiviral compound

ATP EBOV antiviralA small molecule antiviral compound has been shown to protect rhesus monkeys against lethal Ebolavirus disease, even when given up to three days after virus inoculation.

The compound, called GS-5734, is a nucleoside analog. After uptake into cells, GS-5734 is converted to a nucleoside triphosphate (illustrated, bottom panel) which is incorporated by the viral RNA dependent RNA polymerase as it copies the viral genome. However, the nucleoside is chemically different from ATP (illustrated, top) and no further nucleotides can be incorporated into the growing RNA strand. RNA synthesis ceases, blocking production of infectious virus particles.

In cell culture GS-5734 inhibits viral replication at micromolar concentrations, in a variety of human cell types including monocyte-derived macrophages, primary macrophages, endothelial cells, and a liver cell line. The drug inhibits replication of several strains of Zaire ebolavirus, including Kikwit and Makona (from the West African outbreak); Bundibugyo ebolavirus, and Sudan ebolavirus. It also inhibits replication of another filovirus, Marburg virus, as well as viruses of different families, including respiratory syncytial virus, Junin virus, Lassa fever virus, and MERS-coronavirus, but not chikungunya virus, Venezuelan equine encephalitis virus, or HIV-1.

The RNA dependent RNA polymerase of Ebolaviruses has not yet been produced in active form, so the authors determined whether GS-5734 inhibits a related polymerase from respiratory syncytial virus. As predicted, the compound was incorporated into growing RNA chains by the enzyme, and caused premature termination.

Typically tests of antiviral candidates begin in a small animal, and if the results are promising, proceed to nonhuman primates. While a mouse model of Ebolavirus infection is available, the serum from these animals degrades GS-5374. Consequently a rhesus monkey model of infection was used to test the compound.

After intravenous administration of GS-5374, the NTP derived from it was detected in peripheral blood mononuclear cells, testes, epididymis, eyes, and brain within 4 hours. All 12 monkeys inoculated intramuscularly with Zaire ebolavirus died by 9 days post-infection. In contrast, all animals survived after administration of GS-5374 2 or 3 days after virus inoculation. These animals also had reduced virus associated pathology as measured by liver enzymes in the blood and blod clotting. Viral RNA in serum reaches 109 copies per milliliter on days 5 and 7 in untreated animals, and was undetectable in 4 of 6 treated animals.

It is likely that resistant viruses can be obtained by passage in the presence of GS-5734; whether such mutant viruses emerge early in infection, and at high frequency, is an important question that will impact clinical efficacy of the drug. The authors did not detect changes in the viral RNA polymerase gene that might be assoicated with resistance, but further work is needed to address how readily such mutants arise.

These promising results have lead to the initiation of a phase I clinical trial to determine whether GS-5734 is safe to administer to humans, and if the drug reaches sites where Ebolaviruses are known to replicate. However, determining the efficacy of the compound requires treatment of acutely Ebolavirus infected humans, of which there are none. It might be of interest to determine the ability of GS-5734 to clear persistent virus from previously infected individuals.

You can bet that GS-5734 has already been tested for activity against Zika virus.

TWiEVO 5: Looking at straw colored fruit bats through a straw

TWiEVOOn episode #5 of the science show This Week in Evolution, Sara Sawyer and Kartik Chandran join Nels and Vincent to talk about how the filovirus receptor NPC1 regulates Ebolavirus susceptibility in bats.

You can find TWiEVO #5 at microbe.tv/twievo, or you can listen below.

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Zika from sex, the byway but not the highway

FlavivirusCan Zika virus be sexually transmitted? Perhaps in very rare cases, but the main mode of transmission is certainly via mosquitoes. That’s why I’ve shamelessly stolen a quote on this topic from Dr. William Schaffner of Vanderbilt University:

Mosquito transmission is the highway, whereas sexual transmission is the byway. Sexual transmission cannot account for this sudden and widespread transmission of this virus.

If you just read the news headlines, which many people do, you will think that Zika virus spreads like HIV. But it does not.

Let’s make a clear distinction between sexually transmitted viruses (like HIV – sex is the main mode of transmission, along with contaminated blood), versus sexually transmissible viruses. The latter includes viruses that now and then might be sexually transmitted under certain circumstances, but which normally are transmitted by another route. Zika virus is transmitted among humans by mosquitoes. If sexual transmission occurs, it is very, very rare, given the large number of Zika virus infections that have been documented.

Is Zika virus sexually transmissible?

The first hint of sexual transmission of Zika virus came from the story of two American scientists working in Senegal in 2008, where they were sampling mosquitoes. Between 6-9 days after returning to their homes in Colorado, they developed a variety of symptoms of infection including fatigue, headache, chills, arthralgia, and a maculopapular rash. The wife of one patient had not traveled to Africa, yet she developed similar symptoms three days after her husband. Analysis of paired acute and convalescent sera from all three patients revealed antibodies against Zika virus. The authors of the study do not conclude that transmission from husband to wife was via sexual activity – they suggest it as a possiblity. Their data could not prove sexual transmission.

More recently infectious Zika virus was detected in semen of a French Polynesian male who had recovered from infection. The presence of virus in semen is compatible with sexual transmission, but the patient was not known to have transmitted infection to anyone.

The CDC has concluded that Zika virus was transmitted to an individual in Texas who had sex with a traveler returning from Venezuela. As of this writing I do not know exactly how the CDC came to this conclusion.

What would be needed to prove that Zika virus is sexually transmissible?

Polymerase chain reaction (PCR) is used to diagnose many viral diseases. This assay detects small fragments of viral nucleic acid and can be very specific. However as we are trying to establish for the first time that Zika virus can be transmitted sexually, more than PCR must be done – infectious virus should be recovered from the donor and recipient. A positive PCR result does not mean that infectious virus is present in the sample, only fragments of the genome, which of course would not be infectious. It is important to correlate the presence of infectious virus with sexual transmission.

Not only should infectious virus be recovered from both donor and recipient, but the viral genome sequences should be nearly identical, providing strong evidence for sexual transmission. If the viral genome sequences were substantially different, this result could imply that the infection was acquired from someone else.

Looking for anti-viral antibodies in serum is a good way to confirm virus infection when virus is no longer present. However it is not as specific as PCR or virus isolation, and does not provide information about the genome of the donor and recipient virus.

Sexual transmission of Ebolavirus still remains speculative. There are several suspected cases, and many examples of PCR positive semen samples from men who have recovered from the disease. It’s not easy to prove that a virus can be transmitted sexually, especially when it is a rare event.

Just as we are not sure that Zika virus causes microencephaly, we are not sure if it can be sexually transmitted.

TWiV 370: Ten out of 15

On episode #370 of the science show This Week in Virology, the TWiVomics review ten captivating virology stories from 2015.

You can find TWiV #370 at www.microbe.tv/twiv.

TWiV 361: Zombie viruses on the loose

On episode #361 of the science show This Week in Virology, the TWiVsters discuss Frederick Novy’s return from retirement to recover a lost rat virus, and evidence for persistence of Ebolavirus in semen.

You can find TWiV #361 at www.microbe.tv/twiv.

Lassa virus origin and evolution

arenavirusI have a soft spot in my heart for Lassa virus: a non-fictional account of its discovery in Africa in 1969 inspired me to become a virologist. Hence papers on this virus always catch my attention, such as one describing its origin and evolution.

Lassa virus, a member of the Arenavirus family, is very different from Ebolavirus (a filovirus), but both are zoonotic pathogens that may cause hemorrhagic fever. It is responsible for tens of thousands of hospitalizations, and thousands of deaths each year, mainly in Sierra Leone, Guinea, Liberia, and Nigeria. Most human Lassa virus outbreaks are caused by multiple exposures to urine or feces from the multimammate mouse, Mastomys natalensis, which is the reservoir of the virus in nature. In contrast, outbreaks of Ebolavirus infection typically originate with a crossover from an animal reservoir, followed by human to human transmission. Despite being studied for nearly 50 years, until recently the nucleotide sequences of only 12 Lassa virus genomes had been determined.

To remedy this lack of Lassa virus genome information, the authors collected clinical samples from patients in Sierra Leone and Nigeria between 2008 and 2013. From these and other sources they determined the sequences of 183 Lassa virus genomes from humans, 11 viral genomes from M. natalensis, and two viral genomes from laboratory stocks. All the data are publicly available at NCBI. Analysis of the data lead to the following conclusions:

  • Lassa virus forms four clades, three in Nigeria and one in Sierra Leona/Liberia (members of a clade evolved from a common ancestor).
  • Most Lassa virus infections are a consequence of multiple, independent transmissions from the rodent reservoir.
  • Modern-day Lassa virus  strains probably originated at least 1,000 years ago in Nigeria, then spread to Sierra Leone as recently as 150 years ago. The lineage is most likely much older, but how much cannot be calculated from the data.
  • The genetic diversity of Lassa virus in individual hosts is an order of magnitude greater than the diversity of Ebolavirus. Furthermore, Lassa virus diversity in the rodent host is greater than in humans, likely a consequence of the longer, persistent infections that take place in the mouse.
  • The gene encoding the Lassa virus glycoprotein is subject to high selection in hosts, leading to variants that interfere with antibody binding.
  • Genetic variants that arise in one rodent are not transmitted to another.

Perhaps the most important result from this work is the establishment of laboratories in Sierra Leone and Nigeria that can safely collect and process samples from patients infected with Lassa virus, a BSL-4 pathogen.

TWiV 349: One ring to vaccinate them all

On episode #349 of the science show This Week in Virology, Vincent, Alan and Rich explain how to make a functional ribosome with tethered subunits, and review the results of a phase III VSV-vectored Ebolavirus vaccine trial in Guinea.

You can find TWiV #349 at www.microbe.tv/twiv.

An Ebolavirus vaccine in Africa

filovirionAn Ebolavirus vaccine has shown promising results in a clinical trial in Guinea. This vaccine has been in development since 2004 and was made possible by advances in basic virology of the past 40 years.

The ability to produce the Ebolavirus vaccine, called rVSV-EBOV, originates in the 1970s with the discovery of the enzyme reverse transcriptase, the development of recombinant DNA technology, and the ability to rapidly and accurately determine the sequence of nucleic acids. These advances came together in 1981 when it was shown that cloned DNA copies of RNA viral genomes (a bacteriophage, a retrovirus, and poliovirus), carried in a bacterial plasmid, were infectious when introduced into mammalian cells. Production of an infectious DNA copy of the genome of vesicular stomatitis virus (VSV) was reported in 1995. In their paper the authors noted:

Because VSV can be grown to very high titers and in large quantities with relative ease, it may be possible to genetically engineer recombinant VSVs displaying foreign antigens. Such modified viruses could be useful as vaccines conferring protection against other viruses.

This technology was subsequently used in 2004 to produce replication competent VSV carrying the genes encoding the glycoproteins of filoviruses, which others had shown are the targets of neutralizing antibodies. When injected into mice, these recombinant viruses induced neutralizing antibodies that were protective against lethal disease after challenge with Ebolavirus.

In a series of experiments done over the next 10 years, rVSV-EBOV was shown to protect nonhuman primates from lethal disease. In these experiments, animals were injected intramuscularly with the vaccine and challenged with Ebolavirus. The vaccine induced protection against lethal disease and prevented viremia. Extensive studies of the VSV vector in ~80 nonhuman primates showed no serious side effects, and only transient vector viremia.

The rVSV-EBOV was originally developed by Public Health Agency of Canada, and subsequently licensed to NewLink Genetics. Financial support has been provided from Canadian and US governments and others. From 2005 to the present, the NIH Rocky Mountain Laboratory in Hamilton, Montana has also been involved in this work, particularly with nohuman primate challenge studies. In November 2014 Merck entered an agreement with NewLink to manufacture and distribute the vaccine.

In August 2014, well into West Africa Ebolavirus outbreak, Canada donated 800 vials of vaccine to WHO, which then established the VSV Ebola Consortium (VEBCON) to conduct human trials.

The results of Phase I trials of rVSV-EBOV in Africa (Gabon, Kenya) and Europe (Hamburg, Geneva) were published on 1 April 2015. These trials comprised three open-label, dose-escalation trials, and one randomized, double blind controlled trial in 158 adults. Each volunteer was given one injection of 300,000 to 50 million plaque-forming units of rVSV-EBOV or placebo. No serious vaccine related events were reported, but immunization was accompanied by fever, joint pain, and some vesicular dermatitis. A transient systemic infection was observed, followed by development of Ebolavirus-specific antibody responses in all participants, and neutralizing antibodies in most.

The interim results of a phase III trial of rVSV-EBOV, begun on 23 March 2015 in Guinea, have just been published. It is a cluster-randomized trial with a novel design that is modeled on the ring vaccination approach used for smallpox eradication in the 1970s. In ring vaccination, individuals in the area of an outbreak are immunized, in contrast to treating a larger segment of the population. During this trial, when a case of Ebolavirus infection was identified, all contacts and contacts-of-contacts were identified. Some of these individuals were immediately immunized intramuscularly with 2 x 107 PFU, and others (randomly chosen) were immunized three weeks later. The primary outcome was Ebolavirus disease confirmed by PCR. As new cases arose in other areas (clusters), these were treated in the same way, hence the name of cluster-randomized trial.

The press has widely reported that the vaccine was ‘100% protective’. This outcome sounds much better than is represented by the data, so let’s look at the numbers.

Zero cases of Ebolavirus disease were observed in 2,014 immediately vaccinated people, while 16 cases were identified in those given delayed vaccine (n=2,380). These numbers were used to calculate the vaccine efficacy of 100%. While statistically significant, the numbers are small.

More telling are the results obtained when we consider all individuals eligible for immunization, not just those who were immunized (some were excluded for a variety of reasons). Of 4,123 eligible individuals, 2,014 were immunized as noted above, but 2,109 did not receive vaccine. Eight cases of Ebola virus disease were noted in the non-immunized population. This number is small, a consequence of the fact that the outbreak is waning.

On the basis of these interim results, the data and safety monitoring board decided that the trial should continue. However because the board felt that the vaccine is a success, they decided to curtail randomization of subjects into immediately vaccinated and delayed vaccinated groups. Now all contacts and contacts-of-contacts will immediately receive vaccine. As a consequence of this change, it will not be possible to improve the accuracy of vaccine efficacy. For example, when many more individuals are immunized in the future, many fewer that 100% might be protected from disease.

There are two lessons I would like you to remember from this brief history of an Ebolavirus vaccine. Developing a vaccine takes a long time (minimum 11 years for rVSV-EBOV) and depends on advances made with both basic and clinical research.  Don’t believe anyone who says that this vaccine was made in a year. And always look at the numbers when you hear that a vaccine has 100% efficacy.

TWiV 342: Public epitope #1

On episode #342 of the science show This Week in Virology, the TWiVniks discuss the structure of a virus that reproduces in an extreme environment, long-term consequences of Ebolavirus infection, and VirScan, a method to identify the different virus infections you have had in your lifetime.

You can find TWiV #342 at www.microbe.tv/twiv.