Category Archives: Science

H5N1 in the US

From NBC News, January 22, 2015:

A green-winged teal shot by a hunter in northern Washington state has tested positive for H5N1 bird flu — a relative of the virus that’s infected nearly 700 people globally and killed 400 of them.


To make matters more complicated, this strain of H5N1 found in the teal appears to be a mix of H5N1 and the H5N8 found in Washington state and elsewhere in the U.S. as well as in Europe, South Korea, Japan and Taiwan.

The pandemic potential of this version of H5N1 is unknown.


Filed under Outbreak, Science

Ebola Myths vs Facts (with references!)

Myth: New Ebola has not shown any significant mutations.

Fact: New Ebola is accumulating mutations at twice the rate of previous outbreaks. Further, sequence analysis shows that it appears to be under “incomplete purifying selection” (Gire et al. 2014). This suggests that the New Ebola is in the process of adapting to the human host.

Myth: New Ebola is not very contagious. It is hard to get.

Fact: Ebola is now transmitting to people at the same rate as the flu. R0 for seasonal influenza is about 1.3 (Cobum et al 2009). R0 for Ebola is currently calculated to be 1.4 to 1.8 (WHO Ebola response team, 2014).

Myth: The new Ebola hasn’t become more transmissible.

Fact: One of the top experts on Ebola, Dr. Peter Jahrling, has reported: ‘We are using tests now that weren’t using in the past, but there seems to be a belief that the virus load is higher in these patients [today] than what we have seen before. If true, that’s a very different bug.

‘I have a field team in Monrovia. They are running [tests]. They are telling me that viral loads are coming up very quickly and really high, higher than they are used to seeing.

‘It may be that the virus burns hotter and quicker.’ Daily Mail, October 18, 2014.

Myth: Quarantines don’t work.

Fact: Quarantines work very well if they are strictly enforced (McLeod et al. 2007).


Coburn BJ, Wagner BG, Blower S. Modeling influenza epidemics and pandemics: insights into the future of swine flu (H1N1). (2009) BMC Med. 7:30.

Gire SK et al (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345: 1369-1372.

McLeod MA, Baker M, Wilson N, Kelly H, Kiedrzynski T, Kool JL (2008) Protective effect of maritime quarantine in South Pacific jurisdictions, 1918-19 influenza pandemic.Emerg Infect Dis. 14:468-70

WHO Ebola Response Team (2014) Ebola Virus Disease in West Africa — The First 9 Months of the Epidemic and Forward Projections. N Engl J Med 371:1481-1495.


Filed under Science

Expellamis Ebolis Scientia! The use of the word “Science” as an incantation to silence different opinions

In Harry Potter world, people with recessive mutations in the Magic gene can point a stick, enunciate some pseudo-Latin and make cool stuff happen.

In Science world, one must observe reality closely, formulate reasonable hypotheses and then test them with carefully designed experiments. A scientist must then make his results and conclusions public so that they can be scrutinized by other scientists. Quite a chore compared to Harry Potter world. But that’s the way it is.

Lately, I’ve noticed that politicians have been using the word science as a sort of magical incantation with which to silence those who disagree with them. They provide no data or even simple logic. They just say “the Science shows”. This is a perversion of the scientific method. And it is time for real scientists to call bullshit on this tactic.

More to come.


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New Ebola – Evolution of a Virus

Recently, a paper describing the sequencing of many samples from patients in Sierra Leone with Ebola was published in Science by Gire et al.:

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

There have been many headlines referring to this paper with variants of this phrase: “Ebola rapidly mutating!” The meaning and implications of such statements is not always clear due to an incomplete understanding of evolution. Therefore, I think it is worth defining some terms and explaining how viruses evolve generally and how Ebola may be evolving specifically.

First, I should like to clarify the difference between the rate at which mutations occur and the rate at which mutations are observed. Mutations are changes in the genetic sequence. They can occur for several reasons including mistakes which occur during replication of viruses. The rates at which these mutations occur thus depend in part on how accurately enzymes copy genetic sequence. This mutation rate is unlikely to change for a given species unless there is a change in the enzymes involved in copying genetic material. This is a very rare occurence. However, changes in the rate at which mutations are observed is much more common because another important force, selection, affects this process.

Many mutations occur but are never observed. How can this be? If a mutation occurs which is deleterious, it will decrease the likelihood that an organism will survive. Such mutations are common in viruses. However, although unfavorable mutations have always been occuring in Ebola, they were unlikely to be observed because the individual viruses which possesed them did not produce many additional viruses. We say that such viruses were selected against.

One of the key concepts of evolution is that selection can change. If the environment of an organism changes, then what constitutes a “bad” mutation, from the viewpoint of the organism, can also change. For a virus, the host is the environment. If the host for Ebola changes from, say, a fruitbat, to a human, then the environment has changed and the effect of a mutation on the ability of the virus to survive and replicate may change. In fact, a mutation which was selected against in fruitbats may be selected for in humans if it helps the virus survive in its new environment – humans. This will lead to a change in observed mutations in viruses which have colonised a new host even if the rate at which mutations actually occur has not changed.

Thus far, this has been a relatively academic discussion.  But now we come to the public health implications of the Science paper.  One interpretation of these results is that Ebola is adapting to its new host, humans, by acquiring new genetic sequences which allow it to replicate and spread person to person more effectively. Indeed, given that the virus has apparently been spreading human to human since December 2013, it would be surprising if this were not occuring.

In the past, Ebola would spread from its animal host to humans, pass human to human a few times, and then die out.  It never had a chance to adapt to humans.  The current outbreak is different. Because Ebola now has had many “passages” through the novel human environment, it has had many more opportunities to adapt to humans.  This may be reflected in some of the changes in genetic sequence observed in the Science paper.  It may also be reflected in changes in the ability of the virus to replicate and spread in humans.  People who expect Ebola to remain unchanging in its new human host are ignoring evolution.  If mutations can occur which will allow the virus to spread more efficiently in humans, then, given enough time, such mutations will occur.

Ebola was an animal virus.

It is becoming a human virus.

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New Ebola can spread by people without obvious signs of the disease

From CNN, July 29, 2014

Brantly’s family had been with him in Liberia, according to the Centers for Disease Control and Prevention, but left for the United States before he became symptomatic; as such it is highly unlikely that they caught the virus from him. Out of an abundance of caution they are on a 21-day fever watch, the CDC said.

Nancy Writebol from Charlotte, North Carolina, has also been infected. She is employed by Serving in Mission, or SIM, and had teamed up with the staff from Samaritan’s Purse to help fight the Ebola outbreak in Monrovia when she got sick. She, too, is undergoing treatment.

It is believed one of the local staff was infected with Ebola and came to work with the virus on Monday and Tuesday, Isaacs told CNN. “We think it was in the scrub-down area where the disease was passed to both Nancy and Kent,” he said. That staff member died on Thursday.

Dr. Brantly is a doctor with obvious experience in diagnosing Ebola cases. Yet, he was unable to detect infection in the co-worker who infected both him and Mrs. Writebol. Further, the co-worker was able to function for two days while still being able to infect at least two other people.

This suggests that we are indeed dealing with a “New Ebola” (as Pixie has put it at PFI Forum). This New Ebola apparently leaves people well enough, while they are infectious, to both travel and work without being detected. This makes this new Ebola pandemic-capable.

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Two ways Ebola could become a pandemic

Here are two possible ways Ebola could become a pandemic:

1. It could slow down.

In the past, Ebola patients were only infectious when they were very ill and obviously infected with this disease. If the virus were to change in such a way that patients were well enough to travel while they were infectious, they could spread the virus to others before they died, especially if it was not obvious that they had Ebola. There are anecdotal reports that this may be happening in the current outbreak in West Africa.

2. It could become airborne.

In the past, Ebola was spread strictly by bodily fluids. If it changed so that it was transmitted through respiratory droplets, Ebola might spread to others much easier. There is no evidence of this in the current outbreak. However, another strain of Ebola, the Reston virus, was shown to be capable of respiratory transmission. So conversion of any Ebola virus to a respiratory form is a theoretical possibility.


Filed under Outbreak, public health, Science

Virus Storm

The number of lethal new viruses now assaulting the human species is striking:


Since all of these viruses can kill otherwise healthy young adults, when a new outbreak of an infectious agent occurs, it can be difficult to know which of the many, and growing number, of viruses is responsible. Testing should now involve rapid sequencing of samples. This should not be left to local public health departments. There should be a national system for sample preparation and sequencing with clear protocols for hospital and private practitioners to follow and designated laboratories for the samples to be sent to. The goal should be identification of the virus within 24 hours of a death or a cluster of people with severe illness. If the CDC is unwilling or unable to meet these metrics, States should set up their own protocols and networks. Many States have sufficient expertise and equipment to get this done.

There should be no “mystery” viruses in the 21st Century.

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