Karo cluster plus more cases?
I have been working on the correlating specific H5N1 sequences with the patients they were obtained from. I’m working on the Karo cluster from Indonesia now. I may have obtained some interesting results, but my interpretation depends on resolving some discrepancies between the ages of the victims as reported by the WHO in their situation updates and by the people who sequenced the virsuses.
I have found six sequences that clearly represent the same strain of H5N1. Based on WHO reports, I believe that four of them can definitely be assigned to the Karo cluster. Two of them are from patients with different ages than reported by the WHO. I believe that one of these sequences may actually be from the Karo cluster. The other may be from an 18 year old in East Java. If anyone has information correcting the ages of the 15 year old and 17 year old from the Karo cluster, please post on this thread. Thanks.
Links to WHO and sequence data below.
15 year old and 17 year old from the Karo cluster http://www.who.int/csr/don/2006_05_18b/en/index.html
18 year old from East Java http://www.who.int/csr/don/2006_05_29/en/index.html
I think the 17 year old from the Karo cluster may correspond to this sequence that was presumably taken from a 19 year old. http://tinyurl.com/y2qpxe
/strain=“A/Indonesia/CDC594/2006″ /serotype=“H5N1” /isolation_source=“gender:M; age:19; Pleural Fluid” /specific_host=“Human” /country=“Indonesia” /collection_date=“9-May-2006″
The link below will take you to a sequence collected from an 18 year old. The only 18 year old I can find with the right dates is the one from East Java.
http://tinyurl.com/y2y4m6 /strain=“A/Indonesia/CDC597/2006″ /serotype=“H5N1” /isolation_source=“gender:M; age:18; Throat Swab” /country=“Indonesia” /collection_date=“10-May-2006″
In layman terms, what does this mean?
Thanx in advance.
JWB,
If the sequence that is supposedly from an 18 year old came from the 18 year old in East Java, it would mean that the same strain of H5N1 spread human to human off of Sumatra, where the Karo cluster occurred, to another island in Indonesia. This would mean that we were very, very close to pandemic onset in May of 2006. It would mean that efficient human to human transmission has already been achieved. It was not sustained transmission, perhaps because of the tamiflu blanket or other interventions.
I should also point out that the seriousness of this possibility should’ve prompted the WHO and CDC to resolve the age discrepancy or else acknowledge that the Karo cluster strain spread to East Java, most likely by human to human spread. They are either very sloppy in their work, unable to do simple sequence analysis or deliberately neglecting to report a serious event. I am now trying to determine which of these three possibilities is true.
Monotreme, I’ll also post in the new place.
This is very interesting. Would you say that since the Karo cluster was H2H, the virus is now “organized” for lack of a better word, and that right now, all that is needed is the right situation, ie, someone going untreated, and traveling, ect.? Just trying to get a handle on this. Thanks for posting Monotreme.
Thanks DemFromCT and cottontop.
gs posted a timeline with corrected ages for the two boys over at PFI.
It looks like the boy that WHO says was 15 was actually 19 years old. The boy that the WHO said was 17 was actually 18 years old. So, all six of the sequences I have are probably from Karo. None would appear to be from East Java.
So, from my post at 15:00, it looks like option 1 was the answer. There is an uncorrected error in the WHO situation updates.
I knew I could count on our community solving this problem.
cottontop,
One woman infected 6 people. One of these 6 infected another person. I think it is possible that a pandemic strain already exists and only needs the proper environment to start a pandemic. There may be a number of “sparks” before there is enough “kindling” to start the fire.
I’ve long thought the same thing, Monotreme. The pot bubbles, and we wait while the heat rises beneath it. Some days I am reduced to hoping that there is ‘only’ one pandemic strain.
I came across this at CE, and thought it was a brilliant idea as the others did, As long as Monotreme is here, he can comment if he wishes. I think this is perhaps a viable solution to getting the message out about H5N1. http://www.curevents.com/vb/showthread.php?t=65785
cottontop,
Here is a related thread at PFI
Canada Sue gives me entirely too much credit. I know that the SoapBlox FW had a video on coughing and I’m sure others have had this idea as well.
In any case, the idea would be to offload server storage of instructional prepping videos onto YouTube and to have links from the flu sites. YouTube would serve as our central repository. People from different flu sites could contribute. Examples would include proper handwashing technique, how to put on a N-95, how set up a solar panel, battery and inverter, etc.
Monotreme- Oh I definately think it’s worth trying out. At this stage, we have gotten to the point of being desperate in getting this message out. People will not give folks the time of day, family members are ready to lock some of us up, and the frustration has reached it’s peak with alot of us, and we are left asking, “What can be done to get this out there?” If we are to truely take this into our hands, and forget about TPTB, I believe this could work. YouTube could be the instrument we have been looking for. And I agree that we do need the diversity of other flu sites. The flu community is like a huge town, with streets. I visit several, but post on two. Having read your first post earlier, I think the urgency, just got a little more urgent. I hope your prepping, not only for BF, but for whatever comes our way and throws a challenge at us. Thanks for your. time.
One woman infected 6 people. One of these 6 infected another person. I think it is possible wouldn’t it be good to merge the forums, so you needn’t post such things on 4 or more different forums ?
> that a pandemic strain already exists and
> only needs the proper environment to start
> a pandemic. There may be a number of
> “sparks” before there is enough “kindling”
> to start the fire.
we saw these clusters with other strains too. This particular Karo-strain is very rare and doesn’t happen elsewhere. It is a bird-strain, not a mamal-strain like most other human viruses in Indonesia. And there is much more H5N1 in China with many other strains , probably unreported human cases and clusters, but no pandemic yet.
>One woman infected 6 people. One of these 6
>infected another person
they earlier said, the sequences would prove this, but apparantly the sequences were “corrected” and now they don’t. They could all have got it from the same non-human source. Not so likely IMO but possible.
.