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St.Francis

gsgs

gsgs

Registered User
On Sunday, 19.April 12 students of St.Francis,Prep.school,NY ,7 from one class,
returned from Cancun, they all felt well.
On Monday 20.April school reopened after easter holiday.
#Students reporting onset of symptoms on 8.April - 27.April:
1,5,4,2,2,2,3,4,3,3,3,4,8(20.Apr.),19,88,254,116,80,33,7,1
http://www.nyc.gov/html/doh/downloads/pdf/cd/h1n1_stfrancis_survey.pdf
So it started as early as 20.April, the day when the school opened.
Within 4 days 369 students (out of 2686) had symptoms.
~30% of sick students later reported that another household member had it too.

----------------------------------

starting on ~May 16, this virus spread all over New York infecting probably more
than a million people in 3 weeks.
http://www.nyc.gov/html/doh/images/cd/h1n1-hosp-adm-ed-large.jpg
but causing only ~1000 hospitalizations and 50 deaths.
~85% of the published sequences seem to be this Cancun-virus, while the
other 15% are from other introductions.



how could it be, that 12 people, all feeling well on April 19, going to school on April 20,
caused more than 300 infections until April 23 ?
Has such a thing been reported elsewhere ?


--I keep editing this---
 
Re: St.Francis

NYC is a big place. Don't you think it is possible that other infected travelers from Cancun arrived in New York during this same period?
 
Re: St.Francis

yes, and 15% of introductions are another substrain.
The Cancun virus was introduced independently at the same time
in some other places in USA.
But none compares with the explosive spread with hundreds of cases
within a few days at St.Francis.
And New York was hit hardest and earliest, i.e. the surroundings
of St.Francis (Queens, ?..link)
Other introductions often show mutations which can be recognized.

But it may well be that most uploaded sequences were from St.Francis
students and their contacts, thus falsifying the total picture.
---Indeed, only 2 sequences (out of 141 !) from New York since the real outbreak
started on May 15 : 3532(72y,16.May) and 3468(4y,17.May), both Cancun-strain
 
Re: St.Francis

gsgs said:
yes, and 15% of introductions are another substrain.
The Cancun virus was introduced independently at the same time
in some other places in USA.
But none compares with the explosive spread with hundreds of cases
within a few days at St.Francis.
And New York was hit hardest and earliest, i.e. the surroundings
of St.Francis (Queens, ?..link)
Other introductions often show mutations which can be recognized.

But it may well be that most uploaded sequences were from St.Francis
students and their contacts, thus falsifying the total picture.
Click to expand...
As has been noted many times in the past, a number of different agenies submit sequences, but there is considerable bias in the database. Only a small subset of sequences are full sequences, and selecting only the full sequences introduces more bias. For New York, many sequences are being generated under the influenza geneome project and they are pretty easy to see, because all have full sequences (and have detail, including age and gender, so it is pretty easy to see which sequences are from St Francis, since about 150 samples were collected over a two day period, and the patient are high school age).

Thus, the composition of the data is quite clear and it has limited diversity in general, and selecting a subset from the total introduces considerable bias, especially when full sequneces are generated by a small subset of labs.

Thus, the cause for the "falsified" data is rather clear (and has been clear for years).
 
Re: St.Francis

it's pretty useless to generate 78 full genomes from that St.Francis episode
and then only 2 or 3 from the real outbreak, which made ~99% of infections.
(>500000 estimated)

But several travelors from NY were sequenced too, and they all had the
Cancun-virus AFAIK.


Cancun virus outside New York:

Ankara/1/2009//
Athens/761/2009/05/26
Athens/793/2009/05/28
Athens/893/2009/06/09
Athens/918/2009/06/11
Athens/919/2009/06/11
Athens/920/2009/06/11
Athens/924/2009/06/12
Athens/926/2009/06/12
Athens/939/2009/06/12
Athens/940/2009/06/12
Athens/943/2009/06/12
Athens/948/2009/06/13
Athens/987/2009/06/15
Athens/996/2009/06/16
Bayern/63/2009//
CA/14/2009/04/25
Canada-AB/RV1532/2009//
Canada-ON/RV1527/2009/04/24
Canada-ON/RV1529/2009//
Catalonia/329/2009/06/03
Finland/553/2009/05/10
Fujian/1/2009/05/22
Fuzhou/01/2009/05/28
Georgia/01/2009/04/27
Guangdong/02/2009/05/27
Guangdong/05/2009/05/29
Italy/43/2009/06/03
Italy/44/2009//
Italy/45/2009/06/05
Italy/46/2009/06/05
Italy/47/2009/06/05
Italy/48/2009/06/05
Italy/49/2009/05/27
Italy/50/2009/06/08
Italy/60/2009//
Larisa/1001/2009/06/14
Larisa/1002/2009/06/14
Massachusetts/07/2009/04/26
Moscow/01/2009/05/21
Moscow/02/2009/05/26
Moscow/IIV03/2009/06/03
Nevada/03/2009/04/26
NY/3262/2009/04/27
Ohio/07/2009/04/24
Rio de Janeiro/290/2009/05/24
Rio de Janeiro/307/2009/05/27
Rio de Janeiro/332/2009/05/30
Shanghai/37T/2009/05/24
Shanghai/60T/2009/05/28
Shiga/3/2009//
Shizuoka/759/2009/06/02
Switzerland/01/2009/04/28
Toronto/3141/2009/04/
Toronto/3145/2009/04/
Toronto/3146/2009/04/
Yokohama/1/2009//
Zhejiang/1/2009/05/23
Zhejiang/2/2009/05/31
 
Re: St.Francis

gsgs said:
it's pretty useless to generate 78 full genomes from that St.Francis episode
and then only 2 or 3 from the real outbreak, which made ~99% of infections.
(>500000 estimated)
Click to expand...
I believe you have a serious misunderstanding how isolates are selected and what does and doesn't go in the database, which is rather glaring (and not new).
 
Re: St.Francis

if this makes you comfortable (and I know, it does !) then yes,
I may have a "serious misunderstanding how isolates are selected".
Or better I don't know much about the process.

My point is, that it doesn't make much sense. (does it ?)

BTW. no Qinghai genomes since years with hundredths in 2006,7.
How does it evolve ?
 
Re: St.Francis

gsgs said:
if this makes you comfortable (and I know, it does !) then yes,
I may have a "serious misunderstanding how isolates are selected".
Or better I don't know much about the process.

My point is, that it doesn't make much sense. (does it ?)

BTW. no Qinghai genomes since years with hundredths in 2006,7.
How does it evolve ?
Click to expand...
They don't evolve in the database!
 
Re: St.Francis

niman said:
I believe you have a serious misunderstanding how isolates are selected and what does and doesn't go in the database, which is rather glaring (and not new).
Click to expand...

There are many of us on the forum who are totally ignorant when it comes to how they are selected and what goes into the database.

Maybe you could enlighten us?
 
Re: St.Francis

J Infect Dis. 2010 Feb 26. [Epub ahead of print]

Household Transmission of 2009 Influenza A (H1N1) Virus after a School-Based Outbreak in New York City, April-May 2009.
France AM, Jackson M, Schrag S, Lynch M, Zimmerman C, Biggerstaff M, Hadler J.

Epidemic Intelligence Service, Office of Workforce and Career Development, and 2National Center For Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia; and 3New York City Department of Health and Mental Hygiene, New York, New York.

In April 2009, an outbreak due to infection with the 2009 pandemic influenza A (H1N1) virus (pH1N1) was investigated in a New York City high school. We surveyed household contacts of ill students to characterize the extent of transmission within households, identify contact groups at highest risk for illness, and assess the potential for preventing household transmission. Influenza-like illness (ILI) was reported by 79 of 702 household contacts (11.3% attack rate). Multivariate analysis showed that older age was protective: for each increasing year of age, the risk of ILI was reduced 5%. Additional protective factors included antiviral prophylaxis and having had a household discussion about influenza. Providing care for the index case patient and watching television with the index case patient were risk factors among parents and siblings, respectively. Fifty percent of cases occurred within 3 days of onset of illness in the student. These factors have implications for mitigating the impact of pH1N1 transmission.

PMID: 20187740 [PubMed - as supplied by publisher]


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