usafsam epidemiology laboratory service distribution statement a: approved for public release;...
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USAFSAMEpidemiology
Laboratory Service
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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USAFSAM “EPI Lab”
SSgt Anthony Lowman
SSgt Rhonda Sullivan
Lucinda Sinclair
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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USAFSAM “EPI Lab”
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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MOLECULAR/VIROLOGY
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USAFSAM/ PHE Molecular and Virology Department work hand-in-hand
Flu A and Flu B Results Are CorrelatedActs as a checks and balances system
Increases result confidence
Viral Sample is Received Via Central Operations
1 aliquot goes to Molecular for testing
1 aliquot goes to Virology for testing
remaining aliquots are archived
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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SEASONAL INFLUENZA
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Seasonal Influenza (SI) virusesInfluenza A, Subtype H1
Influenza A, Subtype H3
Influenza B
SI Typically Peaks Jan-Feb09’ Molecular Lab-8700 samples
08’ Molecular Lab-12000 samples
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Nucleic Acid Extraction Nucleic Acid Extraction
Automated methods M48 (48 specimens)
MDX (96 specimens)
Manual methods QIAamp DNA Blood Mini Kit
RNAqueous-Micro Kit
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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TEST METHODS
X-TAG RESPIRATORY VIRAL PANEL (RVP)Luminex Platform
13 target real-time multiplex assay
11 viral targets, 1 run control, and 1 internal control
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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TRADITIONAL RT-PCR
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Traditional Polymerase Chain Reaction (PCR)
specific primer sets for specific targets
used for Flu B, Flu A (H1/H3), and Adenovirus 14
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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PROCESSING TIMES
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Automated extractions (sample prep to nucleic acid)
M48-approx. 4 hrs. for 48 samples
MDX-approx. 5 hrs. for 96 samples
Traditional PCR (sample prep. to results)
approx. 6 hrs for a full 96 well plate
Luminex X-Tag RVP (sample prep. to results)
approx. 9 hrs for a full 96 well plateDistribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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OPS TEMPO
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Molecular 2009 1st Quarter Personnel
6 contractors, 4 military, and 1 civilian
Sample # processed prior to H1N1 surge
Jan 09’-4500
Feb 09’-4200
Mar 09’-6000
Work Shifts (Peak)
Two 9 hr. shifts
0700-2100Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Enter -H1N1
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H1N1 hits, USAFSAM’s viral sample workload almost TRIPLES.
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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USAFSAM “EPI Lab”
Normal Virology Operations/ Pre-Surge Testing
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Respiratory Culture Workload
Virology H1N1 Surge Operations
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Normal Virology Ops/ Pre-Surge Testing
Receive 10-50 respiratory samples / dayMolecular pulls first Aliquot
Respiratory Sample Testing:Aliquot 3 cryo vials for specimen archiving
Inoculate:1 PMK Tube
1 A-5 Tube
1 PMK Shell Vial
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Normal Ops/ Pre-Surge Testing
Respiratory Sample Testing Cont…Work up Shell Vials on Day 2 (48 hrs)
Read Tubes for CPE average of 5 times
Positive Tubes/SV identify virus by DFA staining
Archive Isolates of Positive samples
Negative Tubes Day 10:
Perform Hemadsorption (HAd) for R/O
<2 yrs old – Resp. Pool DFA
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Respiratory Culture Workload
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0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
16,000
Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep
FY 09 FY 10
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Virology H1N1 Surge Ops
Dropped “Cadillac Method”Utilized frozen ready cells
Read tubes minimum of 3 times
HAd’s only on questionable tubes
Called Suppliers ASAP for overages
Augmented staff w/ techs from local areaTrained on “easy tasks” to free up Viro Techs
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Virology H1N1 Surge Ops
Combined Molecular aliquoting w/ Viro2 step hr process to a 1 step ½ hr process
Upped Saturday OpsReceived/Processed Saturday Samples
Asked WHMC to send courier
Reduced Isolate BacklogAssigned 2 new techs to manage Archiving/Freezer works
Utilized augmentees
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Virology H1N1 Surge Ops
BSL 2 + precautionsCDC requirement
BSL 2 hood w/ additional PPE
N95 respirator maskFit Test requirements
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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Virology Lessons Learned
Communication, Communication, Communication!
Logistics, Management, Public Health
Capable of higher Ops than projected300 VS. 200 Samples per day
Surge plan adequate/flexible
Training is key
Utilizing BSL2 Hood space
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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USAFSAM’S VIROLOGY LAB
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Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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2009 P H1N1 Surge Plan2009 P H1N1 Surge Plan
Can you spell…SET -UP
How it all started
Surge Strategy20082009
Lessons Learned
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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WHAT HAD HAPPEN’D WAS
16 & 17 Apr 09 – requests are winding downUnusual subtyping results …..Contact CDC
21 Apr 09CDC-have you heard about MexicoShip Tues…BTW we contacted TDHHS…Gee, thanks
22 Apr 09 - Emergency courier….aaaarrrrr!
Does Brooks have an air strip??25 Apr 09
Test 9 RAFB suspect specimens…Full MOPPRun’s done @ 10:30pm…COOL!; Sorta kinda need you to repeat, tonight….Not Cool!
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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WHAT ARE WE DOING???WHAT ARE WE DOING???
27 Apr 09 Did you hear….how’re YOU feeling
27 Apr – 1 May 09 All initial unsubtypables:Quarantine RepeatShipment….notify CDCLab Director/PHR250 specimens…1-7500….2 hr test…WHAT DO YOU WANT!!
All stressed out, and no one
to choke!
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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2008 SURGE PLAN, 200/DAY2008 SURGE PLAN, 200/DAY
Central OPs = 20
CustServiceTeam = 3
Virology Lab = 8
Mole = 11
Personnel from other sections are cross– trained
Suspend other testing
1 Inputs Viro/Mole
Continued focus
Virology Lab = 8
6 trained on 7500
New procedure & processes, cross-training not implemented
Good idea, but ….No need
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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NEW STRATEGY, 400/DAYNEW STRATEGY, 400/DAY
Testing:New Swine Flu assayOIC ordering from home, new lab assistant
Equipment:Easy Mag - get 2 more3 more 7500s coming
PersonnelTrainingSchedules
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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LIMITATIONSLIMITATIONS
Laboratory Footprint – Unidirectional FlowProcessing AreaExtraction Area/PCR Set-upMasterMix
Logistics/ Storage- specimens, suppliesWorking Conditions
Full MOPP – lose dexterity, scope of visionAmbient temps – too hot for full MOPP
TrainingDistribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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WHATEVER THE ROYAL COURT SAYS GOES!!
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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2009 P H1N1 SURGE PLAN2009 P H1N1 SURGE PLANIMPLEMENTEDIMPLEMENTED
Trained Augmentees-2- WHMC (JBAIDS trained)2- Advanced Tech Center (Mole experienced)Addtn’l Central OPs
Outsourced Specimen Processing-Managed by Immunology – Augmented by USAFSAM Chemistry Div
Commandeered lab space (Bacti)3 Easy Mags 2 hoods for extraction prep
Extended lab coverage – 15 crept up to 24hrStreamlined Testing – Dropped InfB
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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LESSONS LEARNEDLESSONS LEARNED
Trained Augmentees-
Next time start in-house (Maybe)
Outsourced Specimen Processing-
3-day training…slow down
Lab space (Bacti)
Great!! Could not have done it
Extended lab coverage – 15 crept up to 24hr
Better usage of augmentees
Streamlined Testing – Dropped InfB
Sooner
29 vs 45 specimens/plate...$400 kit/100 testsDistribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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SO, ARE YOU LOOKING FOR SO, ARE YOU LOOKING FOR YOUR SET-UPYOUR SET-UP
Trusted laboratorians/scientist to perform testing
Detected 2nd strain CDC used as reference
Trusted to roll-out DoD training program
Trusted specimens for annual vaccine production
SET -
UP
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10
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QUESTIONS?QUESTIONS?
Distribution Statement A: Approved for public release; distribution is unlimited. 311 ABG/PA No. 10-085, 16 Mar 10