DoD Global, Laboratory-Based Influenza Surveillance Program Sequence Analysis and Vaccine Effectiveness Overview Maj Thomas Gibbons, PhD, Virologist Chris Myers, PhD, Molecular Biologist Angela Owens, MPH, Epidemiologist Jason Garner, MS, Molecular Biologist Anthony Hawksworth, Epidemiologist

Background Seasonal Influenza Sentinel site surveillance - DoD military sites worldwide - Countries collaborating with DoD overseas research sites MCRD San Diego Frt Benning Fort Jackson MCRD Parris Island CGTC Cape May NRTC Great Lakes Fort Leonard Wood Lackland AFB Population-based surveillance -DoD recruit training sites (8) -Select Navy ships -Border Infectious Disease Surveillance (BIDS)

Background Collection Methods - Patients must have Fever ≥ 100.5ºF and cough or sore throat (for less than 72 hrs) - Specimen collection kits are provided to collect 6-10 specimens/week - Surveillance Questionnaire (vaccination, symptom, and travel history) Laboratory Methods - Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) Universal Influenza A and Influenza B - Viral Culture Influenza A, Influenza B, Adenovirus, Parainfluenza, Respiratory Syncytial Virus (RSV), and Enterovirus - 100% of influenza isolates are subtyped and sequenced

Season (as of 19 Feb 08)

Vaccine Effectiveness Descriptive Review – Preliminary Data Period of Review  30 Sept 2007 – 09 Feb 2008 (non-recruits)  01 Aug 2007 – 09 Feb 2008 (recruits) Population  US military recruits (population-based surveillance)  US Active Duty members (sentinel site surveillance)  DoD beneficiaries (sentinel site surveillance) Outcome  Laboratory-confirmed influenza Reverse Transcriptase polymerase chain reaction (RT-PCR) Viral culture Covered by Vaccination  Vaccination date >14 days prior to clinic visit date Patients with vaccination date prior to August classified as unvaccinated

Sentinel Site Surveillance Preliminary Data 2,570 specimens; 562 (21.9%) influenza isolates 36.1% (203 of 562) identified vaccination status 77.3% (157 of 203) identified as “covered by vaccine” 68.1% (n=107) LAIV; 30.0% (n=47), Injection, 1.9% (n=3) Not Specified Influenza Subtype - A-type pending: 31.8% (n=50) - A/H1: 39.5% (n=62) - A/H3: 24.2% (n=38) - B-type pending: 4.5% (n=7)

Population-Based Surveillance Preliminary Data 205 lab-confirmed influenza A cases Aug 07 – Feb 08  59 (29%) A/H1  74 (36%) A/H3  72 (35%) type pending (weeks 4 and 5)

Vaccine effectiveness calculation  Only consider periods when all trainees on base are 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  Previous estimates of 86-94% VE against lab-confirmed influenza using this method during past 4 seasons Results from Basic Trainees  102 lab-confirmed cases (40 H1, 61 H3, 1 type pending) in this analyses 34 cases among vaccinated, rate = 2.9/10,000 trainee-weeks 68 cases among unvaccinated, rate = 18.6/10,000 trainee-weeks  VE = 85% (95% CI, 77-90) Other assumptions (7 days for coverage; 10% less vaccination) resulted in VE estimates of 89% and 75%, respectively  VE by subtype VE (H1) = 54% Mostly Clade 2b strains VE (H3) = 92% Brisbane strain variants

Overall VE remains strong among basic trainees  On the low end of previous four years of VE estimates Reduced effectiveness against Influenza A/H1 subtype Population-Based Surveillance,

Influenza B Field Isolates HA1 HA Phylogenetic Analysis 78.0% (39 0f 50) isolates collected in Nepal, Thailand, & the Philippines 66.7% (4 of 6) isolates collected in 2008 within US are of the Yamagata lineage 58.0% (29 of 50) isolates belong to B/Victoria lineage: sequence identity Victoria Lineage Yamagata Lineage vaccine strain Current Reference Strain Population: US Active Duty, DoD beneficiaries, and non-D0D personnel Timeframe: July 2007 to present Location: US, Africa, Antarctica, Asia, & South Pacific

Influenza A (H1N1) Field Isolates HA1 HA Phylogenetic Analysis Clade vaccine strain vaccine strain Clade 1 Population: US Active Duty, DoD beneficiaries, and non- D0D personnel Timeframe: July 2007 to present Location: US, Africa, Middle East, Asia, & South Pacific 9.8% (5 of 51) isolates characterized as Clade 1 – all collected from Honduras Clade 2 isolates collected from US (Alaska, HI, SD, TX), Guam, Saipan, Philippines, South Korea, Nepal, Japan, Thailand, Qatar, Kenya Clade 2 subgroup highlighted by change at position 46 S46N T90R T90K R149K E276K T90K Y101H R212K K144E T269N Y256F

T90K, Y101H, V169A, N190D,R212K, K144E, W254R, T269N, H324P D45N R192K E276K R149K T197K S46N, I56K, K90R, R192M, A193T A193T, G240R F263L Amino Acid Substitutions (x100) A_California_NHRC_04_2008(H1N1).seq A_Missouri_NHRC_01_2008(H1N1).seq A_California_NHRC_33_2007(H1N1).seq A_Illinois_NHRC_33_2007(H1N1).seq A_Illinois_NHRC_35_2007(H1N1).seq A_Illinois_NHRC_36_2007(H1N1).seq A_Illinois_NHRC_37_2007(H1N1).seq A_Illinois_NHRC_38_2007(H1N1).seq A_Illinois_NHRC_39_2007(H1N1).seq A_Illinois_NHRC_40_2007(H1N1).seq A_Illinois_NHRC_41_2007(H1N1).seq A_Illinois_NHRC_42_2007(H1N1).seq A_Illinois_NHRC_45_2007(H1N1).seq A_Illinois_NHRC_52_2007(H1N1).seq A_Missouri_NHRC_02_2008(H1N1).seq A_Missouri_NHRC_03_2008(H1N1).seq A_Missouri_NHRC_04_2008(H1N1).seq A_Missouri_NHRC_05_2008(H1N1).seq A_Illinois_NHRC_51_2007(H1N1).seq A_Illinois_NHRC_50_2007(H1N1).seq A_Illinois_NHRC_46_2007(H1N1).seq A_Illinois_NHRC_44_2007(H1N1).seq A_Illinois_NHRC_43_2007(H1N1).seq A_South Carolina_NHRC_15_2008(H1N1).seq A_Texas_NHRC_11_2007(H1N1).seq SolomonIslands_Vaccine.pro A_NewCaledonia_20_1999(H1N1)official.pr Influenza A (H1N1) Field Isolates continued Clade 2 isolates collected from US (CA, IL, MO, SC, TX) Majority of isolates are Clade 2B vaccine strain vaccine strain Population: US military recruits and Border Infectious Disease Surveillance (BIDS) Timeframe: July 2007 to present Location: US

Influenza A (H3N2) Field Isolates HA1 HA Phylogenetic Analysis 85.3% (58 of 68) of representative H3N2 isolates possess changes G50E, D122N, K140I, I223V H3N2 isolates collected in 2008 within the US possess additional changes: L3F, K83N, L157S and K173N 14 overseas and domestic H3N2 isolates collected in 2007 of the season antigenically characterized by CDC as A/Brisbane/10/2007-like via HAI assays Population: US Active Duty, DoD beneficiaries, and non-D0D personnel in allied countries. Timeframe: July 2007 to present Location: US, Central America, Asia, Africa, & South Pacific G50E D122N K140 II223V R142G L3F K83N L157S K173N current vaccine strain N144D

All sequenced representative isolates possess changes G50E, D122N, K140I, and I223V All sequenced isolates collected in 2008 within the US possess additional changes: L3F, K83N, L157S and K173N All BIDS sequenced isolates have either N96K or E280K mutations G50E, D122N, K140I, H195Y, I223V E280K N96K N7D G5R I58V K173E L3F, K83N, L157S, K173N R150K K173Q S199P V20L Amino Acid Substitutions (x100) A_Georgia_NHRC_24_2008(H3N2).seq A_South Carolina_NHRC_18_2008(H3N2).seq A_South Carolina_NHRC_14_2008(H3N2).seq A_South Carolina_NHRC_09_2008(H3N2).seq A_South Carolina_NHRC_23_2008(H3N2).seq A_Georgia_NHRC_21_2008(H3N2).seq A_Missouri_NHRC_13_2008(H3N2).seq A_South Carolina_NHRC_11_2008(H3N2).seq A_South Carolina_NHRC_01_2008(H3N2).seq A_Georgia_NHRC_17_2008(H3N2).seq A_South Carolina_NHRC_24_2008(H3N2).seq A_Georgia_NHRC_23_2008(H3N2).seq A_Georgia_NHRC_25_2008(H3N2).seq A_South Carolina_NHRC_02_2008(H3N2).seq A_California_NHRC_20_2008(H3N2).seq A_Georgia_NHRC_02_2008(H3N2).seq A_Georgia_NHRC_07_2008(H3N2).seq A_Georgia_NHRC_13_2008(H3N2).seq A_Georgia_NHRC_18_2008(H3N2).seq A_Oklahoma_NHRC_03_2008(H3N2).seq A_South Carolina_NHRC_07_2008(H3N2).seq A_California_NHRC_03_2008(H3N2).seq A_California_NHRC_34_2007(H3N2).seq A_California_NHRC_06_2008(H3N2).seq A_Oklahoma_NHRC_02_2008(H3N2).seq A_California_NHRC_01_2008(H3N2).seq A_California_NHRC_35_2007(H3N2).seq A_California_NHRC_07_2008(H3N2).seq A_California_NHRC_11_2008(H3N2).seq A_California_NHRC_05_2008(H3N2).seq A_California_NHRC_02_2008(H3N2).seq A_California_NHRC_36_2007(H3N2).seq A_Wisconsin_67_2005(HA).pro Population: US military recruits and BIDS Timeframe: July 07 to present Location: US current vaccine strain Influenza A (H3N2) Field Isolates continued

Acknowledgements Global Emerging Infections Surveillance and Response System (GEIS) Centers for Health Promotion and Preventive Medicine (CHPPM) / Army Medical Surveillance Activity (AMSA) Air Force Clinical Informatics Branch Centers for Disease Control and Prevention (CDC) Landstuhl Regional Medical Center Sentinel sites in the DoD Global Influenza Surveillance Program

Contact Information Air Force Institute for Operational Health - Sentinel Site Surveillance Naval Health Research Center - Population-Based Surveillance

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Season (as of 19 Feb 08)