Identical H5N1 Sequences from Unrelated Individuals -
Evidence of a Geographical Cluster. [Updated Feb 28, 2007]
[Update 2/28/2007. For the CDC response to the results presented here, see this blog:
Original blog follows].
I have been analyzing some of the sequences from the 2007 Indonesian outbreak. To my surprise, I have found that the sequences from all 8 genomic segments from a strain (A/Indonesia/CDC1047/2007) isolated from a nasal swab from the 26/27 year old woman from South Jakarta are completely identical to sequences from a strain from a throat swab from a 22 year old woman from Banten province (A/Indonesia/CDC1046T/2007). Interestingly, a second sample from the 26/27 year old woman, isolated from a suction tube wash, has a single SNP in the PB1 gene with respect to the nasal swab strain from the same patient. There were also three SNPs observed between the two samples from the 22 year old woman. Thus, the two patients were each infected with identical strains of H5N1 but also had new strains that had mutated. This is as clear a smoking gun of common exposure as you are ever going to get.
Amazingly, neither the WHO or the CDC has commented on this fact. If this is some kind of mistake (mislabeling or incorrect annotation) they should have announced this by now.
H5N1 may have graduated from H2H within families to H2H among unrelated individuals who have nothing in common other than youth and geographical proximity. If so, then a pandemic may be imminent. I hope that the CDC and the WHO grasp why it is important to clarify what is going on with these sequences very quickly.
The following information regarding the two cases was compiled from a variety of sources including GenBank, WHO situation updates and the detective work of many in Flublogia (hat-tip, Laidback Al, cactus, FrenchieGirl, Commonground, imersion, Theresa42 and the many others in Flublogia who contributed to this information)
Name: Ani Apriani (AA)
Sex: F
Age: 22
Location: Warung Mangga village, Pinang subdistrict, Tangerang City, Banten province
From Croftsblog "On Dec. 30 th, AA went to a wet market and bought chicken for the holiday Idi Adah as requested by her mother who lives nearby. A slaughterhouse for chickens is nearby as well as the city dump or a field which is used as a dump. Chicken, pidgeons are in the neighbourhood. Ducks were not seen but are said to be there."
From WHO update 2: "An initial investigation into the source of her exposure found reports of chicken deaths near her home in the days prior to symptom onset. "
Symptom onset: 1/6/2007 - local media reports (WHO onset date, 1/3/2007)
Hospital Admission Date: 1/11/2007
Hospital: Friendship Hospital, Jakarta East
Death: 1/12/2007
Name: Zulfa (Zuraini)
Sex: F
Age: 26 or 27
Location: Mampang, Southern Jakarta
Occupation: Physics teacher at a Senior High School
From WHO update 3: "Investigations into the source of her exposure found reports of bird deaths near her home in the days prior to symptom onset. "
Symptom onset: 1/6/2007
Hospital Admission Date: January 10 at Friendship Hospital
Hospital: First Jakarta Medical Centre in Mampang then Friendship Hospital, Jakarta East
Death: 1/12/2007
Estimates of the proximity of their residences range from 8-20 miles.
Tuesday, January 30, 2007