1. DoD Global, Laboratory-Based Influenza Surveillance Program USAF School of Aerospace Medicine Brooks City-Base, TX Victor MacIntosh, MD, MPH Lieutenant Colonel, USAF, MC Thomas Gibbons, PhD Major, USAF, BSC Alicia C. Guerrero, MPH Vaccines and Related Biological Products Advisory Committee Meeting February 18,2009 Naval Health Research Center San Diego, CA Patrick Blair, PhD, Commander, MSC, USN Chris Meyers, PhD Anthony Hawksworth Distribution Statement A: Approved for public release; distribution is unlimited. 311 HSW/PA No. 09-066, 17 Feb 09

2. Outline Introduction & history Overview of sentinel & population-based surveillance Description & highlights: epidemiology, laboratory, vaccination, molecular analysis Discussion

3. Origin of the program 1976 US Air Force begins influenza surveillance Aims: –Isolate and identify circulating influenza virus –Detect emerging variants –Evaluate effectiveness of vaccine

4. DoD laboratory-based influenza surveillance program Sentinel (etiology) based surveillance USAF School of Aerospace Medicine (USAFSAM)* Brooks City-Base, Texas Population based surveillance** Naval Health Research Center (NHRC) San Diego, California *Formerly the program was located in the Air Force Institute for Operational Health (AFIOH) **Recruits, Shipboard and Border Populations

5. Specimen collection Collection methods (USAFSAM) –Patient criteria: fever ≥ 100.5ºF and cough or sore throat (< 72 hr duration)  Case definition for Influenza-like Illness ->USAFSAM & sentinel sites – Collection kits are provided to sentinel sites Instructed to collect 6-10 specimens / week Preferred specimen is nasal wash – Surveillance questionnaire (e.g. vaccine, symptom and travel history)

6. DoD Global Influenza Surveillance.................IN ACTION

7. DoD-GEIS Epi Services Laboratory Funding & Guidance

8. DoD Global Influenza Surveillance.................IN ACTION DoD-GEIS Epi Services Laboratory Collect & ship Samples Participating Sites Supplies FedEx, etc, Support Funding & Guidance Program guidance, routine reports and notifications

9. DoD Global Influenza Surveillance.................IN ACTION DoD-GEIS Epi Services Laboratory Collect & ship Samples Supplies FedEx, etc, Support Funding & Guidance Flu Isolated Conventional/ Molecular Laboratory Methods Program guidance, routine reports and notifications Participating Sites

10. DoD-GEIS Epi Services Laboratory Collect & ship Samples Program guidance, routine reports and notifications Supplies FedEx, etc, Support Funding & Guidance Flu Isolated Conventional/ Molecular Laboratory Methods Selected Samples CDC Vaccine Decisions All Molecular Sequences DoD Global Influenza Surveillance.................IN ACTION Participating Sites

11. 2007-2008 & 2008-2009 Seasons Results by Week Collected 200720082009 2007- 08 season 2008- 09 season 2007-2008 6,751 Specimens Influenza30.9% Flu A72.7% H140% H360% Flu B 27.3% 2008-2009 2,155 Specimens ( 12 FEB) Influenza26.6% Flu A90% H156.3% H343.7% Flu B 10%

12. Comparison of seasons 2007-2008 (full seasonal year) & 2008-2009 2007-2008 Season  Specimens processed: 6,751  Countries: 20 For example: Antarctica Embassy sites in Asia (US Staff) Nepal  Ft. Gordon Cluster, Dec 2007 A/H1  Ellsworth AFB, vaccine strain contribution July 2007 A/H3 2008-2009 Season  Specimens processed: 2,155  Countries: 13 For example: Saipan Deployed sites: Kyrgyzstan, Kuwait, Iraq, Afghanistan  Guam early season B Yamagata  S. Korea Dec 2008 A/H3 from Osan AB, then A/H1 from Army hospital in Seoul

13. A Subtype & B Lineage Results by Week Collected (USAFSAM) CURRENT SEASON – ALL SITES 2008-2009 2,155 Specimens (10 FEB) Influenza551 Flu A488 H1278 H3210 Flu B 57

14. Influenza Subtype Results for Season 2008-2009 Across DoD Commands

15. Pacific Sites South Korea 2008-2009 307 Specimens Influenza144 Flu A134 H1119 H324 Flu B 0

16. Non DoD Beneficiaries Global, Lab-Based Influenza Surveillance Sites (USAFSAM) DoD Military-based Sites Developing Partners USACHPPM-SNMRC-DUSAMRU-KAFRIMSUSACHPPM-EUR NHRC

17. Vaccination Rates AF AD 95.8% ANG 92.0% AFR 84.0% All recruits are vaccinated – all services AD = Active Duty ANG = Air National Guard AFR = Air Force Reserve

18. Naval Health Research Center (NHRC), San Diego Influenza Surveillance among US Military Basic Trainees NHRC conducts population-based surveillance for febrile respiratory illness (FRI) at 8 US military basic training centers – FRI rates tabulated weekly – Specimens and clinical data are collected systematically from consenting trainees – PCR and viral culture testing for influenza A/B, adenovirus, etc. – Clinical data include vaccination status, type of vaccine, and vaccination date MCRD San Diego Frt Benning Fort Jackson MCRD Parris Island CGTC Cape May NRTC Great Lakes Fort Leonard Wood Lackland AFB

19. NHRC Influenza Surveillance, 2008-09 70 lab-confirmed influenza A cases Oct 08 – Jan 09 –67 (96%) A/H1 HA sequencing of A/H1 isolates from recruits shows they are similar to an A/H1 strain circulating in the U.S. that has 5 amino acid mutations from the current A/H1 vaccine strain –3 (4%) A/H3

20. Vaccine effectiveness calculation –Only considered periods when all trainees on base were vaccinated Majority of recruit vaccination Oct-Jan was LAIV, > 90% –Trainees assumed “covered by vaccination” 14 days after arrival/receiving the vaccine –Proportion “unvaccinated” at each site estimated as those within their first 14 days of arrival e.g., in 8-week training programs, 2/8 (25%) of the population was assumed to be “unvaccinated” at any given time –Previous estimates of 81-94% VE against lab-confirmed influenza using this method during past 5 seasons 2008-09 Results –62 lab-confirmed cases (all A/H1) in this analysis 26 cases among vaccinated, rate = 1.0/10,000 person-weeks 36 cases among unvaccinated, rate = 5.1/10,000 person-weeks –VE (A/H1) = 79% (95% CI, 66-87%) Other assumptions (7 days for coverage; 10% less vaccination) resulted in VE estimates of 83% and 66%, respectively –Vaccine appeared to be effective against A/H1 among U.S. military recruits NHRC Influenza Surveillance, 2008-09

21. Preliminary Vaccine Data USAFSAM 2,155 specimens; 551 (25.6%) influenza isolates 37.6% (207 of 551) identified vaccination status (quest avail) 62.3% (129 of 207) characterized as vaccinated 77.5% (n=100) LAIV; 22.5% (n=29) Injection Vaccinated (N=129)Un-Vaccinated (N=78) Influenza A% (n) A sub pending0.8% (1)1.3%(1) A/H181.4% (105)53.8% (42) A/H315.5% (20)23.0% (18) Influenza B% (n) B lineage pending2.3% (3)3.8% (3) B/Victoria00 B/Yamagata017.9% (14) % Distribution of Influenza Subtypes/Lineage by Vaccination Status (as of 07 Feb 2009)

22. Laboratory method Molecular analysis –Nucleic acid extraction –PCR analysis – A/H1, A/H3 and B –Sequencing of HA1 region for positive flu’s –Sequence analysis performed - data to CDC Tissue culture analysis –Influenza A, B, PIV 1,2,3, RSV, Adeno –All positive tissue culture archived for additional testing Archiving –Repeat or additional testing as requested by provider –CDC request for egg culture production and possible use as vaccine seed virus

23. Amino Acid Substitutions (x100) 0 6.8 246 A/Japan---1 A/Japan/717y/2009 A/Japan/718y/2009 A/Japan/723y/2009 A/Japan/719y/2009 A/Kw-4,J-2,H-1,Kr-32,Kn-1 A/Korea/468k/2009 A/Korea/489s/2009 A/Korea/967s/2009 A/New Jersey-1 A/Korea/219s/2009 A/Korea/490s/2009 A/Korea---1 A/Korea/482s/2009 A/Japan/670k/2009 A/Korea-2 A/Korea/469k/2009 A/Korea/491s/2009 A/Japan--1 A/Korea/250s/2009 A/Japan/721y/2009 A/Korea--1 A/Korea/218s/2009 A/Kuwait/689b/2009 A/Kuwait/553a/2009 A/Korea/593s/2009 A/Korea/397s/2009 A/Korea/972s/2009 A/Korea-----1 A/Korea/485s/2009 A/Saipan/907/2009 A/Korea/488s/2009 A/Korea/92s/2009 A/Japan-1 A/Japan/864k/2009 A/Korea/597s/2009 A/Korea/976s/2009 A/Korea/974s/2009 A/Korea-1 A/Korea-25 A/Korea/467k/2009 A/Korea/473k/2009 A/Korea/474k/2009 A/Korea/475k/2009 A/Korea/477s/2009 A/Korea/478s/2009 A/Korea/398s/2009 A/Korea------1 A/Hawaii--1 A/Kr----1,NJ--1 A/Washington/257m/2009 A/Alaska/710/2009 A/Texas/402w/2009 A/Texas/382w/2009 A/Texas/601w/2009 A/Texas-1 A/Texas/641w/2009 A/Texas/615w/2009 A/TX-5, Kw--4 A/Texas/385w/2009 A/Texas/622w/2009 A/Texas/437w/2009 A/Arkansas/505/2009 A/Texas/519r/2009 A/Illinois/589/2009 A/Texas/590s/2009 A/Texas/293r/2009 A/Illinois/925/2009 A/Kuwait-1 A/H-3,Nv-1 A/South Carolina/588b/2009 A/South Dakota/661/2009 A/South Carolina/715b/2009 A/New Jersey/944/2009 A/Texas/683w/2009 A/Texas/697w/2009 A/Texas/698w/2009 A/Oklahoma/938t/2009 A/Guam-1 A/Illinois-1 A/Texas/392w/2009 A/Germany/535/2009 A/Kuwait/552a/2009 A/Nevada--1 A/Kenya-6 A/California/669t/2009 A/Kenya--1 A/Kenya---1 A/Kenya----1 A/Kenya------1 A/Kenya-5 A/Kenya-----1 A/Honduras----1 A/Honduras---1 A/Brisbane/59/2007 A/Honduras-1 A/Honduras--1 A/Honduras-3 A/Solomon Islands/3/2006 A/New Caledonia/20/1999 A/Beijing/262/95 K162M E169G I184M S141N S141K G185A S141R G152E D272G L69S S257I G185V H192R N183S G185S I213V G185N A189T All annotated aa changes are comparisons of submitted specimens to A/Brisbane/59/2007 and do not relate to previous vaccine strains 2008 – 09 Vaccine strain Previous Vaccine strains January 09 (collection date) “_” Parallel Mutation Site Influenza A/H1 HA (HA1) Phylogenetic Analysis Overall amino acid sequence identity for the 184 specimens sequenced 98.1 – 100% 3 at 98.1% 88 at 99.1% or more 93 greater than 98.1% but less than 99.1% Parallel amino acid changes at 141 and 185

24. Overall amino acid sequence identity for the 118 specimens sequenced 97.9 – 99.4% 15 at 97.9% 73 at 99.1% or more 30 greater than 97.9% but less than 99.1% Parallel amino acid changes at 173 All annotated aa changes are comparisons of submitted specimens to A/Brisbane/10/2007 and do not relate to previous vaccine strains 2008 – 09 Vaccine strain Previous Vaccine strains January 09 (collection date) December 08 (collection date) ^ Create glycosylation motif & Loss of glycosylation motif “_” Parallel Mutation Site P194L K173E K158R K173Q K173E ^S45N L3F, I25L, T131N, R142G, K173N, K173Q V112I &N144S T48A I267V N278K Influenza A/H3 HA (HA1) Phylogenetic Analysis

25. 2008 – 09 Vaccine strain Previous Vaccine strains January Yamagata Lineage Victoria Lineage Overall amino acid sequence identity for the 35 B Yamagata lineage specimens sequenced to date 98.2 – 99.7%* Overall amino acid sequence identity for the 11 B Victoria lineage specimens sequenced to date 97.3 – 97.9%** Influenza B HA (HA1) Phylogenetic Analysis

26. A Ten Seasonal Year Review 1998-1999 through 2008-2009 Seasonal Year Specimen Result 1998-19991999-20002000-20012001-20022002-20032003-20042004-2005* 2005-20062007-20082008-2009 Negative 73%59%66%61%58% 63%59%42%45% Adenovirus 3%33%16%18%20%11%5%3%22%12% Enterovirus 0% 1% 2%1%0.5% Herpes Simplex Virus 2%1% 2%1% 2%1% ------- Influenza A 15%6% 14%8%25%26%16%23% Influenza B 5%1%7%3%8%2%3%8% 3% Parainfluenza 2%1% 2% 1%3%2%1% Respiratory Syncytial Virus 0% 1% 0% 0.4%1%3% Metapneumovirus ------- 0.2%0.5% TOTAL 3194693345614094435743112610448567512155 *2008-2009 data includes specimens collected from 28 Sept 2008 through 7 Feb 2009.

27. Acknowledgements Armed Forces Health Surveillance Center DoD-Global Emerging Infections Surveillance and Response System (GEIS) NHRC, USAFSAM Overseas Research Laboratories & Host Countries (AFRIMS, USAMRU-K & NMRCD-Lima) Military Health System –Landstuhl Regional Medical Center –Tripler Army Medical Center Medical & public health staff USACHPPM-S, USACHPPM-EUR Contact Us! influenza@brooks.af.mil (210) 536-3471 or DSN 240-3471 https://gumbo2.brooks.af.mil/pestilence/influenza/

28. Questions & Discussion

29. Backup Slides

30. Vaccine effectiveness calculation –Only considered periods when all trainees on base were vaccinated –Trainees assumed “covered by vaccination” 14 days after arrival/receiving the vaccine –Proportion “unvaccinated” at each site estimated as those within their first 14 days of arrival e.g., in 8-week training programs, 2/8 (25%) of the population was assumed to be “unvaccinated” at any given time –From Dec 08 – Jan 09, there were 319,002 person-weeks at the 6 centers included in the analyses Estimated 248,107 vaccinated and 70,895 unvaccinated Influenza rates (cases/10,000 person-weeks) were: –Vaccinated: 26/248,107 = 1.0 –Unvaccinated: 36/70,895 = 5.1 Results in a VE of 79% Backup slide - NHRC VE Calculation Methods

31. Interim VE estimates among patients with medically attended ILI illness, specimen was collected for USAFSAM testing Influenza typeFlu + (n=213)Flu (-) (n=402) Relative Risk Ratio VaxNot VaxVaxNot Vax All ILI patients5715661341 1.5 (48.3%/31.4%) Influenza A5713561362 1.8 (48.3%/27.2%) Influenza A/H14110877389 1.6 (34.7%/21.7%) Influenza A/H31526103471 2.4 (12.7%/5.2%) Preliminary Vaccine Data USAFSAM

32. Proposed VE Study – USAFSAM VE Case Control Study Period of Review –27 Sept 2008 – 07 Feb 2009 Population –Patient Medical Encounters – AF Clinics –Cases : lab confirmed influenza patients –Controls 1:4 match based on DMIS (clinic), date of encounter, and age group Selected from non-ILI visits –Excluded cases: deployed AD, BMTs, Lackland AD aged 18-19. Vaccination Status –Matched cases and controls against the AFCITA database. Questionnaire data not used.

33. Preliminary VE Analysis USAFSAM Among cases of lab confirmed influenza matched to non-ILI patient controls matched by age, base clinic visited and date of visit Influenza cases and controls by Vaccination status Influenza cases and controls by Vaccination with FluMist CasesControlsORCI Vaccinated (any vaccine type)601901.15(0.78, 1.67) Unvaccinated83301 CasesControlsORCI Flu Mist (vaccinated)481352.04(1.02, 4.1)* Not vaccinated w FluMist1269 *Statistically significant, p<0.05

34. Amino Acid Substitutions (x100) 0 5.2 24 A/Korea/7995s/2008 A/Korea/8072k/2008 A/Korea/7859o/2008 A/Korea/7858o/2008 A/Korea/7855o/2008 A/Korea/7854o/2008 A/Korea/7853o/2008 A/Korea/7851o/2008 A/Korea/7723o/2008 A/Korea/7722o/2008 A/Korea/7719o/2008 A/Korea/7714o/2008 A/Korea/248s/2009 A/Korea/115o/2008 A/Korea/60k/2008 A/Korea/90s/2009 A/Korea/93s/2009 A/Korea/330s/2009 A/Korea/487s/2009 A/Brisbane/10/2007 A/Wisconsin/67/2005 A/California/7/2004 A/Wyoming/03/2003 A/Panama/2007/1999 A/Sydney/5/1997 *15/19 previously vaccinated HA1 Phylogenetic Analysis South Korean Influenza A/H3 Specimens with completed vaccine questionnaires* All annotated aa changes are comparisons of submitted specimens to A/Brisbane/10/2007 and do not relate to previous vaccine strains HA1 Protein sequence identity = 97.9 – 99.4% 2008 – 09 Vaccine strain Previous Vaccine strains L3F I25L T131N R142G K158R K173Q P194L

35. Amino Acid Substitutions (x100) 0 4.6 24 A/Japan/7338x/2008 A/California/455t/2009 A/Guam/7178/2008 A/Japan/154y/2008 A/Guam/7124/2008 A/Alaska/464/2009 A/Guam/7261/2008 A/Kuwait/494aa/2009 A/Kuwait/291aa/2009 A/Guam/7396/2008 A/Guam/6981/2008 A/Guam/7054/2008 A/Kuwait/688b/2009 A/Brisbane/10/2007 A/Wisconsin/67/2005 A/California/7/2004 A/Wyoming/03/2003 A/Panama/2007/1999 A/Sydney/5/1997 HA1 Phylogenetic Analysis Non-South Korean Influenza A/H3 Specimens with completed vaccine questionnaires* All annotated aa changes are comparisons of submitted specimens to A/Brisbane/10/2007 and do not relate to previous vaccine strains HA1 Protein sequence identity = 99.1– 99.4% 2008 – 09 Vaccine strain Previous Vaccine strains *4/13 previously vaccinated

36. DoD authority/policy for global influenza surveillance MilestoneDescriptions 1992IOM Report Emerging Infections: Microbial Threats to Health in the United States 1 Scientific community identifies EID problem, factors favoring worsening of the problems and makes recommendations for action 1995 CISET Report Infectious Disease a Global Threat: Report of the National Science and Technology Council 2 US Government Executive Office CISET committee issues report prepared by the National Science and Technology Council on infectious disease global threat from emerging and re-emerging diseases 1996 Presidential Directive Presidential Decision Directive NSTC-7: Emerging Infections 3 The President issues Directive that says the US is not prepared for the threat from emerging infectious diseases and assigns roles and responsibilities to federal departments/agencies, including expanding the mission of DoD 1998 DoD Strategic Plan - GEIS Addressing Emerging Infectious Disease Threats: A Strategic Plan for the Department of Defense 4 DoD publishes its EID strategic plan that includes the establishment of the DoD-GEIS as a tri-service organization 1999DoD PolicyPolicy for DoD Global, Laboratory-Based Influenza Surveillance 5 Assistant Secretary of Defense for Health Affairs issues policy for global, laboratory-based, influenza surveillance and assigns executive agency to the Air Force 1 IOM. 1992. Emerging Infections: Microbial Threats to Health in the United States. Washington, DC: National Academy Press. 2 CISET (Committee on International Science, Engineering, and Technology). 1995. Infectious Disease a Global Threat: Report of the National Science and Technology Council. Working Group on Emerging and Re-emerging Infectious Disease. Washington, DC: Committee on International Science, Engineering, and Technology 3 NSTC (National Science and Technology Council, Executive Office of the President). 1996. Presidential Decision Directive NSTC-7: Emerging Infections. Washington, DC: National Science and Technology Council, Executive Office of the President. 4 DoD-GEIS (Department of Defense Global Emerging Infections Surveillance and Response System). 1998. Addressing Emerging Infectious Disease Threats: A Strategic Plan for the Department of Defense. Washington, DC: Walter Reed Army Institute of Research. 5 Bailey S. 1999. Policy for DoD Global, Laboratory-Based Influenza Surveillance. Memorandum for Surgeon General of the Army, Surgeon General of the Navy, Surgeon General of the Air Force, Deputy Director for Medical Readiness, J-4, the Joint Staff. U.S. Department of Defense, Health Affairs, Washington, DC, February 3, 1999.

37. Vignette:Ft Gordon Dec 2007 Vignette 1: Investigation of an Influenza A Outbreak at an Advanced Military Training Site, Ft. Gordon, GA An influenza outbreak occurred among active duty (n=28) and dependents (n=2) stationed at Fort. Gordon U.S. Army Garrison in Georgia in December of 2007. Fort Gordon houses several active duty units and includes training facilities for Advanced Individual Training in Signal Corp military occupational specialties, the Dwight D. Eisenhower Army Medical Center (EAMC) and is home to the Southeast Regional Medical Command. There are approximately 30,000 military and civilian employees on post. In January of 2008, the USAFSAM laboratory received 33 influenza A isolates for molecular characterization from Fort Gordon US Army Garrison in Georgia. Molecular analysis revealed that the Ft. Gordon strains were antigenically unique compared to other US strains previously sequenced by the USAFSAM laboratory. USAFSAM matched these record results with SADR data and results were forwarded to USACHPPM for a comprehensive follow up epidemiologic investigation. Thirty cases were contacted for interview via email and telephone and interviewed between April and May 2008. The active duty members averaged 19 yrs of age, with 67% (20) males and 33% females (10). The predominant symptoms among interviewed cases were fever >90% cough 88%, fatigue 88% and congestion 71%. A large majority of cases were hospitalized, 88% with an average of about 2 self reported bed days upon admission to Eisenhower Army Medical Clinic.

38. Vignette: Submission of Vaccine Strain Ellsworth AFB July 2007 Vignette 2: Submission of Vaccine Strain from Ellsworth AFB, SD The 2008-09 trivalent influenza vaccine contains an A/Brisbane/59/2007 (H1N1)-like virus, an A/Brisbane/10/2007 (H3N2)-like virus, and a B/Florida/4/2006-like virus. One of these strains, the Brisbane/59-like, was identified through the DoD Lab-Based, Global Influenza Surveillance Program at the USAF School of Aerospace Medicine (SAM) and served as the seed virus for the H1 component of the live, attenuated influenza virus (LAIV) vaccine (aka FluMist ® ). A prior Air Force member and current Army National Guard member and their beneficiaries were assigned to Ellsworth Air Force Base, South Dakota for their primary care. Four members of this family were seen at the base clinic in July 2007 presenting with influenza-like illness (i.e. fever, cough, sore throat). A travel history was noted, which may explain the presence of influenza illness in the northern hemisphere during non-influenza season. Specimens were collected and sent to the laboratory at USAFSAM, where they were processed through the standard procedures of viral culture and molecular characterization. Two of the patients were reported to have Influenza A by USAFSAM. Specimens underwent further molecular characterization at the USAFSAM laboratory, and were then sent to CDC for antigenic characterization. One of them was selected as a seed virus by MedImmune, Inc. for the LAIV. Although the strain was selected for the LAIV and not the traditional, injectable trivalent influenza vaccine (TIV), this contribution to the LAIV is still significant since use of the LAIV is on the rise in military populations.

39. Non DoD Beneficiaries Global, Lab-Based Influenza Surveillance Sites (USAFSAM) DoD Military-based Sites Developing Partners USACHPPM-SNMRC-DUSAMRU-KAFRIMSUSACHPPM-EUR NHRC