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.


The return of H1N1

pH1N1 has been quiet the past few years. But now its back. And its killing people.

From KHOU, December 19, 2013

Health officials say there have been six confirmed deaths from H1N1 in the Houston area recently, KHOU 11 News confirmed Thursday afternoon. That includes the four deaths at Conroe Regional Medical Center.

At least 14 people have become critically ill in Harris, Montgomery and Jefferson counties, including the four patients at Conroe Regional Medical Center.

Although public health officials are saying that this is the same strain that caused the pandemic of 2008/2009, we won’t really know that until the sequences from Conroe Texas have been made publicly accessible. In the meantime, it would be wise not to assume that either previous exposure or vaccine status is protective. They may be. But I woudn’t bet my life on it.

Given demonstrated problems with detection of the virus and its ability to kill, public health authorities are recommending prescription of Tamiflu based on symptoms alone. This is a wise policy.

Thousands of unreported H7N9 flu cases in China

Recent news stories have highlighted a new “study” suggesting that the actual case fatality rate for H7N9 is lower than the apparent 30% rate. What most of these stories don’t mention is that to achieve these lower rates, the authors of the study must assume that there have been thousands of unreported H7N9 cases in China.

Here’s the math:

Case fatality rate = Deaths / Cases

The reported number of cases is 131.
The reported number of deaths is 39.

39/131 = 29.77%

The new “study” asserts that the case fatality rate is actually between 0.16% and 2.8%. They come to this conclusion by assuming there must be unreported cases. The news stories don’t say how many unreported cases are required to get these lower case fatality rates. I will.

For a case fatality rate of 2.8% we would have:

39/cases = .028
1/cases = .028/39
cases = 39/.028
cases = 1,393

For a case fatality rate of 0.16% we would have:

39/cases = .0016
1/cases = .0016/39
cases = 39/.0016
cases = 24,375

Is it believable that there have been tens of thousands of cases of H7N9 in China – all from contact with birds at poultry markets? This is patently ridiculous. A case fatality rate of 0.16% requires that there be over 24,000 cases which implies efficient human to human spread of H7N9.

A case fatality rate of 2.8% would be similar to the 1918 pandemic – one of the most lethal disease outbreaks in human history. To reduce the apparent case fatality rate to even this level, we must assume over 1,200 unreported cases. This number pushes the limits as to what is believable in terms of bird to human spread of the virus. More likely, there would have to be substantial human to human spread, perhaps limited by the currently unfavorable weather for influenza transmission.

One can make all the assumptions one wants about missing data. However, anyone who repeats these assumptions should do the math and report the implications of these assumptions.

note: I have just found a story that does mention the number of unreported cases:

From Fox News, June 23, 2013

“Human infections with avian influenza A H7N9 virus seem to be less serious than has been previously reported,” they wrote.

But many mild, unreported cases may have occurred — between 1,500 and 27,000 — said the study, urging “continued vigilance and sustained intensive control efforts”.

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.


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 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.


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.


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