TWiV 327: Does a gorilla shift in the woods?

On episode #327 of the science show This Week in Virology, the eTWiVicators review evidence that the HIV-1 group O epidemic began with a single cross-species transmission of virus from western lowland gorillas.

You can find TWiV #327 at

WHO assessment of experimental Ebola virus vaccines

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.

TWiV 305: Rhymes with shinola

On episode #305 of the science show This Week in Virology, Vincent, Alan, and Kathy continue their coverage of the Ebola virus outbreak in West Africa, with a discussion of case fatality ratio, reproductive index, a conspiracy theory, and spread of the virus to the United States.

You can find TWiV #305 at

Ebola virus enters the United States

Filovirus virion

Image credit: ViralZone

Given the extent of the Ebola virus outbreak in West Africa, transport of an infected individual to the US was bound to happen. The case is an adult who had contact with an Ebola virus-infected woman in Liberia, then traveled to Dallas. He had no symptoms before arriving in the US and therefore did not likely transmit the infection to airplane passengers. He sought medical care on 26 Sep 2014 and was admitted to Texas Health Presbyterian Hospital 28 Sep 2014 where he is currently under isolation. Samples sent to the CDC tested positive for Ebola virus. There are excellent summaries of the events at ProMedMail and the CDC website.

Apparently the Dallas patient told a healthcare worker during his first hospital visit that he had been in Liberia. This information was not transmitted to his physician. The word ‘Liberia’ should have set off alarm bells. Furthermore, if the physician did not receive the patient’s recent travel history, he/she should have requested it. There is no room for error when dealing with Ebola virus infection.

It is puzzling that travel (excluding healthcare workers) out of the affected West African countries is still permitted. As moderator JW notes on ProMedMail: “This chain of events illustrates the danger that anybody arriving from Liberia, even without symptoms on departure from there or on arrival in the USA (or anywhere else in Africa or overseas) may be incubating Ebola — but not international volunteers who have only been in contact with Liberians while wearing adequate PPE (personal protection equipment).”

Why is it important to stop travel out of the affected countries? While I’m confident that the US can detect and properly contain imported Ebola virus infections, not all countries will be able to do so. There are dozens of other countries that are unprepared to deal with an infected case, from diagnosis to isolation to treatment. I can easily imagine infection quickly getting out of control in such countries: millions are at risk. While the economics of stopping air travel out of Liberia, Sierra Leone, and Guinea will be severe, they cannot approach the devastation of having outbreaks burning simultaneously in multiple countries.

Update: NPR has a good explanation of the reproductive index, or the number of persons who can be infected by another infected person during an outbreak. For Ebola virus, this number is 1-2. This low number is why quarantine can be effective.

Could the Ebola virus epidemic have been prevented?

Ebola is comingThe cover of this week’s issue of Businessweek declares that ‘Ebola is coming’ in letters colored like blood, with the subtitle ‘The US had a chance to stop the virus in its tracks. It missed’. Although the article presents a good analysis of the hurdles in developing antibody therapy for Ebola virus infection, the cover is overstated. Why does Businessweek think that Ebola virus is coming to the US? (there is no mention of this topic in the article). Are we sure that antibody therapy would have stopped the outbreak? (no, as stated in the article).

How the U.S. Screwed Up in the Fight Against Ebola is an analysis of why ZMapp, the cocktail of monoclonal antibodies that block infection with Ebola virus, has not yet been approved for use in humans. ZMapp was given to two American workers who had become infected with the virus while working in Africa. The two workers recovered, but the role of ZMapp in their recovery is unknown – as the authors of the article note. Although ZMapp can prevent lethal infection of nonhuman primates with Ebola virus, it is not known if it would work in humans. Answering that question requires a clinical trial, and the article explores why this phase was not done years ago. Only after the large Ebola virus outbreak in west Africa did the US provide funds to conduct a phase I trial of the drug.

The article discusses how development of ZMapp languished for years, because the US government did not consider the Ebolaviruses to be a pressing problem. In hindsight they were wrong, and now anyone can seem smart by saying we should have pushed development of Ebola virus vaccines and therapeutics.

The real question is whether we will learn from this experience, and be better prepared for the next viral outbreak. Just because infections are rare or geographically localized should not lessen their importance, as these features can change. Knowing the animal source of a viral infection may also lead to developing ways to prevent infections. For example, because people acquire Hendra virus from horses, immunization of these animals should prevent human infections.

What other antiviral vaccines and drugs should we be developing? This question is difficult to answer because we discover new viruses regularly and making therapeutics for all of them is not possible. Testing an antiviral drug or vaccine against rare viruses is difficult because identifying populations that are at risk for infection may be a hit or miss proposition.

Influenza viruses are at the top of the list for vaccine and drug development, because nearly everyone gets infected. Other viruses we should be ready for include SARS and MERS coronaviruses, dengue virus, chikungunya virus, Lassa virus, Nipah and Hendra viruses. I’m sure you can think of other viruses that belong on this list.

Developing antiviral vaccines and drugs is expensive. For some of the viruses on my list (dengue, chikungunya) there are currently large enough markets that permit involvement of for-profit pharmaceutical companies. Development of therapeutics against viruses that cause rare infections must be supported largely by governments.

The US does not spend enough money on basic life sciences research. We do spend a great deal of money on the military. President Obama recently declared Ebola virus to be a top national security priority. Why not view all infectious diseases in this way, to ensure that they receive the funding for research that they deserve?

While the Businessweek cover is misleading, intended to stimulate sales, the article does make us think about the problems we confront when dealing with rare but lethal diseases. No one should conclude that Ebola virus outbreak in Africa could have been prevented, because antiviral therapies have not yet been tested in humans. But we won’t know if we never do the research.

TWiV 304: Given X, solve for EBOV

On episode #304 of the science show This Week in Virology, the TWiV team consults an epidemiologist to forecast the future scope of the Ebola virus epidemic in West Africa.

You can find TWiV #304 at

Transmission of Ebola virus

jet nebulizerAs the West African epidemic of Ebola virus grows, so does misinformation about the virus, particularly how it is transmitted from person to person. Ebola virus is transmitted from human to human by close contact with infected patients and virus-containing body fluids. It does not spread among humans by respiratory aerosols, the route of transmission  of many other human viruses such as influenza virus, measles virus, or rhinovirus. Furthermore, the mode of human to human transmission of Ebola virus is not likely to change.

What is aerosol transmission? Here is a definition from Medscape:

Aerosol transmission has been defined as person-to-person transmission of pathogens through the air by means of inhalation of infectious particles. Particles up to 100 μm in size are considered inhalable (inspirable). These aerosolized particles are small enough to be inhaled into the oronasopharynx, with the smaller, respirable size ranges (eg, < 10 μm) penetrating deeper into the trachea and lung.

All of us emit aerosols when we speak, breathe, sneeze, or cough. If we are infected with a respiratory virus such as influenza virus, the aerosols contain virus particles. Depending on their size, aerosols may travel long distances, and when inhaled they lodge on mucosal surfaces of the respiratory tract, initiating an infection.

Viral transmission can also occur when virus-containing respiratory droplets travel from the respiratory tract of an infected person to mucosal surfaces of another person. Because these droplets are larger, they cannot travel long distances as do aerosols, and are considered a form of contact transmission. Ebola virus can certainly be transmitted from person to person by droplets.

Medical procedures, like intubation, can also generate aerosols. It is possible that a health care worker could be infected by performing these procedures on a patient with Ebola virus disease. But the health care worker will not transmit the virus by aerosol to another person. In other words, there is no chain of respiratory aerosol transmission among infected people, as there is with influenza virus.

In the laboratory, machines called nebulizers (which are used to administer medications to humans by inhalation) can be used to produce virus-containing aerosols for studies in animals. A human would likely be infected with an Ebola virus-containing aerosol generated by a nebulizer (theoretically; such an experiment would be unethical).

A variety of laboratory animals have been infected with Ebola virus (Zaire ebolavirus) using aerosols. In one study rhesus macaques were infected with aerosolized Ebola virus using a chamber placed over the animals’ heads. This procedure resulted in replication of the virus in the respiratory tract followed by death. Virus particles were detected in the respiratory tract, but no attempts were made to transmit infection from one animal to another by aerosol. In another study, cynomolgous macaques, rhesus macaques, and African Green monkeys could be infected with Ebola virus aerosols using a head-only chamber. Virus replicated in the respiratory tract, and moved from regional lymph nodes to the blood and then to other organs. Virus titers in the respiratory tract appeared to be lower than in the previous study. No animal to animal transmission experiments were done.

When rhesus macaques were inoculated intramuscularly with Ebola virus,  virus could be detected in oral and nasal swabs; however infection was not transmitted to animals housed in separate cages. The authors conclude that ‘Airborne transmission of EBOV between non-human primates does not occur readily’.

Pigs can also be infected with Ebola virus. In one study, after dripping virus into the nose, eyes, and mouth, replication to high titers was detected in the respiratory tract, accompanied by severe lung pathology. The infected pigs can transmit infection to uninfected pigs in the same cage, but this experimental setup does not allow distinguishing between aerosol, droplet, or contact spread.

In another porcine transmission experiment, animals were infected oronasally as above, and placed in a room with cynomolgous macaques. The pigs were allowed to roam the floor, while the macaques were housed in cages. All of the macaques became infected, but their lungs had minimal damage. However it is not known how the virus was transmitted from pigs to macaques. The authors write: ‘The design and size of the animal cubicle did not allow to distinguish whether the transmission was by aerosol, small or large droplets in the air, or droplets created during floor cleaning which landed inside the NHP cages’. The authors also indicate that transmission between macaques in similar housing conditions was never observed.

While these experimental findings show that animals can be infected with Ebola virus by aerosol, they do not provide definitive evidence for animal to animal transmission via this route. It is clear is that the virus does not transmit via respiratory aerosols among nonhuman primates.

We do not know why, in humans or non-human primates, Ebola virus does not transmit by respiratory aerosols. The virus might not reach sufficiently high titers in the respiratory tract, or be stable in respiratory secretions, to be efficiently transmitted by this route. There are many other possibilities. A careful study of Ebola virus titers in the human respiratory tract, and in respiratory secretions, would be valuable. However during Ebola virus outbreaks the main concern is to save people, not conduct experiments.

These experiments reveal the large gaps in our understanding about virus transmission in general, and specifically why Ebola virus is not transmitted among primates by respiratory aerosols.

Whither 2009 H1N1?

When will the 2009 swine-origin influenza virus become a seasonal strain? While prediction is very hard, especially of the future (at least according to Yogi Berra), examining past pandemics can be informative.


The 1968 pandemic began with the emergence of a novel H3N2 influenza virus in Hong Kong in July 1968. First isolates (stars) were obtained globally throughout the summer. The previous seasonal H2N2 strain was last isolated in August 1968 in Australia and was subsequently not seen again. There were sporadic H3N2 outbreaks for several months (hatched lines). Epidemic spread (solid lines) ensued in the northern hemisphere throughout the winter, and then ceased in the spring of 1969. In the southern hemisphere the first epidemic occurred from January through October. There were second seasons of epidemic spread in both hemispheres, ending in the summer of 1970. After that time the H3N2 strain became a seasonal strain, causing local epidemics each year as the virus underwent antigenic drift.

If the pattern of H3N2 serves as a guide, we might predict that the 2009 swine-origin H1N1 virus will display pandemic spread for at least one more season. In the northern hemisphere, the second season would comprise November 2010 – April 2011. However, immunity in older individuals might blunt the spread of the virus beyond the current first season. It also remains to be seen how much immunization will impact pandemic spread.

At one point the 2009 H1N1 swine-origin influenza virus will become a seasonal strain, and the monovalent vaccine will no longer be produced. At that time the season influenza vaccine will likely comprise a ‘drifted’ version of the 2009 H1N1 strain and an influenza B virus. By all current indications the previous seasonal H1N1 and H3N2 strains will soon disappear from humans – although not from the globe.

Viboud, C., Grais, R., Lafont, B., Miller, M., Simonsen, L., & , . (2005). Multinational Impact of the 1968 Hong Kong Influenza Pandemic: Evidence for a Smoldering Pandemic The Journal of Infectious Diseases, 192 (2), 233-248 DOI: 10.1086/431150

Swine flu A/Mexico/2009 (H1N1): Questions and answers

questionHere are my answers to questions about swine flu sent by readers of virology blog:

Q: Am I missing something?  How can a summer pandemic be unprecedented?  You cited a pretty famous example of one.  In fact nearly all of your examples seem to have occurred partly or mostly “out of season”.

A: You are correct; it is true that there were cases of influenza over the summer of 1918, even in the northern hemisphere. These were mainly in troops; I believe this situation was anomalous due to massive troop movements. But in 1968 the seasonal pattern was clear.

Q: I haven’t seen anyone address death rates for cases treated with antivirals vs. cases not treated with antivirals. For that matter, reporting of the cases in the US has been rather unclear about the extent to which confirmed and suspected cases are being treated with antivirals. Couldn’t it be that Mexico has only relatively recently started to consistently treat suspected cases with antivirals within the short window of effectiveness, and that most US cases have received treatment? This would explain a leveling off of the increase in number of deaths in Mexico and the “mild” cases we’re seeing in the U.S.  If this is not made clear, the public will mistakenly believe this flu to be benign and will not take the appropriate steps to mitigate its spread. And couldn’t this turn political as countries have different incentives to shut down their economies with quarantines and bans on public gatherings given their respective antiviral stockpiles?

A: I don’t have any information on the extent of use of antivirals anywhere. There are still so few confirmed cases that it would be premature to speculate, although it’s a good point.

Q: How are influenza viruses classified as H1, H2, etc? I had always thought it was serological, but that would imply that the seasonal H1N1 vaccine might have some efficacy against this H1N1 “swine” virus. Is there a more modern method for classification based on nucleotide sequence?

A: The subtyping (H1, H2, etc) is done by serology, using a panel of antibodies against the 17 known HA subtypes. This would imply some cross-reactivity among the H1 HAs of the swine flu strain and the previous H1N1 strain. Such cross-reactivity might confer perhaps not protection against infection but could lead to milder disease. CDC asserts that “Vaccination with seasonal influenza vaccine containing human influenza A (H1N1) would not be expected to provide protection against swine influenza A (H1N1) viruses” but it could reduce disease severity.

Q: I found these statistics on the newspaper “Reforma” so I have added the population for each state (in thousands) and calculated morbidity and mortality by adding all up (deaths, proven cases and probable (maybe) cases) and it turns out that the states with the highest morbidity do not have the highest mortality… for instance Tlaxcala has the highest morbidity for such a small state and San Luis Potosi has the highest mortality with a much lower morbidity….Could be that we are dealing with two different types of H1N1 viruses? one is the California that is not too virulent and a mutated one that is highly virulent and is not spreading that much….

A: These are certainly possible scenarios. Until we have sequences from the Mexican isolates we won’t know the answers. I do think the absence of sequence information from Mexico is exacerbating the panic.

Q: What are the chances of swine flu developing resistance against Tamiflu and other currently available antiviral drugs ?  Do you think that the distribution of Tamiflu and other drugs over the course of the last few years have been a mistake that leaves us less well-prepared in front of the current epidemic ?

A: The chance of swine flu becoming resistant to Tamiflu is very high; last season a high proportion of all circulating H1N1 viruses were resistant to the drug. Remember, the current H1N1 viruses are already resistant to adamantanes. I don’t think distribution of the drugs was a mistake; their use probably saved lives. What is a mistake is not having a deeper arsenal of antiviral drugs. We need to have at least 6 drugs for an effective antiviral approach.

Q: I live in Mexico and we are very confused here about the measures the government is taking against the flu. I have heard that it is not possible in the first 7 days passing the virus person-person, but only in the moment that the symptoms are already visible. Is that true?

A: Peak virus shedding occurs about a day before peak symptoms. I would not say it is not impossible to shed virus without symptoms, but in most cases, shedding is quickly followed by symptoms.

Q: I read somewhere that this new strain is one that contains parts of the H5N1 virus (bird flu) and other flues, including the H1N1 strain (human), and some genetic material from swine flu, but they’re just calling it the H1N1 virus. This is all very confusing, because that would have had to be genetically engineered in a lab and then released into the general public. They (the media) is also saying that it is a rapidly mutating virus (RNA, obviously, because they are unstable). Could this be genetically engineered? If someone could explain, that would be great.

A: Pigs are infected with many different influenza virus subtypes (H1N1, H3N2) and viruses with different sets of RNA segments can emerge. It does not have to be engineered in a lab to have RNAs from so many different viruses. This is not a virus anyone has seen before, and no scientist is smart enough to have made it so that it would be transmitted among humans.

We receive quite a few anxious emails from Mexico. Following is an example:

Q: I am living in Baja, Mèxico. This  swine influenza issue is getting really scary. And I suspect authorities  give one information then they give contradictory information, I think they don´t want people to panic. As we already are anyway.

a) La Paz, is really  hot weathered, unfortunately… and the hot weather hasn`t come yet, do you think hot weather would help to attenuate the spreading of the virus?

A: Yes, hot weather should interfere with aerosol transmission. But it is possible that the virus might continue to spread through contact.

b) How long do you think it would take to make a vaccine?

Six months. I have read that some companies feel it can be done faster, but the vaccines we have used successfully in the past require six months.

c) Now it is really difficult to find the Relenza or Tamiflu, but I have heard that some natural products sometimes help reinforced the inmunological system , like the onion, would you recommend to eat something in particular?

I am not aware of natural antiviral sources, but I would caution you against using natural products that might contain other dangerous materials (not onions, of course).

Q: I was reading that some countries do not have the techniques for testing if a virus is of the present H1N1 type. Which exactly is the procedure for this test and why it is so complex/expensive?

A: It is true that some of the assays are complex, and several are used. One method is to isolate the virus in cell culture by inoculating a nasal swab or throat wash specimen into cultured cells. Then a panel of antibodies against the 16 known HA subtypes are used in a variety of assays, such as neutralization assays, in which the capacity of the antibody to block infection is determined. For example, if the virus is an H1 virus, only antibodies against the H1 HA would block infectivity. Other diagnostic methods include direct fluorescent antibody testing, immunoassays, real-time reverse transcription-polymerase chain reaction, nucleotide sequencing, and multiplex reverse transcriptase-polymerase chain reaction. Some of these assays can be done directly on the nasal swab or throat wash. Viral culture is the “gold standard” for typing and subtyping of influenza viruses, but takes 3 to 7 days to culture the virus. In experienced hands they are not complex, but they must be done properly to have confidence in them. Lab personnel need to be trained in the methods because clearly a great deal depends upon a reliable test.

Q: Why does the CDC recommend against face masks when the science clearly shows they are exceedingly beneficial at stopping the transmission of flu-like disease? Here’s a study I found on the CDC’s own site clearly demonstrating the efficacy of properly fitted N95 face masks during the SARS outbreak.

A: I did not mean to imply that CDC advises against using face masks. My statement was based on the fact that on the CDC’s swine flu page, there are no recommendations for face masks. This is the page that most of the public will see. Face masks will work if used properly; if not used according to directions, they will not prevent transmission or infection and will convey a false sense of security.

Oseltamivir resistance decreases influenza aerosol transmission

tamifluThe isolates of influenza virus obtained in the current global outbreak have proven to be resistant to the adamantane antivirals, but susceptible to oseltamivir (Tamiflu) and zanamivir (Relenza). Consequently the two neuraminidase inhibitors will likely be used extensively to control the outbreak until a vaccine is available. Extended use of the antiviral drugs will undoubtedly lead to the selection of drug resistant influenza virus mutants. However, there might be a silver lining to this otherwise dismal prediction.

Transmission of oseltamivir-resistant influenza viruses was studied in a guinea pig model for infection. Viruses with either one or two amino acid changes that lead to drug resistance multiplied normally in guinea pigs, but the viruses were transmitted very poorly to other animals by aerosols. Oseltamivir-sensitive viruses were transmitted efficiently by aerosol among animals. Interestingly, both oseltamivir-sensitive and oseltamivir-resistant viruses transmitted efficiently by the contact route among guinea pigs placed in the same cage.

These observations indicate that mutations that cause resistance to oseltamivir reduce aerosol, but not contact transmission of influenza virus. The authors speculate that the amino acid changes associated with drug resistance also decrease the enzymatic activity of the viral NA (neuraminidase) protein. One of the functions of this viral protein is to facilitate release of newly synthesized virus particles from the surface of the infected cell. Mutations that cause drug resistance may lead to impaired virus release, and therefore poor transmission by the aerosol route.

Although these results are encouraging, it is not clear if drug resistance mutations would have a similar effect on aerosol transmission of the current A/Mexico/2009 (H1N1) influenza viruses. A high proportion of the influenza H1N1 viruses from the previous season were resistant to the drug, yet the viruses spread extensively. One possible explanation for the discrepancy is that influenza in guinea pigs does not lead to coughing or sneezing. Hence, the virus-laden aerosols produced by guinea pigs are a consequence of normal breathing. In humans, air turbulence caused by coughing and sneezing might be sufficient to dislodge virus particles that in the guinea pig would remain firmly attached to the epithelial surface. Nevertheless, the results suggest that simple hygienic measures could slow the spread of a drug resistant virus that transmits by efficiently by contact and poorly by aerosol.

Bouvier, N., Lowen, A., & Palese, P. (2008). Oseltamivir-Resistant Influenza A Viruses Are Transmitted Efficiently among Guinea Pigs by Direct Contact but Not by Aerosol Journal of Virology, 82 (20), 10052-10058 DOI: 10.1128/JVI.01226-08