DoD Global, Laboratory-BasedInfluenza 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 MayNRTC 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 CultureInfluenza A, Influenza B, Adenovirus, Parainfluenza, Respiratory Syncytial Virus (RSV), and Enterovirus

- 100% of influenza isolates are subtyped and

sequenced

2007-2008 Season (as of 19 Feb 08)

Vaccine EffectivenessDescriptive 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 SurveillancePreliminary 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

0

4

8

12

16

20

45 46 49 50 51 52 1 2 3 4

Week Collected

A-type pending

A/H1

A/H3

B-type pending

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 SurveillancePreliminary Data

Vaccination Status of Confirmed Influenza Cases Among Military Basic Trainees, 2007-08

0

10

20

30

40

50

60

70

30 32 34 36 38 40 42 44 46 48 50 52 2 4 6 8 10 12 14 16 18 20

Week of Illness

Num

ber

of C

ases

0

10

20

30

40

50

Per

cen

t F

lu P

osit

ive

Flu A -Vaccinated

Flu A - Unvaccinated orVaccinated < 14 DaysFlu B -Vaccinated

Flu B - Unvaccinated orVaccinated < 14 DaysPercent Flu Positive

2007 2008

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

2007-2008 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, 2007-2008

Influenza B Field IsolatesHA1 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: 99.0-99.7 sequence identity

Nucleotide Substitutions (x100)0

6.8

246

B.Thailand.136.2007.seqB.Thailand.158.2007.seq

B.Thailand.5193.2007.seq.seqB.Thailand.4793.2007.seq

B.Thailand.4797.2007.seqB.Thailand.139.2007.seq

B.Thailand.191.2007.seqB.Thailand.137.2007.seqB.Thailand.5282.2007.seq

B.Thailand.189.2007.seqB.Thailand.4785.2007.seqB.Thailand.5285.seqB.Thailand.5190.2007.seqB.Thailand.130.2007.seqB.Thailand.94.2007.seqB.Kenya.5624.2007.seq

B.Nepal.116.2007.seqB.Nepal.5208.2007.seq

B.Thailand.4523.2007.seqB.Thailand.166.2007.seqB.Kenya.5616.2007.seqB.Kenya.5619.seqB.Kenya.5621.2007.seqB.Kenya.5620.2007.seqB.Thailand.87.2007.seqB.Thailand.89.2007.seq

B.Malaysia.2506.2004NH.seqB.South Carolina.771.2008.seqB.South Carolina.1297.2007.seq

B.Ohio.01.2005.seqB.Hong Kong.330.2001.seq

B.Nepal.170.2007.seqB.Nepal.173.2007.seqB.Nepal.223.2007.seqB.Nepal.1469.2007.seqB.Nepal.1481.2007.seqB.Nevada.1762.2007.seq

B.Arizona.730.2008.seqB.Nebraska.746.2008.seqB.Texas.728.2008.seq

B.Texas.701.2008.seqB.Thailand.258.2007.seq

B.Thailand.264.2007.seqB.Thailand.5187.2007.seq

B.Thailand.262.2007.seqB.Thailand.81.2007.seqB.Thailand.100.2007.seqB.Thailand.184.2007.seq

B.Philippines.1401.2007.seqB.Thailand.1511.2007.seq

B.Florida.4.2006.seqB.Antarctica.1183.2007.seq

B.Nepal.118.2007.seqB.Shanghai.361.2002.seq

Victoria Lineage

Yamagata Lineage2006-07 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

Nucleotide Substitutions (x100)0

3.1

2

A.Hawaii.6910.2007.seqA.Hawaii.6914.2007.seqA.Hawaii.6921.2007.seq

A.Nepal.197.seqA.Nepal.216.2007.seq

A.Nepal.4719.2007.seqA.Qatar.1123.2007.seq

A.Nepal.4304.2007.seqA.Nepal.4715.2007.seq

A.Nepal.4606.2007.seqA.Nepal.217.2007.seq

A.Alaska.1702.2007.seqA.Alaska.1704.2007.seq

A.Thailand.1439.2007.seqA.Nepal.202.2007.seq

A.Kenya.5623.2007.seqA.Thailand.1409.2007.seq

A.South Dakota.4344.2007.seqA.South Dakota.4345.2007.seq

A.Japan.335.2007.seqA.Philippines.5306.2007.seq

A.Thailand.1389.2007.seqA.Nepal.220.2007.seq

A.Hawaii.6915.2007.seqA.Saipan.526.2007.seq

A.Guam.6835.2007.seqA.Texas.6668.2007.seqA.Hawaii.6913.2007.seqA.Guam.6730.2007.seq

A.Guam.6495.2007.seqA.Guam.6716.2007.seq

A.Hawaii.6911.2007.seqA.Texas.6669.2007.seqA.South Korea.6612.2007.seq

A.Philippines.1408.2007.seqA.Philippines.1609.2007.seq

A.Philippines.1645.2007.seqA.Hawaii.6908.2007.seqA.Hawaii.5717.2007.seq

A.Hawaii.6909.2007.seqA.Hawaii.6917.2007.seqA.Hawaii.6918.2007.seqA.Hawaii.6919.2007.seqA.Hawaii.6922.2007.seqA.Hawaii.6926.2007.seqA.Hawaii.6927.2007.seq

A.Solomon Islands.3.2006ref.seqA.Honduras.597.2007.seq

A.Honduras.3869.2007.seqA.Honduras.5567.2007.seq

A.Honduras.643.2007.seqA.Honduras.5564.2007.seq

A.New Caledonia.20.1999.seq

Influenza A (H1N1) Field IsolatesHA1 HA Phylogenetic Analysis

Cla

de 2

2006-07 vaccine strain

2007-08 vaccine strain

Cla

de 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

D45NR192KE276K

R149KT197K

S46N, I56K, K90R, R192M, A193T

A193T, G240R

F263L

Amino Acid Substitutions (x100)0

3.5

2

A_California_NHRC_04_2008(H1N1).seqA_Missouri_NHRC_01_2008(H1N1).seq

A_California_NHRC_33_2007(H1N1).seqA_Illinois_NHRC_33_2007(H1N1).seqA_Illinois_NHRC_35_2007(H1N1).seqA_Illinois_NHRC_36_2007(H1N1).seqA_Illinois_NHRC_37_2007(H1N1).seqA_Illinois_NHRC_38_2007(H1N1).seqA_Illinois_NHRC_39_2007(H1N1).seqA_Illinois_NHRC_40_2007(H1N1).seqA_Illinois_NHRC_41_2007(H1N1).seqA_Illinois_NHRC_42_2007(H1N1).seqA_Illinois_NHRC_45_2007(H1N1).seqA_Illinois_NHRC_52_2007(H1N1).seqA_Missouri_NHRC_02_2008(H1N1).seqA_Missouri_NHRC_03_2008(H1N1).seqA_Missouri_NHRC_04_2008(H1N1).seqA_Missouri_NHRC_05_2008(H1N1).seqA_Illinois_NHRC_51_2007(H1N1).seqA_Illinois_NHRC_50_2007(H1N1).seqA_Illinois_NHRC_46_2007(H1N1).seqA_Illinois_NHRC_44_2007(H1N1).seqA_Illinois_NHRC_43_2007(H1N1).seq

A_South Carolina_NHRC_15_2008(H1N1).seqA_Texas_NHRC_11_2007(H1N1).seq

SolomonIslands_Vaccine.proA_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

2006-07 vaccine strain2007-08 vaccine strain

Population: US military recruits and BorderInfectious Disease Surveillance (BIDS)

Timeframe: July 2007 to present

Location: US

Nucleotide Substitutions (x100)

0

3.9

2

A.South Carolina.79.2007.seqA.Texas.138.2007.seq

A.Alabama.700.2008.seqA.Colorado.608.2008.seqA.Illinois.498.2008.seqA.Nebraska.595.2008.seqA.Nevada.1963.2007.seqA.Oklahoma.555.2008.seqA.Texas.281.2008.seqA.Virginia.547.2008.seq

A.Oklahoma.556.2008.seqA.Philippines.1436.2007.seq

A.Philippines.1535.2007.seqA.Philipines.5315.2007.seqA.Philippines.1429.2007.seq

A.Thailand.291.2007.seqA.Alabama.618.2008.seq

A.Maryland.416.2008.seqA.Arkansas.414.2008.seqA.Texas.136.2007.seq

A.Arkansas.417.2008.seqA.Maryland.238.2007.seq

A.North Carolina.500.2008.seqA.Oklahoma.502.2008.seqA.Illinois.198.2007.seq

A.Washington.616.2008.seqA.Alaska.486.2008.seq

A.Nevada.1962.2007.seqA.Texas.1308.2007.seqA.Texas.1322.2007.seq

A.Lousiana.386.2008.seqA.Lousiana.558.2008.seq

A.South Carolina.247.2007.seqA.Texas.5910.2007.seq

A.North Carolina.271.2008.seqA.Honduras.1038.2007.seq

A.Honduras.5566.2007.seqA.Thailand.82.2007.seq

A.Thailand.1391.2007.seqA.Thailand.95.2007.seqA.Thailand.271.2007.seqA.Maryland.505.2008.seq

A.Kenya.5622.2007.seqA.Hawaii.5718.2007.seqA.Nepal.207.2007.seq

A.Honduras.6374.2007.seqA.Brisbane.10.2007.seq

A.Honduras.601.2007.seqA.Honduras.6337.2007.seq

A.Honduras.6253.2007.seqA.Honduras.5559.2007.seq

A.Kenya.5618.2007.seqA.Philippines.5302.2007.seq

A.Philippines.5307.2007.seqA.Philippines.5305.2007.seq

A.Philippines.1486.2007.seqA.Philippines.5321.seq

A.Kenya.4100.2007.seqA.Kenya.5625.2007.seq

A.Thailand.1484.2007.seqA.Kenya.5617.2007.seq

A.Philippines.5326.2007.seqA.Philippines.5333.2007.seq

A.Wisconsin.67.2005.seqA.Kenya.5627.2007.seq

A.New York.55.2004.seqA.California.7.2004.seq

A.Fujian.411.2002.seqA.Panama.2007.99.seq

Influenza A (H3N2) Field IsolatesHA1 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 2007-8 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

N96KN7DG5R

I58V

K173E

L3F, K83N, L157S, K173N

R150K

K173Q

S199P

V20L

Amino Acid Substitutions (x100)0

2.3

2

A_Georgia_NHRC_24_2008(H3N2).seqA_South Carolina_NHRC_18_2008(H3N2).seq

A_South Carolina_NHRC_14_2008(H3N2).seqA_South Carolina_NHRC_09_2008(H3N2).seqA_South Carolina_NHRC_23_2008(H3N2).seqA_Georgia_NHRC_21_2008(H3N2).seq

A_Missouri_NHRC_13_2008(H3N2).seqA_South Carolina_NHRC_11_2008(H3N2).seqA_South Carolina_NHRC_01_2008(H3N2).seqA_Georgia_NHRC_17_2008(H3N2).seqA_South Carolina_NHRC_24_2008(H3N2).seq

A_Georgia_NHRC_23_2008(H3N2).seqA_Georgia_NHRC_25_2008(H3N2).seqA_South Carolina_NHRC_02_2008(H3N2).seq

A_California_NHRC_20_2008(H3N2).seqA_Georgia_NHRC_02_2008(H3N2).seqA_Georgia_NHRC_07_2008(H3N2).seqA_Georgia_NHRC_13_2008(H3N2).seqA_Georgia_NHRC_18_2008(H3N2).seqA_Oklahoma_NHRC_03_2008(H3N2).seqA_South Carolina_NHRC_07_2008(H3N2).seq

A_California_NHRC_03_2008(H3N2).seqA_California_NHRC_34_2007(H3N2).seq

A_California_NHRC_06_2008(H3N2).seqA_Oklahoma_NHRC_02_2008(H3N2).seq

A_California_NHRC_01_2008(H3N2).seqA_California_NHRC_35_2007(H3N2).seq

A_California_NHRC_07_2008(H3N2).seqA_California_NHRC_11_2008(H3N2).seq

A_California_NHRC_05_2008(H3N2).seqA_California_NHRC_02_2008(H3N2).seqA_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

Influenza@brooks.af.mil

Naval Health Research Center- Population-Based Surveillance

NHRC-FRI@med.navy.mil

BACKUP SLIDES

2007-2008 Season (as of 19 Feb 08)