Zika Alert

The CDC has gone to its highest alert level due to concerns about the Zika virus.

From US News & World Report, February 8, 2016:

The Centers for Disease Control and Prevention said Monday that the agency’s command center is going to its highest level of alert, a measure reflecting growing concern about the prospect of Zika virus gaining a foothold in the mainland U.S


This represents the fourth time that CDC’s command center has declared a Level 1 alert. The other emergencies were Hurricane Katrina, the H1N1 flu threat in 2009 and the Ebola epidemic in West Africa.


So far, 50 cases been identified in the U.S., with several in Texas, Illinois, California and Washington, D.C. Five days ago, Florida Gov. Rick Scott declared a state of emergency in four counties, where health officials have diagnosed nine cases of Zika virus in travelers returning from Zika-affected areas.


“Once Zika got a foothold in Brazil, it spread like wildfire through Latin America, the Caribbean and Central America. Now it’s on our doorstep,” Vasilakis says. “There’s a lot of traffic between the U.S. and many countries in Latin America. If an infected individual ends up on our shores, it’s quite possible they could infect local mosquitoes and start a transmission cycle in the U.S., especially the southern U.S.”

“We already had three dozen infected individuals in the U.S. Starting in late March and April, when the weather becomes hotter and more rainy, the mosquito population will greatly increase in the Gulf states, increasing the risk,” he says.


Since it was first identified in Brazil last May, the virus has spread to more than 25 countries and territories in the Americas and Caribbean. It has been linked with a neurological ailment, called Guillain-Barre syndrome, which can cause paralysis, and at least 4,000 cases of a devastating birth defect, microcephaly. Babies born with microcephaly have malformed craniums and smaller brains, which often leads to lifelong cognitive impairment and disability.


H7N9 Flies from China to Canada – On a Plane

From SCMP, January 27, 2015

North America’s first case of bird flu in humans has been identified in a Vancouver-area woman who returned to the city on a flight from Hong Kong this month.

Canadian health authorities said the patient, who tested positive to the H7N9 strain of avian flu on Monday morning, is not gravely ill.


The Globe and Mail newspaper reported that the patient and her husband, both aged in their 50s, had travelled together and both were now sick at home. Tests have not yet confirmed the man’s suspected H7N9 infection.

The newspaper quoted Bonnie Henry, BC’s deputy provincial health officer, as saying the couple “did some touring of areas and villages in China where poultry are seen throughout the village, but there was not a particularly high-risk exposure that we were able to identify.

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.

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.

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.

Temporal and quantitative framework for intervention in the Ebola pandemic

The following projection involves estimates based on media accounts of reported cases as well as estimates of unreported cases.

First some assumptions:

1 HCW is needed for every 10 Ebola patients
There are 10,000 to 20,000 patients not receiving care currently.
By mid-November, this number will jump to 100,000-200,000, without immediate intervention.
By some time in January, this number will reach 1-2 million.

Second, some math:

1,000 to 2,000 additional HCWs are needed immediately, as in, on this very day. This number could be reasonably be acheived if it was made a priority.

If additional HCWs are delayed until mid-November, 10,000 to 20,000 HCWs will be required. Although technically possible, it is unlikely that this number could be mobilised.

If additional HCWs are delayed until January, 100,000 – 200,000 will be needed. This number almost certainly will not be acheived.


Plans to plan, plans to meet to plan, speeches about plannning, speeches about potential deployments, promises to deploy at some point in the future are all equally useless. Either HCWs deploy within the next few weeks or Africa is doomed. Plan B will be to let the virus burn through the continent and attempt to limit it to there while more developed countries develop vaccine for their own populations.

That is all.

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.