Immaculate Infection – Death from Dubai

The recent SARS2 (new SARS) infection of a French visitor to Dubai, which is part of the United Arab Emirates (UAE), is a bit of a mystery. Because government officials from the UAE claim that they have no cases of SARS2.

So how did the French visitor get infected? There are really only three possibilities:

1. Animal transmission. What are the odds that a French visitor was the only person in Dubai infected in this way? Slim to none, imo.

2. Targeted infection by an unknown evildoer. This is possible. And, despite its conspiracy-theory associations, an entirely legitimate speculation if there really are no other cases in Dubai.

3. There are many SARS2 cases in Dubai, but government officials are lying about them on orders from the Emir, a medieval tyrant with unlimited powers of life and death over everyone in Dubai. The motive would be economic. Dubai is a trade center and playground for the rich. If it got out that a virus as lethal as Ebola were spreading human to human in Dubai, the Emir’s income stream might be severely reduced.

The WHO isn’t recommending travel restrictions (it almost never does despite the danger of country to country spread). But people can think for themselves.

Dubai is dangerous. Go there at your own risk.

Two pandemics? SARS 2 and H7N9

There are currently two viruses with apparent pandemic potential circulating in the world today – SARS 2 (nCoV) and H7N9.

Although many details are being suppressed, SARS 2 appears to be spreading human to human:

From Gulf News, May 6, 2013

The 13 cases linked to one Saudi hospital suggest the spread of nCoV may have reached a dangerous new stage in which it is spreading from one human to another, rather than infecting humans from another source such as an infected animal, according to infectious disease experts.

The virus has spread quickly: 13 people were infected between April 14 and May 1, nearly half of the 30 total cases that have been reported to the World Health Organisation. Of those 30 cases, 18 have died, giving the disease a case fatality rate similar to that of the feared H5N1 avian flu.

[snip]

Two terse emails posted on Promed over the past few days by the Saudi government suggest the virus spread multiple times from one person to another.

“It has to be person to person — I can’t imagine any other way,” said Michael Osterholm, director of the Centre for Infectious Disease Research and Policy at the University of Minnesota.

“Animal contact doesn’t appear to play a role at all” in the latest cases, he said. Moreover, he said, the length of time between the dates of onset of disease in the 13 people-from April 14 to May 1 — suggests “multiple chains of transmission”.

From the Wall Street Journal, May 6, 2013

“People are sending messages, SMSs, saying, ‘stay home.’ That all the hospitals have the virus. All,” said one man, a cousin to one of the men who died and to two other men who have been sickened in the current outbreak and are still being treated.

The man confirmed an account from a hospital official in Hofuf that his three relatives had gone to three different hospitals in Eastern Province.

“The Ministry of Health just wants to close the books” by saying the latest outbreak is limited to one hospital, the man said, speaking on a Hofuf street lined with medical centers and pharmacies.

It is possible that the virus has infected a number of people in hospitals. This is primarily how the original SARS spread. If so, the virus can likely be contained with aggressive testing and infection control. However, if the virus is spreading easily in community settings, containment will be more difficult. We won’t know which of these possibilies to expect until the Saudi government stops hiding information.

There are now 129 reported infections and 31 deaths from H7N9 in China. The official story is that all of these cases are due to bird to human infection. This is almost certainly false because a number of clusters have been reported. Further, there are adaptive changes in the virus isolated in humans that have not been seen in birds. Release of all sequences from human cases would provide a better indication of what is going on in China, but this information has been suppressed by the government.

Both SARS 2 and H7N9 have the potential to cause pandemics. However, unless the relevant governments change their policy of data suppression, we may not know a pandemic has started until large numbers of cases have been observed in multiple countries.

And that is too late.

H7N9 case in Taiwan – Implications for a pandemic

The recent report of a businesman who traveled to China and came back with a severe case of H7N9 has implications for the probability of a pandemic. The population of Taiwan is only about 23 million. I don’t know how many people from Taiwan traveled to China last month, but lets say it was 200,000. Of these, at least one developed a life-threatening infection. The population of the area in China with reported infections is at least 200,000,000. If we apply a 1 in 200,000 incidence to this group we would expect 1,000 severe infections, an order of magnitude higher than those reported. Given the Chinese government’s past history of covering up SARS and H5N1 cases, a underreport by a 1,000 cases is all too possible.

The reported cases of 100+ are already straining the boundaries of what can be explained without assuming a pandemic has begun. A 1,000 cases would go right past that barrier. And I think there is a good chance that is exactly what has happened.

H7N9 sequencing in China – Where is BGI?

There have been some news stories recently suggesting that although the Chinese authorities are doing their best, they just don’t have the experience or resources to properly test or sequence the samples they have.

This is complete nonsense written by people with little or no knowledge of the state of Chinese biotechnology.

BGI, originally the Beijing Genomics Center, is perhaps the best funded sequencing center in the world. They have received billions of dollars from the Chinese government. With this money, they have bought massive numbers of Next Generation sequencers, some of the biggest computers in the world and hired an army of bioinformaticians. All to sequence and analyze DNA.

When a novel bacteria was killing people in Germany, they had sequenced the complete genome in three days. A viral genome is much smaller than a bacterial genome. They could sequence every single incoming clinical sample of H7N9 on a daily basis. Developing assays to test samples for the presence of H7N9 would be childs play for them. So why aren’t they?

Jun Wang, executive director of BGI, is not a shy man. I’m sure he would love to be publishing and analyzing all of the H7N9 sequences. But he’s not talking. Why not?

Don’t let anyone tell you China can’t do more testing or sequencing of H7N9 samples. They quite easily could. They are making a conscious decision not to.

Reference

Inside China’s Genome Factory, MIT Technology Review, February 11, 2013

The complete map of the Germany E coli O104 genome released. June 16, 2011.

How to stop a H9N7 pandemic – containment

Although officially all cases of H7N9 have resulted from bird to human contact, there are strong indications that this assertion is false:

1. There is no virological link between between birds and affected humans.
2. Mutations have been found in humans but not birds which indicate that the virus is adapting to a human host rather than an avian host.
3. The rapid spread of cases in China is consistent with human to human dissemination but not bird to human transmission.

At the least, the precautionary principle should be invoked given the available evidence and the apparent lethality of the virus. Insisting on a high bar before considering the possibility that this virus could cause a pandemic would be foolhardy.

Is it still possible to prevent a pandemic from starting? Maybe. Viruses vary in their infection efficiency. Models suggest that viruses with lower R0′s, say under 1.6, would be relatively easy to stop from causing pandemics. I am somewhat dubious of these models. But it does make sense to intervene at the earliest possible timepoint in viral spread. H7N9 may still be in the process of adapting to the human host. Hence, it may transmit at a slow rate now. However, once it is fully adapted, the spread may accelerate. The only way to prevent adaptation is to stop the spread among humans. With each passage from one human to another, selective pressures will force the virus to adapt more completely to humans increasing the efficiency with which it is spread.

What can be done? Increase surveillance: we need a massive effort to test large numbers of people wherever cases have been reported as soon as possible; Social distancing: closing schools, theaters, shopping centers and other venues where people meet; Tamiflu blanket: give this antiviral to all contacts of infected patients; Travel restrictions: limit travel from and to affected areas.

The Chinese government and its hand-picked Director of the WHO may hesitate to take these actions for fear of the economic costs. But the consequences of not acting now, when there may still be time, could be far higher.

Reference

Longini et al. 2005 Containing Pandemic Influenza at the Source. Science. 309: 1083-1087

H7N9 adaptation to humans – evidence for ongoing human to human transmission

From The University of Wisconsin-Madison News, April 12, 2013

A genetic analysis of the avian flu virus responsible for at least nine human deaths in China portrays a virus evolving to adapt to human cells, raising concern about its potential to spark a new global flu pandemic.

The collaborative study, conducted by a group led by Masato Tashiro of the Influenza Virus Research Center, National Institute of Infectious Diseases, and Yoshihiro Kawaoka of UW-Madison and the University of Tokyo, appears in the current edition (April 11, 2013) of the journal Eurosurveillance. The group examined the genetic sequences of H7N9 isolates from four of the pathogen’s human victims as well as samples derived from birds and the environs of a Shanghai market.

“The human isolates, but not the avian and environmental ones, have a protein mutation that allows for efficient growth in human cells and that also allows them to grow at a temperature that corresponds to the upper respiratory tract of humans, which is lower than you find in birds,” says Kawaoka, a leading expert on avian influenza.

[snip]

Although it is too early to predict its potential to cause a pandemic, signs that the virus is adapting to mammalian and, in particular, human hosts are unmistakable, says Kawaoka.

From CNN, April 12, 2013 [hat-tip, Pixie]

One concerning mutation, known as “Substitution Q226L,” was found in two of the first three victims. Past experiments have shown it to make viruses — including the H5N1 bird flu virus — more likely to infect ferrets, which are commonly used in flu research. The same mutation was also found in the viruses that caused the 1957 and 1968 flu pandemics.

A second mutation, known as “PB2 E627K,” was found in all three virus samples.

According to Dr. Ron Fouchier, a Dutch virologist, this mutation allows the virus to reproduce at much lower temperatures than a standard avian influenza virus. The change lets it grow in a human respiratory tract, which is cooler than the virus’ natural home: a bird’s gastrointestinal tract.

In mice, Fouchier said, the mutation makes the infection as much as 1,000 times more virulent.

A number of other mutations were found as well, including changes that are characteristic of viruses found in mammals.

“Known normal bird viruses have to adapt substantially to infect people, but not these,” said Fouchier, who said the changes are enough that he would no longer call the H7N9 strain “bird flu.”

For a virus to adapt to humans, such an adaptation must confer a selective advantage to the viruses tuned to infect humans rather than birds. The only way that I can see that happening is if the virus is being passaged from one human to the next. That would mean that the virus is likely already moving human to human. I would be interested if anyone can think of an alternative explanation for these results.

References

Eurosurveillance, Volume 18, Issue 15, 11 April 2013
Genetic analysis of novel avian A(H7N9) influenza viruses isolated from patients in China, February to April 2013
T Kageyama, S Fujisaki1, E Takashita, H Xu, S Yamada, Y Uchida, G Neumann, T Saito, Y Kawaoka, M Tashir

New England Journal of Medicine, April 11, 2013
Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus
Gao et al.

The Chinese military and flu as a biological weapon

In a speech alleged to have been written in 2005 by Chi Haotian, then Minster of Defense and vice-chairman of China’s Central Military Commission, he is reported as saying the following:

What kind of special means is there available for us to “clean up” America? Conventional weapons such as fighters, canons, missiles and battleships won’t do; neither will highly destructive weapons such as nuclear weapons. We are not as foolish as to want to perish together with America by using nuclear weapons, despite the fact that we have been exclaiming that we will have the Taiwan issue resolved at whatever cost. Only by using non-destructive weapons that can kill many people will we be able to reserve America for ourselves. There has been rapid development of modern biological technology, and new bio weapons have been invented one after another. Of course we have not been idle; in the past years we have seized the opportunity to master weapons of this kind. We are capable of achieving our purpose of “cleaning up” America all of a sudden.

You can read the whole speech here.

There has been no authoritative debunking or confirmation of the authenticity of this speech. In another blog, I gave my reasons for suggesting that it appears to be genuine.

One of the things that did bother me about the speech was the inclusion of pseudoscientifc nonsense and dumb conspiracy theories. Some examples:

According to the speech, the Chinese people have a special evolutionary history and are separate from all other humans. This is refuted by literally tons of genetic data. It is further claimed that China is benefiting from Israeli research on genetic weapons directed against Arabs. This is really stupid. Anyone who knows anything about the genetics of the Middle East knows that such a weapon would be impossible, even in theory. Finally, the old conspiracy theory that Bill Gates and other powerful businessmen want to decrease the world population is presented as fact. I have problems with some Microsoft products, but only a loon would think that Mr. Gates, who has given generously to many charities that save lives, wants to wipe out 80% of the world population.

Do members of the Chinese military and government really believe such nonsense or at least say they do?

The answer is yes.

From the Washington Post, April 9, 2013:

Colonel Dai Xu of the People’s Liberation Army wrote online that the new strain of bird flu hitting China, known as H7N9, is an American “bio-psychological weapon” meant to destabilize China. The rant, posted to Dai’s account on the Twitter-like service Weibo, had already been shared by more than 30,000 fellow users by the time that the South China Morning Post reported it on Monday. Dai now has a quarter million followers on Weibo, which is quite a platform.

In general, Chinese Web users appear to have rejected Dai’s argument. In response to the criticism, though, he’s only dug in. “It is common knowledge that a group of people in China have been injected with mental toxin by the U.S.,” he wrote at one point. “I will not retreat even half a step.” He urged Chinese officials to ignore the virus’s apparent spread and argued that the disastrous 2003 SARS outbreak was also an American plot.

The terms “bio-psychological weapon” and “mental toxin” have the same pseudoscientific flavor as the speech alleged to have been given by Chi Haotian. So too does the endorsement of a ridiculous conspiracy theory.

Given the alarming lethality and spread of H7N9, it is not surprising that the Chinese government would want to evade responsibility for the virus. But why allow, or more likely direct, a member of the Chinese military to spread such a silly rumor? We really don’t know what is the origin of H7N9. The involvement of the PLA in a cover story is concerning, especially in light of the speech by Chi Haotian.