Tag Archives: R0

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).

References

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.

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H7N9 – R0 vs CFR

16 people have been reported infected with H7N9 in China thus far. 6 of them have died. This represents a case fatality rate (CFR) of almost 40%. This would place H7N9 among the most lethal diseases known to man. However, there have been rumors that there have been many more cases that have not been reported. If we suppose that many cases that have not resulted in death have not been reported then the CFR would be lower.

Most flu viruses have a CFR of less than 0.1%. If H7N9 was no more lethal than “regular” flu, there would have to be 6,000 unreported cases. There is no way so many cases could come from birds in such a short amount of time. Hence, if H7N9 is no more lethal than regular flu, the virus is already spreading human to human in a sustained way.

The Spanish flu of 1918 had a CFR of 2%. If H7N9 is as bad as the worst flu pandemic in human history, then there would already have to be 300 cases. Again, it is unlikely that so many cases could come entirely from birds in such a short period of time. At least some human to human spread would have to be occurring.

R0 describes the efficiency with which flu spreads. How many other people does each infected person infect? This number can be misleading because in the real world many people with flu do not infect anyone else but a few infect many, so-called superspreaders. One H7N9 superspreader in a Shanghai hotel or airport could seed the virus in people who will take it with them to cities around the world.

We don’t know how efficiently H7N9 is spreading in the human population or how lethal it is. However, we do know that either it is much more lethal than regular flu OR it is already spreading sustainably within the human population. Either way, efforts to contain it should be considered an international top priority.

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Contagion Review

[Warning, this review contains spoilers]

I recently saw the new movie “Contagion”, directed by Steven Soderbergh. Although I’ve enjoyed many of his films for their artistic merit, this review will focus on the movie from the standpoint of the accuracy of its science, as well as how it depicts the CDC, the World Health Organisation (WHO), the Department of Homeland Security and the blogosphere.

Briefly, the movie is about how ordinary people, scientists and public health officials respond to a new virus. It was apparently spread both by respiratory droplets dispersed by coughing and by touch (fomites). In addition to coughing, symptoms included bad headaches and seizures indicating that the virus could spread to the brain. The virus starts out with an R0 of 2 but this increases with time. The case fatality rate (CFR) is 20-25%. It’s not a flu virus, but the exact nature of the virus is not described. It apparently originated in bats, was transferred to pigs via a piece of fruit and then to humans at restaurant. It is said to have been based on Nipah virus.

The movie is relatively believable for this genre, partly because of the quality of the script and the acting. The cast includes Gwyneth Paltrow, Jude Law, Matt Damon, Laurence Fishburne, Kate Winslett and Eliot Gould. These are far superior actors to the B-list hacks found in other pandemic movies from recent years. The only false note was provided by Marion Cotillard as a WHO representative.

The quality of the science in the movie was mixed. A highly infectious virus with a CFR of 20-25% is certainly possible, especially if the carriers are asymptomatic but infectious in the early stages of the disease. They appeared to use real equipment in real labs for many of the scenes. One minor flaw was that it was stated that an attenuated virus would be used but one of the scientists was shown injecting herself. Killed viruses are usually injected. Attenuated viruses are usually given orally or nasally. Indeed, some people later in the movie were shown being given nasal sprays similar to Flumist. The most egregious science errors related to the rapidity with which the CDC was depicted sequencing the genome of the virus and characterising the proteins. Last year during the pH1N1 pandemic, it was revealed that the CDC was conducting PCRs one tube at time, by hand, even though they had bought expensive robots which could have greatly increased their throughput. Although the CDC has the budget to perform cutting edge science, they do not have the personnel for even basic tasks like high throughput PCR. De novo assembly of the genome of a novel virus requires a much higher level of expertise currently not available at the CDC. The recent outbreak of the new E coli strain demonstrated this. German and Chinese labs rapidly sequenced the bacteria and made the sequences public. A number of groups then rapidly assembled the genome. The CDC was not among these groups. Further, the depiction of rapid progress in determining the three dimensional structure and function of novel proteins is not realistic. Nucleotide sequencing can go fast, protein work takes much more time.

The depiction of the role of public health officials during this pandemic was mostly laudatory, but not very accurate. A CDC official played by Laurence Fishburne warns his fiancé to leave a city with a high level of infected people but not to tell anyone else of their danger. This is realistic as these sorts of private warnings have occurred before (see Nights of the Weak-Kneed – Past and Future for more). As mentioned above, the CDC scientists are depicted in the movie as performing miracles of discovery while the truth is that they struggle with basic methods. Mr. Soderbergh was likely snookered by convincing PowerPoints and a VIP tour of very elaborate equipment at the CDC. Some epidemic intelligence officers likely are brave and determined as portrayed by Kate Winslett. However, the extensive role of “Risk Communicators”, otherwise known as PR spin “doctors” at the CDC is not given much attention, although it is hinted at in one scene.

The least realistic, and frankly bizzare, subplot of the movie involved the WHO. We don’t see much going on at the WHO itself. Instead, we follow the strangely robotic Marion Cotillard to China to investigate the source of the virus. One of the Chinese scientists suggests that the WHO is in bed with the American drug companies. A strange line given that the WHO is currently run by Margaret Chan, an unqualified incompetent who owes her position to the Chinese Communist Party and billions of dollars in bribes to African countries. In any case, the WHO representative is kidnapped by Chinese scientists and held in a small village in an attempt to acquire vaccine from the WHO. Mr. Soderbergh obviously knows nothing of contemporary China if he thinks this is a serious possibility. Security forces would be blasting away at everyone in that village within hours of such a crazy scheme. The idea that the location of a kidnapped WHO representative could be kept secret from the central government for weeks to months is beyond silly. In any case, if there was such a virus on the loose now, the Chinese governement would get whatever it wanted from Margaret Chan whenever it wanted it. This was demonstrated during the pH1N1 pandemic when China got early access to the virus and was allowed to prepare a vaccine more quickly than other countries.

The depiction of the Department of Homeland Security (DHS) was brief. A DHS representative raises the possibility of a weaponised bird flu virus which was immediately shot down by the CDC official. This is realistic, imo. DHS is far more aware of the negative consequences of a pandemic than the CDC, imo, and much more willing to warn people to prepare. However, the CDC has apparently overruled them on this. In the movie, the DHS representatives are depicted as scary, unappealing guys. A pity, given their message in support of individual preparedness could save a lot of lives. I wish Mr. Soderbergh had taken their concerns more seriously and perhaps assigned one of his A list actors to portray a DHS official.

There was no mention of Flublogia or the preparedness community in general in the movie. Instead, the only blogger mentioned was a quack selling a fake cure to the disease caused by the virus. This character, portrayed by Jude Law, was obviously patterned on Mike Adams of NaturalNews, an anti-vaccine activist who pushes supplements of dubious effectiveness. Although I agree with the charterisation of the blogger in the movie as irresponsible and immoral, I am disappointed that Mr. Soderbergh decided to ignore the rest of the online community which follows and contributes to identifying outbreaks. The SARS cover-up in China was first reported on BOXUN, an anti-Communist ex-patriot website. I am aware of several instances where the online community of flu watchers made positive contributions to science and public health. Too bad that, once again, the mainstream media implies that the online community consists entirely of “those crazy internet people”. Maybe we need to make our own movie.

Commentators at PFI_Forum have characterised the portrayal of everyday events as a mild version of what the real thing would be like. I agree. Although overcrowded ERs, empty grocery shelves, home invasions, and movement restrictions are shown briefly, the full impact of a high CFR pandemic is not depicted. However, for all its faults, this movie might convince some that prepping is not a bad idea. Although I hate to say it, I think the the early scene where Gwyneth Paltrow dies was one that will affect many people the most. If Gwyneth can die from a virus, then surely no-one is safe!

Whatever works.

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