This morning I received this email from President Lee Bollinger:

Dear fellow members of the Columbia community:

As you may have seen in the media, Dr. Craig Spencer is being treated for Ebola at Bellevue Hospital in Manhattan. Dr. Spencer, an emergency department physician at NewYork-Presbyterian/Columbia University Medical Center, recently returned from a humanitarian mission with Doctors Without Borders to one of the outbreak areas in Western Africa. We admire and appreciate all of those willing to do this vital and selfless public health work around the globe.

It’s critical to bear in mind what our public health and infectious disease experts have emphasized – that the risk to people in New York City and at Columbia remains extremely low. If you or anyone has any concerns, please visit the University’s Ebola Preparedness site or the New York City Department of Health Ebola update page. You may also contact Student Health Services or Workforce Health and Safety for Faculty/Staff with Hospital Responsibilities.

We must keep Dr. Spencer in our thoughts and wish him a full and speedy recovery, as we do the vulnerable populations he serves. We will also continue to keep the Columbia community informed as we learn more from City, State, and Federal health officials.

Sincerely,
Lee C. Bollinger

The transition between incubation period (when there are no symptoms) and the first clinical signs is a dangerous period. During this time the patient may continue to move around in public despite having fever and other indications of infection. It will be important to trace as many of this physician’s contacts as possible, a difficult task in a city of over 8 million people. Apparently the physician traveled around the city, using the subways, the night before having a fever. Whether any virus is shed during this time, in amounts sufficient to infect others, is unknown, but could be determined by studying the contacts of such infected individuals.

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crab eating macaqueI have received many questions about whether immunizing with Reston virus could protect against infection with Ebola virus. Usually the question comes together with the statement ‘because Reston virus does not cause disease in humans’. I can think of two reasons why a Reston virus vaccine is not a good idea.

There have been very few confirmed human infections with Reston virus (4 according to Fields Virology 6th Edition), and although these individuals did not show signs of disease, the number is too small to make any conclusions. For example, if the case fatality ratio of Reston virus in humans were 1%, we might not have yet seen any deaths due to the small number of confirmed infections. However if we were to immunize a million people with a Reston virus vaccine, and the case fatality ratio were 1%, there would be 10,000 deaths, obviously an unacceptable rate for a vaccine. As the virus causes disease in nonhuman primates, and there are so few human infections, it is not possible to know the case fatality ratio.

The other problem is that in general, infection with one of the Ebolaviruses does not confer protection against the others*. For example, animals that survive challenge with Ebola virus (Zaire) are not protected from infection with Sudan virus. For this reason, vaccines need to be prepared against representatives of all the species. I am not aware of any animal studies that have assessed whether Reston virus infection protects from infection with the other Ebolaviruses, but there is no reason to believe that such cross-protection would be achieved.

Vaccines are currently being tested against Ebola virus (species Zaire ebolavirus), cause of the outbreak in west Africa.

*Thanks to Andrea Marzi for information on cross-protection.

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When the first case of Ebola virus infection was detected at the Firestone Liberia, Inc. rubber tree plantation in March of this year, the company needed to prevent the virus from spreading among their 8,500 employees. The company established an incident management system, developed procedures for early detection of infection, enforced infection control guidelines, and provided different levels of management for contacts depending on their exposure. The company did a remarkable job of isolating and caring for patients and limiting transmission to health care workers and family members. A description of this program, just issued by Morbidity and Mortality Weekly Report, is a must read.

I found the following paragraph, Community Reintegration of Ebola Survivors, perhaps the most significant in the report:

To prepare communities for the return of Ebola survivors and minimize potential stigmatization, Firestone established a survivor reintegration program. The program consisted of community education, whereby members of the reintegration team explained that the survivor had been declared Ebola-free and no longer contagious, and a survivor welcome celebration. The celebrations were prepared by the community with assistance from the reintegration team and attended by MOHSW, Firestone staff, and clergy. Each survivor was presented a medical certificate and an opportunity to share his or her experience. The celebrations were broadcast on radio and recorded for future programs for Ebola education in the community. In addition, Firestone donated a solidarity package to the survivor, which included essential household items (e.g., mattress, bedding material, and mosquito net).

Among all our discussion of virus fatality, transmission, virulence, fomites, and vaccines, we should remember that people are contracting the virus. At all stages of disease they need to be treated with humanity.

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SkinI received this question about Ebola virus infection via email:

Can you become infected if infected droplet lands on your skin even if there is no abrasion on the skin? I am now hearing this, which surprises me. The virus can enter through the actual skin and does not need mucus membrane to enter?

The skin of most animals is an effective barrier against viral infections. The outer layer of human skin, called the stratum corneum, consists of a layer of dead, keratinized cells (illustrated). Viruses cannot replicate in, or be transported across, dead cells. Therefore any virus that lands on the skin cannot simply replicate in the outer layer or be transported to the underlying living cells.

However, viruses can pass through the dead layer of the skin through cuts or abrasions. Many activities, such as shaving, or even scratching, lead to microabrasions. It is relatively easy to breach the dead layer of cells with a fingernail, and such abrasions cannot be seen.

A patient in the late stages of Ebola virus infection (such as the Dallas patient) is shedding high amounts of virus particles in body fluids. If virus-laden droplets land on the skin, the virus can readily enter via cuts or abrasions. Even if the skin is intact, the droplets could be inadvertently transferred to mucous membranes of the eye, nose, or mouth, initiating infection. For this reason it is important that the skin be entirely covered when caring for Ebola virus infected patients.

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TWiV 307: Ebola aetiology

19 October 2014

On episode #307 of the science show This Week in Virology, Tara Smith joins the TWiEBOVsters to discuss the Ebola virus outbreak in west Africa, spread of the disease to and within the US, transmission of the virus, and much more.

You can find TWiV #307 at www.twiv.tv.

Cost BalancingWHO and CDC recommend that individuals who are potentially infected with Ebola virus should be quarantined for 21 days. Where does this number come from? Charles Haas at Drexel University asked the same question, and provides an answer.

The quarantine period for an infectious disease is based on the incubation period, the time before symptoms of an infection appear. For Ebola virus, the incubation period is 2-21 days after infection. During this time it is believed that individuals infected with the virus are not contagious, but they could produce small amounts of virus. Whether or not a patient is contagious during the incubation period depends on the virus.

It is clearly important to determine the correct quarantine period for Ebola virus to prevent chains of infection. The longer the quarantine period imposed, the less risk of infecting others. However the cost of enforcing quarantine must be balanced with the cost of releasing exposed individuals (illustrated). According to Haas, the optimal quarantine time should be at the intersection of the two curves.

To determine how the Ebola virus quarantine period was set at 21 days, Haas examined the incubation periods calculated for previous outbreaks. In a study of the 1976 Zaire outbreak, the mean time between exposure and disease for 109 cases of person-to-person spread was calculated at 6.3 days with a range of 1 to 21 days. Mean incubation times for the 1995 Congo outbreak (315 cases) and the 2000 Uganda outbreak (425 cases) were 5.3 and 3.35 days, respectively. Two other analyses of the 1995 Congo outbreak gave mean incubation times of 10.11 and 12.7 days. WHO has estimated a mean incubation period for the first 9 months of the current west African outbreak as 11.4 days, with an upper limit (95% confidence) of 21 days.

Haas concludes that the 21 day quarantine value is derived from a ‘reasonable interpretation’ of outbreak data, but it might not be long enough. He estimates that there is a risk of between 0.2% and 12% of developing Ebola virus infection after 21 days.

The current outbreak should allow collection of data for revising and updating the 21 day quarantine period for Ebola virus infection.

 

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The World Health Organization held a conference to assess the status of testing and eventual licensing of two candidate Ebola virus vaccines. The agenda and list of participants and the final report are available. I was interested in the following list of key expected milestones:

October 2014:
Mechanisms for evaluating and sharing data in real time must be prepared and agreed upon and the remainder of the phase 1 trials must be started

October–November 2014:
Agreed common protocols (including for phase 2 studies) across different sites must be developed

October–November 2014:
Preparation of sites in affected countries for phase 2 b should start as soon as possible

November–December 2014:
Initial safety data from phase 1 trials will be available

January 2015:
GMP (Good Manufacturing Practices) grade vaccine doses will be available for phase 2 as soon as possible

January–February 2015:
Phase 2 studies to be approved and initiated in affected and non-affected countries (as appropriate)

As soon as possible after data on efficacy become available:
Planning for large-scale vaccination, including systems for vaccine financing, allocation, and use.

I wonder how a phase 2 study will be conducted, the goal of which is to determine if it is effective and further evaluate its safety. Will this be done in west Africa, where protection against Ebola virus infection can be assessed? If so, will there be controls who receive placebo?

If indeed an Ebola virus vaccine is our best hope in limiting the current outbreak, it won’t be distributed for a while, according to the optimistic expectations of WHO – assuming all proceeds on time, and that the results are favorable.

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Dr. Francis Collins, the head of the National Institutes of Health, believes that we would have an Ebola virus vaccine if not for the past ten years of flat budgets for life science research:

NIH has been working on Ebola vaccines since 2001. It’s not like we suddenly woke up and thought, ‘Oh my gosh, we should have something ready here.’ Frankly, if we had not gone through our 10-year slide in research support, we probably would have had a vaccine in time for this that would’ve gone through clinical trials and would have been ready. (Source: Huffington Post)

I do understand that Collins needs to be a champion of life sciences research, but to promise that a vaccine would be ready by now is overly optimistic. Vaccines are not easy to design, as the efforts to make an HIV-1 vaccine illustrate. There is no guarantee that even unlimited resources would have produced an approved vaccine. However, more money might have allowed clinical trials of the Ebola virus vaccine candidates currently beginning phase I testing.

I believe that Collins should take the Ebola virus outbreak as an opportunity to emphasize the need for continuous, strong support of basic life sciences research. Michael Eisen, who is particularly annoyed with Collins’ statement, is right about what Collins should have said:

But what really bothers me the most about this is that, rather than trying to exploit the current hysteria about Ebola by offering a quid-pro-quo “Give me more money and I’ll deliver and Ebola vaccine”, Collins should be out there pointing out that the reason we’re even in a position to develop an Ebola vaccine is because of our long-standing investment in basic research, and that the real threat we face is not Ebola, but the fact that, by having slashed the NIH budget and made it increasingly difficult to have a stable career in science, we’re making it less and less likely that we’ll be equipped to handle all of the future challenges to public health that we’re going to be face in the future.

Don’t get me wrong. I get what Collins is trying to do. I just think it’s a huge mistake. Every time I see testimony from NIH officials to Congress, they are engaged in this kind of pandering – talking about how concerned they are about [insert pet disease of person asking question] or that and how, if only they could get more money, we’d be able to take make amazing progress. But guess what? It hasn’t worked. The NIH budget is still being slashed. It’s time for the people who run the biomedical research enterprise in this country to make basic research the center of their pitch for funding. Collins had a huge opportunity to do that here, but he blew it.

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EV-D68

Enterovirus D68 by Jason Roberts

An outbreak of respiratory disease caused by enterovirus D68 began in August of this year with clusters of cases in Missouri and Illinois. Since then 691 infections have been confirmed in 46 states in the US.

The number of confirmed infections is likely to increase in the coming weeks, as CDC has developed a more rapid diagnostic test. Previously it was necessary to amplify the viral genome by polymerase chain reaction, followed by nucleotide sequencing to determine the identity of the agent. The new test utilizes real time, reverse transcription PCR which is specific for the EV-D68 strains that have been circulating this summer.

Since its discovery in California in 1962, EV-D68 has been rarely reported in the United States (there were 26 isolations from 1970-2005). Beginning in 2009 it was more frequently linked to respiratory disease outbreaks in North America, Europe, Asia, and Africa. It seems likely that the virus was always circulating, but we never specifically looked for it.

The current EV-D68 outbreak is the largest ever reported in North America. Enterovirus infections are not rare – there are millions every year in the US – but why EV-D68 has been so frequently isolated this year is unknown. One possibility is that the CDC, after the initial outbreak in August 2014, began looking specifically for the virus.

Sequence analysis of the EV-D68 viral genomes indicate that 3 different strains are involved in the US outbreak. These viruses are related to EV-D68 strains that have previously circulated in the US, Europe, and Asia. The sequences are available at GenBank as follows: US-IL-14/18952, US-KY-14/18951, US-MO-14/18950, US-MO-14/18949, US-MO-14/18948, US-MO-14/18947, and US-MO-14/18946.

Most of the illness caused by EV-D68 in the US has been respiratory disease, mainly in children. Five of the 691 confirmed EV-D68 cases were fatal, but whether the virus was responsible is not known.

There have also been some cases of polio-like illness in children in several states associated with EV-D68. In Colorado the virus was isolated from four of 10 children with partial paralysis and limb weakness. Previously there had been one report of an association of EV-D68 with central nervous system disease. In this case viral nucleic acids were detected in cerebrospinal fluid. EV-D68 probably does not replicate in the human intestinal tract because the virus is inactivated by low pH. If the virus does enter the central nervous system, it may do so after first replicating in the respiratory tract, and then entering the bloodstream.

There are no vaccines or antivirals to prevent or treat EV-D68 infection. Most infections will resolve without intervention save for assistance with breathing. As the fall ends in North America, so will infections with this seasonal virus.

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Ledipasvir and SofosbuvirThe Food and Drug Administration has approved the use of a single pill containing two different antiviral drugs for the treatment for hepatitis C. It is the first combination pill approved for the disease, and also the first treatment that does not contain interferon or ribavirin.

The new hepatitis C drug, called Harvoni, is a mixture of the antiviral drugs ledipasvir and sofosbuvir. Ledipasvir (pictured) is an inhibitor of the hepatitis C virus protein NS5A, which has multiple roles in the viral replication cycle that include RNA synthesis and virus particle assembly. The mechanism of NS5A inhibition by ledipasvir is not known. Sofosbuvir is a previously licensed inhibitor that targets the viral RNA-dependent RNA polymerase. It is an analog of the nucleoside uridine, one of the four building blocks of RNA. Sofosbuvir is utilized by the viral RNA polymerase, leading to inhibition of viral RNA synthesis.

The use of single antiviral drugs (monotherapy) to treat RNA virus infections is always problematic because resistance usually arises rapidly. Dual-therapy pills like Harvoni are better, but the best are triple-therapy pills. Triple therapy formulations such as Atripla have been used successfully to treat infections with HIV-1, and presumably there will be mixtures of three antiviral drugs for treating hepatitis C.

Let’s use HIV-1 to illustrate the value of treating infections with multiple antiviral drugs. The HIV-1 viral genome, like that of HCV, is slightly less than 10,000 bases long. Assume that one mutation in the viral genome is needed for drug resistance. If the RNA polymerase mutation rate is 1 out of every 10,000 bases synthesized, then each base in the viral genome is substituted in a collection of 10,000 viruses. An HIV-1 infected person can make as many as 10,000,000,000 virus particles each day, so 1010/104 = one million viruses will be produced each day with resistance to one drug.

If we use two antiviral drugs, developing resistance to both occurs in every 104 x 104 = 108 viruses. In this case 1010/108 = 100 viruses will be produced each day with resistance to two drugs.

If we use three antiviral drugs, developing resistance occurs in every 104 x 104 x 104= 1012 viruses, which is more than what is produced each day.

This is why triple antiviral therapy has been so successful for the treatment of AIDS.

And yes, I’m sure someone has tested Sofosbuvir for inhibition of Ebola virus replication.

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