Rhiza Labs FluTracker Forum

NS sequences of Pennsylvania/40/2010, Wisconsin/12/2010, Minnesota/11/2010 are IDENTICAL.

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In summary, A/Pennsylvania/40/2010 (PA/40) and A/Wisconsin/12/2010 (WI/12) are virrually identical across all 8 gene segments. WI/12 is from a 10 month old male and would have been one of the patients in the original pager alert (described as a 7 month old child from Illinois). The patient developed symptoms on September 8, 2010. The second patient described in the alert was from Pennsylvania. The release of sequences somehat similar to the pager alter was delayed and sequences from an adult male in Pennsylvania, A/Pennsylvania/14/2010 (PA/14) was released along with earlier trH3N2's and PA/14 was similar but distinct from WI/12. Several months later a second Pennsylvania case was announced. sequences were not released and the announcement was delayed because virus couldn't be isolated (but they didn't say they had exhauted the sample and didn't say that virus wasn't isolated, only that an announcement had been delayed. The second case was not described, but disease onset was 2 days prior to WI/12.

Today, as second sequence from PA from a 3M and collected on Sept 13 was released. the collection date is consistant with the prior announcment on the case with a sideason onset date of September 6, strongly suggesting that PA/40 was that case.

Thus, two sequences that were virtually identical across all gene segments were collected from two patients (10 month old male and 3 year old female) in Wisconsin and Pennsylvania, consistant with the locations descibed in the pager alert, but the sequences from the index case were released without notice or labeling on a Sunday, 7 months after the fact.

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The PA/40 sequence relased today (SUNDAY) by the CDC at GISAID was a direct sequence of the sample (no virus was isolated) and the sequence matched WI/12 across all 8 gene segments (patients developed symptoms two days apart in Pennsylvania and Wisconsin), a markedly different result than anoounced last year when WI/12 was relased with PA/14 (developed symptoms 6 weeks after WI/12) and the lack of a match was noted by the CDC.

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Earlier CDC comments on the Pennsylvania stand in (another patient who developed symptoms 6 weeks after the original Pennsylvania case) CDC comments are 2 months after the fact:

http://www.recombinomics.com/News/11121 ... e_CDC.html

CDC Comments On Swine H3N2 Cases In United States
Recombinomics Commentary 21:07
November 12, 2010


Two cases of human infection with a novel influenza A virus were reported: one case by the Wisconsin Department of Health Services and one case by the Pennsylvania Department of Health. Both patients were infected with a swine origin influenza A (H3N2) virus similar to the three other swine origin influenza A (H3N2) viruses previously identified in 2009 and 2010. The Wisconsin case reported contact with pigs in the week preceding symptom onset on September 8, 2010 and required hospitalization. No contact with pigs has been identified in the Pennsylvania case in the week before symptom onset on October 24, 2010; however the case lives in an area close to pig farms. Both patients have fully recovered from their illness. The cases are not related and the viruses from these two cases have some genetic differences, indicating that they did not come from the same source.

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Pager alert describing Pennsylvania stand in:

H3N2 Triple Reassortants in Pennsylvania and Illinois Patients
Recombinomics Commentary 21:40
November 10, 2010

http://www.recombinomics.com/News/11101 ... PA_IL.html
"We have received disturbing information on the WHO alert system that the U.S. two people the virus H3N2: a seven-month child in Illinois and 46-year-old man in Pennsylvania, "- told Interfax Rospotrebnadzor head Gennady Onishchenko.

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Pennsylvania stand in was used to claim that Pennsylvania and Wisconsin patients (who really developed symptoms two days apart) did not match (when PA/40 and WI/12 are virtually identical across all eight gene segments).

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Quick timeline.

Sept 6 - 3 year old female in Pennsylvania develops flu symptoms

Sept 8 - 10 month old male in Wisconsin develops flu symptoms

Oct 24 - 46 year old male in Pennsylvania develops flu symptoms

Nov 9 - WHO issues pager alert on two trH3N2 cases in US

Nov 12 - WHO describes the Sept 8 and Oct 24 cases and says not related

Nov 18 - WHO releases sequences on Sept 8 and Oct 24 cases

Feb 5 - WHO announces Sept 6 case - delay and no sequences because no virus isolated

April 17 - WHO releases seqs from Sept 6 case on SUNDAY, unlabeled, with no comment

April 17 - Analysis of seqs from Sept 6 and Sept 8 cases shows virtual identity

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Commentary

http://www.recombinomics.com/News/04171 ... Match.html

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T462C and A47A tandem pedigree

EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI246023 A/swine/Minnesota/02948/2009 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI242925 A/equine (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242371 A/equine/Tokyo/1971 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242360 A/equine/New Market/1976 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242359 A/equine/Miami/1963 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242353 A/equine/Kascakew/1/1978 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242348 A/equine/Fontainebleau/1976 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242347 A/equine/Algiers/1972 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI242345 A/equi 2/Solvalla /79 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI240796 A/Sweden/SOL/79 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI240127 A/equine/Romania/1980 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI240105 A/equi 2/Aby/84 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI222910 A/swine/Minnesota/7931/2007 (A/H3N2) segment 4 (HA) 27.0 6.31083
EPI184611 A/psittacine/Italy/2873/2000 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI165401 A/equine/Sachiyama/1/1971 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI159280 A/equine/France/1/1967 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI159272 A/equine/Switzerland/2225/1979 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI156249 A/equine/Algiers/1/1972 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI156241 A/equine/Kentucky/2/1980 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI154026 A/equine/Uruguay/1/1963 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI154010 A/equine/Fontainbleu/1/1979 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI154002 A/equine/Sao Paulo/1/1969 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI153994 A/equine/Romania/1/1980 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI153986 A/equine/Switzerland/1118/1979 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI153914 A/equine/Sao Paulo/6/1963 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI133332 A/equine/New York/1/1983 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI133047 A/equine/California/83/1982 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI130345 A/equine/France/1/1976 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI129722 A/equine/Miami/1/1963 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI129720 A/equine/Uruguay/1/1963 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI80608 A/equine/NewMarket/D64/79 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77995 A/equine/New York/VR-297/1983 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77976 A/equine/California/103/1982 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77938 A/equine/Georgia/13/1981 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77919 A/equine/Georgia/10/1981 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77900 A/equine/Georgia/9/1981 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77881 A/equine/Georgia/3/1981 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77862 A/equine/Georgia/1/1981 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77805 A/equine/Miami/1/1963 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77748 A/equine/California/1/1980 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77729 A/equine/Kentucky/4/1980 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI77710 A/equine/Kentucky/1/1978 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI13281 A/pet bird/China/R7/04 (A/H3N8) segment 4 (HA) 27.0 6.31083
EPI13277 A/finch/China/R170/02 (A/H3N8) segment 4 (HA) 27.0 6.31083

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T447C
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI259504 A/swine/Minnesota/03008/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI246027 A/swine/Minnesota/02952/2009 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI246023 A/swine/Minnesota/02948/2009 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI244116 A/swine/Illinois/02940/2010 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI222910 A/swine/Minnesota/7931/2007 (A/H3N2) segment 4 (HA) 27.0 6.31238
EPI222674 A/swine/Oklahoma/008722/2007 (A/H3N2) segment 4 (HA) 27.0 6.31238

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