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**sharon sanders** · December 25, 2009, 09:29 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Thank you Al for this analysis and thank you to everyone who contributes to the collection of data here at FT.

**JJackson** · December 25, 2009, 09:02 PM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Thanks Al.

**Celvin11** · December 26, 2009, 01:45 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Quality posting

**Celvin11** · December 27, 2009, 09:02 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Some statistical data

From Egypt's Statistical bureau - Capmas

http://www.msrintranet.capmas.gov.eg/ows-img2/pdf/2-17.pdf

population (as of 1 January 2009) by governorate
area and density data - note: dots in columns for density seem misplaced by two digits

Only 7.83 % of Egypt's area is populated. That returns a density of 962 people per sq km

Density in Cairo is 24,264 per inhabited sq km and 40,957 in Giza !

**Twall** · January 1, 2010, 08:30 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Thanks, for your efforts.

**Vibrant62** · January 1, 2010, 08:54 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

I would add additional regions to this analaysis.

China, as H5N1 is endemic in multiple regions and mismatched poultry vaccines have produced many silent carriers of H5N1 in birds, both wild and domestic.

Nigeria, as again H5N1 is endemic in this region, and there is no way of knowing what the true H5N1 situation is there due to problems in monitoring. Again there is a high incidence of backyard poultry farming there. The absence of reported cases is not necessarily evdience of absence of human H5N1 infections, and I would suggest that it is quantitatively impossible to quantify risks here without data. All we can do is acknowledge that the problem exists.

India - large regions have endemic levels of H5N1 infection in birds, and again, unless people are wealthy, there is a limited chance that infections would be picked up in the slums, where background mortality rates are high. Again, we cannot be clear of the true extent of the problem here, and we can probably say the same for Bangladesh and Pakistan.

All these regions provide high levels of potential for a reassortment event. All have high levels of backyard poultry and all countries have extremely large populations living in areas of quite high population density.

In a nutshell, if H5N1 and H1N1 are sufficiently synergistic to reassort easily, then the odds of not encountering a viable hybrid offspring in the forseeable immediate future must be quite small as there are multiple opportunites each winter season, globally. Let us hope that this combination is one that is difficult, and that viable strains cannot and do not emerge.

**sharon sanders** · January 1, 2010, 09:18 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

I agree.

**Laidback Al** · January 2, 2010, 01:47 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Originally posted by Vibrant62 View Post

I would add additional regions to this analaysis.

China, as H5N1 is endemic in multiple regions and mismatched poultry vaccines have produced many silent carriers of H5N1 in birds, both wild and domestic.

Nigeria, as again H5N1 is endemic in this region, and there is no way of knowing what the true H5N1 situation is there due to problems in monitoring. Again there is a high incidence of backyard poultry farming there. The absence of reported cases is not necessarily evdience of absence of human H5N1 infections, and I would suggest that it is quantitatively impossible to quantify risks here without data. All we can do is acknowledge that the problem exists.

India - large regions have endemic levels of H5N1 infection in birds, and again, unless people are wealthy, there is a limited chance that infections would be picked up in the slums, where background mortality rates are high. Again, we cannot be clear of the true extent of the problem here, and we can probably say the same for Bangladesh and Pakistan.

All these regions provide high levels of potential for a reassortment event. All have high levels of backyard poultry and all countries have extremely large populations living in areas of quite high population density.

In a nutshell, if H5N1 and H1N1 are sufficiently synergistic to reassort easily, then the odds of not encountering a viable hybrid offspring in the forseeable immediate future must be quite small as there are multiple opportunites each winter season, globally. Let us hope that this combination is one that is difficult, and that viable strains cannot and do not emerge.

Vibrant62 is absolutely correct that there are many other regions and countries where H5N1 is now endemic among wild birds and domesticated poultry. There may be many unreported or unrecognized human H5N1 infections and deaths in these countries.

From a global health perspective it becomes an issue of local surveillance and reporting. Many countries simply lack the public health care infrastructure to adequately treat their citizens much less do they have the testing facilities and supplies necessary to distinguish different influenza strains. Also, there is ample historical evidence that some countries are less than forthcoming about timely reporting of infectious diseases within their borders even when they have strong surveillance capabilities.

Egypt is one of those countries where H5N1 is endemic, but it should be commended for its proactive approach. It has developed a functional influenza surveillance system, it has reported its human H5N1 infections to WHO in a timely manner, and it has made its H5N1 genetic sequences publicly available. By my count, genetic sequences from at least 69 of the 90 confirmed human H5N1 cases in Egypt have been released. Links to the most of the 2009 released sequences can be found here.

As noted by Vibrant62, an H1N1/H5N1 reassortment event could happened wherever these two viruses are cocirculating, not just in Egypt. But at least in Egypt, public health officials would recognize and understand the implications of such a potentially devastating influenza threat.

**Laidback Al** · January 8, 2010, 01:30 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Egypt: H1N1 Mortality Discussion ? Update January 7, 2009
<o:p> </o:p>
Post #1 above discusses 101 H1N1 deaths in <st1:country-region w:st="on"><st1:place w:st="on">Egypt</st1:place></st1:country-region> through December 23, 2009. During the past 15 days an additional 72 individuals have died in <st1:place w:st="on"><st1:country-region w:st="on">Egypt</st1:country-region></st1:place> (link). News releases from the Ministry of Health are no longer stating ?underlying conditions? and, noticeably, deaths of pregnant women are no longer identified, although a number of the women who died since December 23 are of child bearing age.
<o:p> </o:p>
The highest mortality rate is still among individuals in the 20-29 and 30-39 year old age groups (see graph and table). Females represent about 59% of the deaths, while males only represent about 41% (when the sex of the fatal cases is noted). Cairo Governorate still leads the country with at least 34 deaths. Ominously, the number of fatalities per week is continuing to increase with a potential of 50-60 deaths during Week 3 unless the number of infections and deaths start to decrease (see graph with trendline). The Egypt Ministry of Health has already estimated there will be 200 H1N1 deaths during the month of January (link).

**Vibrant62** · January 8, 2010, 03:34 AM

Re: An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

Thank you for your analysis Al.

It would be extremely helpful if data from laboratory H1N1/H5N1 reassortment experiments were made public to allow greater assessments of risks and probabilities of coinfections and reassortments. If the news is bad, it may prompt other regions to follow Egypt's lead and example to bolster prevention measures, and open the debate on a global scale about what measures should be taken internationally.

for example, there are pre-pandemic H5N1 vaccines. Should all persons who keep / work with poultry be more actively encouraged to have vaccines against both H1N1 and H5N1 strains, regardless of their location, and especially if there are grounds to suspect H5N1 is circulating within a natural environment?

Whilst there appears to be more active control measures in place in Asia and Egypt, perhaps regions of Europe could and maybe should be following such a strategy, as H5 outbreaks are still sporadically reported, most likely as a result of wild bird carriers coming into contact with domestic flocks.

There is a great deal more that could be done, if the risks are high - the trouble is that we dont have access to such data to make assessments.

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An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

An Analysis of the H1N1 Fatalities in Egypt and the Potential for H1N1/H5N1 Reassortment

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