1. Influenza Sentinel Site Surveillance Training Addis Ababa, Ethiopia: February, 2010 Council of State and Territorial Epidemiologists United States Centers for Disease Control and Prevention

2. Part 1: Background and Objectives

3. Outline Background Purpose of the Training Guiding Principles Objectives of sentinel surveillance Topics covered in the guidance

4. Global Burden of Respiratory Infections Influenza:  3 – 5 million cases of severe illness  250,000 – 500,000 deaths Lower Respiratory Infections:  Leading cause of death in low-income countries  3 rd leading cause worldwide

5. Need for Improved Surveillance Historically, influenza surveillance data collection:  Virologic data for vaccine selection  Limited epidemiologic data  Lacked international standards Remaining gaps in understanding:  Epidemiology, burden of disease  Social factors, clinical risk factors  Climatic factors

6. Global Surveillance for Influenza WHO Global Influenza Surveillance Network (GISN)  International, laboratory-based (NICs) surveillance network  Provides virus strain information to select seasonal vaccine National Influenza Centres (NICs)  Laboratories designated by national Ministries of Health and recognized by WHO to participate in GISN  131 NICs, in 102 countries (as of Feb. 4, 2010)

7. Pandemic H1N1 (2009) Timely virologic and epidemiologic monitoring at national level: o Track progression of pandemic o Track impact of pandemic o Convey an accurate perspective on severity and risk to population o Prioritize country-specific risk groups for intervention resources

8. Seasonal Influenza Preparedness Pandemic Monitoring Relatedness of Seasonal and Influenza Pandemic Preparedness

9. Surveillance Needs During a Pandemic Is the situation changing? o Total amount of ILI, proportion of outpatient ILI due to influenza o Laboratory data to look at proportion of subtypes circulating in the community o Systematic sampling of viruses by age How severe is the disease and is it changing? o SARI hospitalizations o Deaths (and ICU admissions) from sentinel hospitals o Clinical picture of hospitalized cases Is the virus changing? o Drug resistance, drift and shift from laboratories o Comparison of viruses from less and more severe cases

10. Why is Monitoring the Severity/Virulence of a Pandemic Important? Inform how aggressively we think about interventions, for example:  School closures  Stopping public gatherings  Vaccination priorities  Antivirals priorities Mitigation, gain time to procure vaccine

11. Role of Sentinel Surveillance in Broader Monitoring Systems Reporting of qualitative indicators Aggregate reporting of laboratory-confirmed cases Aggregate reporting of syndromes ILI/SARI/Mortality Embedded sentinel sites to efficiently monitor o Virus characteristics o Severity and change in severity o Risk factors for severe illness o Hospital impact

12. Routine Value of Sentinel Surveillance Routinely produce useful epidemiologic and virologic data o Identify priority groups for intervention (severe outcomes) o Accurately characterize circulating viruses o Monitor seasonality to prepare for influenza season o Compare provinces, countries and regions o Estimate burden of disease Establish standards for surveillance reporting, collection and analysis Provide a platform for the study of influenza and other respiratory pathogens

13. Guiding Principles: Short and Long Term Value Integration into national systems Standard case definitions for comparisons (ILI, SARI) Efficiently monitor pandemic severity, high risk groups, and impact Ongoing surveillance of influenza and other pathogens High quality data in limited amounts

14. Seasonal SurveillancePandemic Monitoring Virologic Objectives Monitoring changes in virus Monitor antiviral susceptibility Monitor known markers of virulence Strain surveillance, by age, for the development of new vaccines Strain surveillance, by severity, to assess virologic risk factors for severe disease Detect novel viruses Monitoring changes in virus Monitor antiviral susceptibility Monitor known markers of virulence Strain surveillance, by age, for the development of new vaccines Strain surveillance, by severity, to assess virologic risk factors for severe disease Detect novel viruses Epidemiologic Objectives Identify priority groups for intervention--risk factors for severe outcomes. Monitor the intensity of influenza season in relation to baselines Estimate burden of disease Monitor the timing/ seasonality of influenza to inform seasonal planning Provide a platform for surveillance that includes additional pathogens Identify priority groups for intervention--risk factors for severe outcomes. Monitor the intensity of influenza season in relation to baselines Estimate burden of disease Inform timely public risk communication messages Monitor treatment practices Support rapid investigations Be useful in the long term

15. Topics Covered in Training Toolkit to establish a few high quality sentinel IP/OP sites Criteria for selecting sentinel SARI and ILI sites Methods to avoid bias in the selection of cases for testing Epidemiologic data collection forms Procedures for laboratory specimens Report templates for weekly and annual data summaries Techniques for routine monitoring of the surveillance system Pandemic support functions

16. Part 2: Case Definitions

17. Goal of Pathogen-based Surveillance: Global Burden of Influenza Deaths Hospitalized SARI Cases Hospitalized SARI Cases Mild Disease, Not Medically-Attended Medically-Attended Outpatient Cases ILI Surveillance SARI Surveillance Pathogen-based surveillance Household Surveys/ Serum Surveys

18. SARI Surveillance Should be priority/minimum basic influenza surveillance for countries with limited resources Recommend adding this measure in countries with existing outpatient surveillance

19. SARI Case Definition > 5 Years Old Any person requiring hospitalization* and presenting with manifestations of acute lower respiratory infection with:  sudden onset of fever (> 38 ºC) and  cough or sore throat and  shortness of breath, or difficulty breathing with or without clinical or radiographic findings of pneumonia, or  any person who died of an unexplained respiratory illness. * hospitalization may not be a required in some sites (i.e. remote from hospitals). Time requirement for onset of illness may vary.

20. SARI Case Definition < 5 Years Old IMCI case definition for pneumonia: Any child aged 2 months to 5 years with cough or difficulty breathing and:  Breathing faster than 40 breaths / minute (ages 1 – 5 years)  Breathing faster than 50 breaths / minute (ages 2 – 12 months) *Note that infants less than 2 months of age with fast breathing of 60 breaths or more per minute should be referred for serious bacterial infection.

21. SARI Case Definition < 5 Years Old IMCI case definition for severe pneumonia: Any child aged 2 months to 5 years with cough or difficulty breathing and any of the following:  Unable to drink or breastfeed, or  Vomits everything, or  Convulsions, or  Lethargic or unconscious, or  Chest indrawing or stridor in a calm child

22. ILI Case Definition A person with: o sudden onset of fever >38°C, and o cough or sore throat in the absence of other diagnosis

23. ILISARI Strengths Less resource intensive as a case definition than SARI. Captures hospitalized component of influenza. Will capture cases with exacerbations of chronic conditions, not just those with pneumonia. Weaknesses Fever requirement may overlook persons without fever, such as elderly and immune-compromised. Not ideal if being used to monitor viral respiratory pathogens other than influenza. Will overlook those that do not present with fever. Will overlook those that do not seek care at a hospital. Fever requirement makes it more specific, less sensitive

24. Considerations When Using the SARI Case Definition Fever requirement: may exclude elderly and immunocompromised Option: do not include fever, or require a measured fever  May detect non-influenza viral pathogens  Will increase resource demands  Should record presence or absence of measured fever on the swab form for comparison to other countries  Ensure consistent application of case definitions across all sites

25. Experiences with SARI Surveillance Early data from Member States in 5 WHO regions suggests routine surveillance for SARI will…. …achieve virologic objectives of seasonal influenza surveillance (pct. positive similar to ILI during influenza season) …provide epidemiologic and virologic data on severe influenza infections …provide a basis for monitoring severe respiratory disease during a pandemic …serve as a platform for assessing burden of multiple viral respiratory pathogens

26. Prioritizing the Focus of the Surveillance System Simple Model Budget: Low, no existing surveillance Surveillance for: SARI as a minimum standard  Epidemiologic data collection (i.e., denominator data = total number of SARI or ILI seen)  Virologic testing  Small number of well-run sentinel sites preferred to large number of poorly-run sites.

27. Prioritizing the Focus of the Surveillance System Intermediate Model Budget: Medium Surveillance for: SARI and outpatient ILI  Virologic testing  Epidemiologic data collection (i.e. denominator data)

28. Prioritizing the Focus of the Surveillance System Advanced Model Budget: High Surveillance for: SARI and ILI surveillance  Virologic testing  Epidemiologic data collection (i.e. denominator data)  Multiple pathogens, possibly reduce fever requirement in inpatient setting as well

29. Part 3: Mechanics of Sentinel Surveillance

30. Outline Sentinel site selection Case sampling strategies Epidemiologic data collection and forms

31. Selection of Sentinel Sites

32. What is sentinel surveillance? One or more designated health care facilities that routinely collect epidemiologic information and laboratory specimens from patients presenting an illness consistent with a specified case definition The system provides an efficient way to obtain high-quality data on relatively common conditions from a manageable number of locations

33. Why Sentinel Surveillance? For monitoring/ identification of:  Identify target groups:  For antiviral use and timing  That might have greatest impact on transmission  Strains to include in vaccine  Appropriate management practices  Hospital staffing and procurement needs

34. Key Attributes of Sentinel Sites Efficient data collection High quality data Limited number of well-chosen sites “A few high quality data are better than a lot of bad data”

35. The Efficiency of Sentinel Sites Systematic testing of inpatient and outpatient (SARI and ILI) cases  Representation of viruses by age and severity  Efficient collection of demographic and epidemiologic data that is linked to virologic data  Can yield measures of disease burden  Valuable seasonally as well as in a pandemic  Can support efforts to monitor surge on hospitals

36. ILI Sentinel Surveillance SARI Sentinel Surveillance Strengths Not a “new” system that must be created in a pandemic. Can be used to monitor progression of pandemic when other testing shifts to focus on only severe cases. Can be compared to meaningful baselines in many places to provide a measure of the relative magnitude of ILI consultations as compared to previous seasons. Efficient way to monitor severity and clinical characteristics of severe cases, and their change over time Monitor the progression and impact of a pandemic by focusing on an important outcome with a standard case definition. Will inform understanding of viruses that cause severe disease Timely feedback of results to clinicians can inform treatment practices. Sentinel hospitals can be used to estimate burden of severe disease. Sentinel hospitals can be used to monitor the impact of a pandemic on health care resources. Weaknesses Does not capture severe illness, which is needed to inform priority groups for intervention Not an easy or highest priority entity to collect epidemiologic data on No viruses from severe cases Not ideal for monitoring if a pandemic is becoming worse. Baselines are less well established at this point in time. It is a change from traditional practices to initiate systematic testing in hospitalized setting Sentinel sites are limited in their ability to characterize geographic spread.

37. Ideal Characteristics of Sentinel Sites Feasibility  People that are motivated to run the system  Political willingness for a site to participate  Sufficient staffing and laboratory capacity to maintain sampling and testing during healthcare surge  Efficient data management and transmission capability

38. Ideal Characteristics of Sentinel Sites Patient representativeness  All ages  Wide range of medical conditions For SARI surveillance, general or community hospitals are preferable to specialty care hospitals For ILI surveillance, general outpatient clinics are often appropriate

39. Ideal Characteristics of Sentinel Sites Quantifiable population denominator o Facilitates estimates of burden of disease o Requires understanding of population served by the sentinel site Large referral hospitals may underestimate community incidence and require extra staff  Difficult to test a large proportion of all SARI cases identified  If calculating rates, may be difficult to assess the total population served by the surveillance site

40. Placement of Sentinel Sites Population representativeness  Ethnicity  Socioeconomics Climatic representativeness  Climate affects virus activity (transmission and viability in environment)

41. Example: Influenza Sentinel Site Selection in Cote d’Ivoire Selection originally based on locations with confirmed AI and high poultry density/activity Other considerations:  Health centers/hospitals that provide care to both adults and children  Availability of staff  Availability of a cold chain  Status of the health center/hospital; public, private, religious  Availability of financial and material resources for setting-up & monitoring

42. Example: SARI sentinel sites in South Africa, 2009 Chris Hani Baragwanath Agincort Edendale Example: SARI Sentinel Surveillance in South Africa, 2009

43. Example: Sentinel Site Selection in Ukraine

44. Integration into National Clinical Reporting Systems Ideally, sentinel sites could be integrated:  Adopt standard case definitions  Establish smaller number of sentinel sites within the broader universal reporting system  Assure high-quality data at these sites through more intensive training and oversight  Systematic laboratory testing only at sentinels  Broader clinical reporting provides valuable indicator of geographic spread within a country

45. Integration into National Clinical Reporting Systems ILI/SARI Case-based epi data collection, laboratory testing ILI/SARI Syndrome Reporting ILI/SARI Syndrome Reporting ILI/SARI Syndrome Reporting ILI/SARI Syndrome Reporting ILI/SARI Syndrome Reporting ILI/SARI Syndrome Reporting ILI/SARI Case-based epi data collection, laboratory testing ILI/SARI Case-based epi data collection, laboratory testing

46. Selection of SARI Cases It is preferable to collect data and specimens from all or most SARI cases from a few facilities rather than a small sample of SARI cases from multiple facilities  Logistically feasible  Less bias  If not possible, an unbiased sampling protocol should be established

47. Selection of ILI Cases Large number of cases at outpatient sentinel sites is likely Total number of ILI cases seen is very important to collect Collect specimens and case-based epidemiologic data from only a sample of ILI cases Select cases for laboratory testing in as unbiased a manner as logistically possible

48. Sampling Methods for Respiratory Specimen and Case- based Epidemiologic Data Collection Select all cases for testing Select every xth case for testing Select all cases on certain days of the week for testing Select the first x cases on a certain day of the week

49. Selecting All Cases For Testing Minimizes bias Requires the most resources May not be feasible in many settings More feasible for sentinel surveillance focused on hospitalized cases (SARI)

50. Selecting Every Xth Case For Testing Less likely to be biased than methods that only select cases on the same day or at the same time Fewer resources than sampling all cases Frequently used for hospital-based (SARI) surveillance

51. Selecting All Cases On Certain Days Of The Week For Testing Does introduces bias o Patient volume and mix is not the same every day of the week o Day(s) of the week should be alternated Reduces logistical challenges of transport to laboratory

52. Selecting the First X Cases On a Certain Day of the Week Can introduce bias by day-of-week or time-of-day Commonly used for ILI surveillance where General Practitioners (GP’s) require convenience sampling models Consider local health seeking behaviors Not desirable for burden estimation of for SARI surveillance

53. SARIILI FeasibilityDesirabilityFeasibilityDesirability Selecting all cases2313 Selecting every xth case3323 Selecting all cases on certain days of the week 31-222 Selecting the first x cases on certain days of the week 3132 1 = least feasible/desirable; 3 = most feasible/desirable

54. Epidemiologic Data Collection

55. Data Collection Tools Forms filled out by designated sentinel site staff At a minimum, collect data 4 weeks before and after typical peak months Assign each patient a unique identification number to link epidemiologic and laboratory data  Recorded on data collection form, swab forms, and laboratory specimen

56. Minimal Data Elements Unique identification number Patient demographics Minimal clinical information including relevant dates of onset and clinical symptoms Pre-existing medical conditions (for SARI only) Vaccine and antiviral use

57. Case-Based Data Collection Forms: SARI Swab Form For all SARI cases tested for influenza o Should be completed as soon as possible after identification Send one copy to laboratory with the specimen, one to the national surveillance centre, keep original at the sentinel site

59. Case-Based Data Collection Forms: Outpatient Swab Form For all ILI cases tested for influenza Complete as soon as possible after selection for laboratory testing Send one copy to laboratory with the specimen, one to the national surveillance centre, keep original at the sentinel site

61. SARI Weekly Aggregate Data Form ID number of sentinel site, and focal point New SARI cases during week New inpatients during week Number of SARI cases selected for influenza testing Number of SARI deaths during the week Ages: 0-4, 5-14, 15-29, 30-64, 65+, Total

62. SARI Weekly Aggregate Data Form

63. ILI Weekly Aggregate Data Form ID number of sentinel site, and focal point Day(s) of week surveillance was undertaken New ILI cases during week New outpatients during week Number of ILI cases selected for influenza testing Ages: 0-4, 5-14, 15-29, 30-64, 65+, Total

64. Unique Identification Numbers Important for linkage between laboratory and epidemiologic information Numbers should be standardized throughout the country Assigned when SARI or Outpatient Swab forms are filled out Same number used on any forms or specimens for each patient

65. Identification Number Example 001 / 09 / 1 / 0001 Sentinel Site Year SARI or ILI Case Number Example: 1 = SARI 2 = ILI

66. Part 4: Roles and Responsibilities Within the Sentinel Surveillance System

67. Sentinel Surveillance Structure Countries implementing a sentinel surveillance system should have: Sentinel sites with a designated focal point National surveillance centre that coordinates the epidemiologic data collection and analyses National Influenza Centre / laboratory that oversees virologic aspects of the surveillance system and laboratory quality WHO / Regional Offices Regional Surveillance Platform Countries Data Summary Reports WHO Global Platforms (FluNet and FLU-ID)

68. Sentinel Site Focal Point Adhere to case definitions Adhere to unbiased systematic sampling strategies Collect respiratory specimens Package, store, and transport specimens Assign unique ID number to specimens and forms All data forms are filled out completely and accurately Manage and transmit epidemiologic data Track daily number of SARI and ILI cases, and number selected for laboratory testing Assure timeliness of data reporting and specimen collection and transport Report SARI laboratory test results to the clinician Ensures that staff at the site carry out the following:

69. National Surveillance Centre Organizational entity assigned to coordinate influenza surveillance in a country Should have a national surveillance focal point who is responsible for implementation and coordination of the national influenza sentinel site surveillance system May be located in different agencies or institutes in different countries

70. National Surveillance Centre Focal Point Assist MOH with selection of sentinel sites Assist with decisions about ILI and SARI sampling and epidemiologic data collection Assure that sites have data collection forms and reporting mechanisms Assure that the data is analyzed correctly Disseminate the weekly and annual flu report Report data into the regional and global platforms Routinely monitor the sentinel surveillance system Responsibilities:

71. National Influenza Centre (NIC) Recognized by WHO Participates in regional influenza network and GISN An up-to-date list of NICS can be found at: http://www.who.int/csr/disease/influenza/centres/en/in dex.html

72. NIC Routine Responsibilities Provide technical support and guidance to sentinel sites Receive, register, and store specimens from SARI and ILI cases Perform analyses on seasonal viruses Perform subtyping of non-seasonal viruses, minimally  Influenza A(H5N1)  Pandemic influenza A(H1N1) 2009 Archive and store original specimens at least one year Share samples with WHO CCs Conduct antiviral susceptibility testing (where possible) Maintain linkage between site and laboratory ID numbers

73. NIC Responsibilities: Data Analysis and Reporting Communicate results of confirmatory tests Consolidate and analyze national laboratory data Report weekly national surveillance data into regional and global surveillance platforms Develop national diagnostic standards and assays, provide training, and organize quality assurance programs (where possible)

74. Sentinel Sites INHP ( Epi Surv, MoH) DGS (Gen. Dir, MoH) IPCI (NIC) Partners: WHO, CDC, UNICEF… Sentinel Site Sentinel Site Example: Surveillance System Organization in Cote D’Ivoire CABINET (Minister)

75. Ukraine Georgia Sentinel site focal point submits data forms Regional surveillance coordinator enters data and verifies accuracy and completeness Regional laboratories test specimens NIC provides confirmatory testing and ensures functioning of the system Smaller population and geographic area Sentinel sites send samples and data forms to NIC within national public health agency National Center for Disease Control and Public Health monitors operation of the system Examples of Surveillance System Organization

76. Notification of Novel Influenza Viruses through the IHR Mechanism Immediate notification to WHO through the IHR mechanism: Human infection with influenza A other than seasonal subtypes  Any combination of H2, or H4-H16 with any of the N1-N9 subtypes  Includes avian influenza subtypes A(H5N1), A(H9N2), and A(H7N7) Human infections of Influenza A viruses that grow poorly in cell culture or react poorly with standard WHO reagents in HAI assays  May have same subtype as seasonal viruses, but be of animal origin (such as pandemic (H1N1) 2009)

77. Participating in WHO External Quality Assessment Project for the Detection of Influenza A Viruses by PCR To improve global laboratory capacity for influenza diagnosis To monitor quality and standards of performance of NICs around the world Requirements:  Laboratories test a panel of simulated H1, H3, H5 specimens twice per year  Each laboratory receives performance report

78. Part 5: Data Reports and Analysis

79. Outline Measures of Burden Weekly Reports Annual Reports Reporting Outside the Country/Publications

80. Measures of Burden Incidence rate o Number of influenza cases per 100,000 population per time unit o Allows for estimate of age-specific burden of disease o International standard for reporting o Incidence of influenza consultations also valuable to monitor seasonal intensity over time Proportion of SARI and ILI at sentinel sites that is caused by laboratory-confirmed influenza o Minimal standard

81. Example: The Netherlands General practitioners  Collect specimens and data from a random sample of persons meeting ILI case definition  Each maintains list of 2,500 patients, which can be used for denominator data Incidence rate  Calculated per 100,000 per week

82. Minimal Analyses and Reports Generate weekly, at least 4 weeks prior and following typical peak months Disseminate to all relevant governmental partners, sentinel sites, and the public Virologic surveillance conducted outside flu season may be reported less frequently

83. Weekly SARI Data During the previous week: Number of new cases at each sentinel site Number of total new hospital admissions at each sentinel site Number of SARI cases selected for influenza testing  % testing positive  By influenza type and subtype Number of inpatient deaths due to SARI Number of sentinel SARI sites reporting Results for all sites stratified by the age groups: 0-4, 5-14, 15-29, 30-64, 65+

84. Example: SARI Surveillance Weekly Report (South Africa) Report comes out weekly Posted on website: http://www.nicd.ac.za/ Includes graph and table portraying virological data  By epidemiological week  By sentinel site

85. Weekly Outpatient Data During the previous week: Number of new ILI cases reported Number of total outpatients seen at ILI sentinel site Number of ILI cases selected for influenza testing  Percent of tested ILI positive for influenza  By influenza type and subtype

86. Additional Data to Report If available, report:  Weekly consultation rates for ILI, or SARI  Antiviral resistance testing results http://www.cdc.gov/flu/weekly/ Data on geographical spread (map) Level of detail will depend on number and location of sentinel sites

87. Annual Analyses and Reports

88. Annual Analyses SARI, ILI, and confirmed influenza cases by age and month Underlying medical conditions of SARI patients Number and percent of positive influenza cases who received vaccination in the current season. Number and percent of positive influenza cases exposed to antivirals 14 days before onset of symptoms Incidence rates

89. All Analyses Optional Stratifications 0-4 years 5-14 years 15-64 years >65 years 0-12 months 15-29 30-64 >75 years Additional age categories that inform vaccination policy Standard Age Stratification

90. Assessment of Seasonality Establish the baseline rate of influenza in a region/ country Inform the timing of vaccination and treatment

91. Example: Using Data in the UK Yearly guidance issued to doctors about when antiviral agents should be prescribed Recommendations are based off of surveillance data and are triggered when: o GP consultation rates rise above 30 consultations per 100,000 population o Community-based influenza surveillance is above baseline

92. Reporting and Publication

93. Regional and Global Reporting for Seasonal Influenza Flu Season (4 weeks before and after typical peak influenza months): epidemiologic and virologic data should be reported regionally Non-flu season: only virologic data Can be used for a regularly published bulletin

94. Example: EuroFlu Weekly Electronic Bulletin Detailed epidemiologic and virologic data for each country and Europe as a whole. Presented with:  Maps  Tables  Graphs  Pie charts National level reporting mechanism is important

95. Example: EuroFlu as a Basis for Synthesizing Regional Information

96. Reports for Posting/Publication Public posting of routine analysis and data should be national surveillance system goal. Peer-reviewed publication is also important. May include:  Routine analyses  Special studies Informs international influenza control efforts Creates advocates for influenza interventions

97. Part 6: System Monitoring

98. Outline Suggested Quality Indicators Timeliness Completeness Validity

99. Timeliness Indicators Expected dates of data reporting from sentinel site to next administrative level compared to actual dates Some examples are time elapsed from:  Specimen collection to arrival at the laboratory  Laboratory receipt of specimens to laboratory processing and testing  Laboratory confirmation results to inclusion of results in Weekly Influenza Reports  Laboratory confirmation results for individual SARI cases to notification of the sentinel site focal point  Laboratory results for individual SARI cases by the sentinel site focal point to notification of the patient’s doctor

100. Quantification of Timeliness Indicators Percent of time site achieves targets for specific time intervals e.g. 90% of specimens received at the laboratory within 48 hours of specimen collection Percent of samples tested within a target time frame e.g. 90% of tested specimens have results within 1 week Percent of sites achieving time targets or time lag averages e.g. 90% of sentinel sites package and transport 90% of specimens within 48 hours of collection Percent of time that doctors receive laboratory results for SARI cases within 48 hours of confirmatory test completion

101. Completeness Percentage of swab forms received from each site with complete data Percentage of total expected swab forms that are received Percentage of total expected cases that have specimens submitted to the laboratory

102. Validity: Data Audits Ensures Validity by determining the following: o Case definitions are understood and adhered to o Cases are counted appropriately (no duplicates) o Reported cases meet the case definition o Uniform sampling procedures are being followed o Laboratory equipment and staff are sufficient o Data values are being recorded correctly (can be compared to gold-standard of chart-review) o Sentinel sites and doctors are receiving timely feedback and SARI test results

103. Validity: Compare to Expected Results Number of cases reported each month at site Number of specimens submitted each month at each site Percent of specimens positive for influenza each month at each site Number and percent of SARI and ILI cases tested Does something look out of the ordinary?

104. Comprehensive System Evaluations Conduct in addition to routine monitoring When to conduct  At start-up  At regular intervals  If aberrations in expected results are observed

105. Part 7: Additional Uses of the System and Surveillance Data

106. Outline Estimating disease burden Establishing baselines and thresholds Pandemic detection, planning, and monitoring

107. Overview Make decisions about health resource allocation Identification of risk groups for targeted intervention Monitoring of the impact of intervention programs, including vaccination

108. Estimating Disease Burden

109. Estimates of Disease Burden Disease burden = amount and impact of influenza in the population represented by a sentinel site(s ) Basic measures o Incidence rates of hospitalized SARI caused by laboratory- confirmed influenza o Estimates of excess mortality o Direct costs of medical care and treatment o Indirect costs due to lost time from employment or costs incurred by family members of a sick person

110. Importance of Disease Burden Assist policy makers  Decisions about allocation of resources by putting influenza in perspective relative to other diseases Judge cost-benefit ratio of interventions Stimulate or target future surveillance activities

111. Estimating Catchment Area Sources of population denominator data: Patient lists from sentinel physicians Well circumscribed municipalities of medium size where sentinel sites capture a large portion of admissions/outpatients Health Utilization Survey can be used if:  Well-defined community  Site does not receive a large proportion of cases from distant areas  See guidance document for more details

112. Establishing Baselines and Thresholds

113. Baseline Incidence Baseline = level of influenza activity typically seen outside the seasonal epidemic Rise above baseline indicates start of seasonal epidemic Serves as an objective threshold for public health action Occasionally influenza activity does not exceed the baseline threshold

114. Pandemic Detection, Planning, and Monitoring

115. Sentinel Surveillance Supports Public Health Response Establishes infrastructure for:  Prioritizing investigation of severe respiratory illness cases  Creating clinical specimen collection and transport network  Building expertise in confirmatory testing for human and novel influenza viruses  Strengthening relationships between laboratory, epidemiologic, and clinical personnel

116. Sentinel Systems and Early Warning Sentinel systems are generally not adequate for detection of unusual events or outbreaks early in their course

117. The Role of the Sentinel System in Monitoring a Pandemic Monitoring the course of a pandemic will use existing routine influenza surveillance data describing:  Location of the virus  Trend in cases  Severity of pandemic  Changes in virulence

118. Part 8: Laboratory Specimen Processing

119. Outline Specimen collection Specimen storage and packaging Specimen testing Shipment of specimens

120. Specimen Collection

121. Collecting Respiratory Specimens For direct detection of antigens or nucleic acids, and for virus isolation (culture) o Take no more than 7 days after onset of symptoms o Ideally take within 3 days o Preferably before antiviral therapy Record time from illness onset to specimen collection Give patient verbal explanation of reason for specimen collection and how it will be collected

122. Specimen Tube Labeling Patient unique identifier Specimen date Type of specimen in the tube Hazard label

123. Upper Respiratory Specimens Best for virus isolation and PCR  Nasopharyngeal (NP) swab  Nasopharyngeal aspirates or washes  Nasal wash Alternatively, collect both  Nasal swab  Throat swab  Combine in single vial of VTM

124. Materials Required Personal protective equipment Swabs Tongue depressors Plastic vials, such as cryovials, containing 2-3 ml of virus transport medium (VTM) stored at 4°C (supplied by the NIC) Serum collection: collection tubes, alcohol, gauze, non-heparin treated needles Alcohol and/or bleach Packaging materials for transport in country

125. Specimen Storage and Packaging

126. Specimen Storage Place in VTM immediately Store at 4°C, up to 24 hours For immunoflourescence:  Refrigerate and process within 1-2 hours For virus isolation:  Refrigerate and inoculate into cell cultures as soon as possible If not processed within 48-72 hours, freeze at or below -70°C

127. Specimen Storage Specimens may be divided into aliquots Freeze-thaw cycles should be minimized Do not store in a household freezer (-20°C) with a “defrost” cycle  Keeping sample on ice up to a week is better than allowing freeze-thaw cycles Blood may be stored at room temperature overnight or incubated at 56°C for 30 minutes  Remove serum and store at 4°C up to a week or put into long term storage at -20°C

128. Preparation of VTM Add 10g veal infusion broth and 2g bovine albumin fraction V to 400 ml sterile distilled water Add 0.8 ml gentamicin sulfate solution (50 mg/ml) and 3.2 ml amphotericin B (250 μg/ml) Sterilize by filtration Store unopened for up to one year

129. Packaging 3 layers of packaging Compliance with P650 requirements for infectious substances in UN 3373 category B 1 st layer  Watertight specimen tube (no more than 500mL)  Absorbent material 2 nd layer  Watertight container (zip- loc or hard plastic) 3 rd layer  Rigid outer packaging

130. Packaging May need to include ice packs or dry ice Example: P650 packaging system in combination with Safetybag

131. Specimen Testing

132. Specimen Processing BSL-2 laboratory Class II microbiological safety cabinet for procedures that may give rise to infectious aerosols Seasonal influenza: disposable gloves and gown Suspect avian influenza / severe respiratory pathogens: BSL-2 laboratory with BSL-3 practices, or BSL-3 laboratory

133. Non-molecular Influenza Detection and Subtyping Viral isolation  Eggs  Cell culture  Followed by HAI assay using WHO reagent kit Immunofluorescence assay  Initial screen to select specimens for viral isolation  Low sensitivity  Requires living cells ELISA  Low sensitivity 1918 influenza virions. CDC/ Dr. Terrence Tumpey

134. Influenza Detection and Subtyping by RT-PCR Higher sensitivity Increased biosafety  Uses low amounts of virus  Viral isolation can be performed on known subtypes Cost effective Rapid  Can provide results in 24 hours

135. RT-PCR is Recommended for Confirmatory Testing and to Select Specimens for Virus Isolation Real-time RT-PCR preferred Assays can be developed locally or obtained commercially  Primers and probes must be validated at least once a year Can be performed in BSL-2 laboratory o Reduces chances that isolation of a novel virus (a BSL-3 practice) will be attempted in BSL-2 conditions

136. Virus Isolation Performed after confirmation of type and subtype Cell or egg culture  Cell line: Madin-Darby canine kidney Results in 2-10 days Followed by HAI, RT-PCR, or IFA Ming Wang, et al. Food Markets with Birds as a Source of Avian Influenza. Emerg Inf Dis Vol. 12, No. 11. Nov 2006

137. Principles for Viral Isolation BSL-2 laboratories test for:  Seasonal influenza A(H1N1)  Seasonal influenza A(H3N2)  Influenza B  Other respiratory viruses (RSV, adenovirus) BSL-3 laboratories test for:  Influenza A, subtype not identified  Influenza A, subtype identified as not being  Human seasonal A(H1N1) or  Human seasonal A(H3N2)

138. Testing Algorithm for SARI and ILI Test one of duplicate specimens by (real time) RT-PCR: type A/B Isolate virus on cell culture or eggs Perform lineage identification or influenza A subtyping Ship an aliquot of to a WHO CC for further virus identification and strain characterisation Subtyping for H1, H1v, and H3 by RT- PCR A+ BSL2: Ship aliquot of specimen to a WHO CC BSL 3: isolate virus on cell culture of eggs from early specimens, and a sample of future specimens Test for other respiratory viral pathogens B + Influenza - H1+ or H3+ H1v

139. Seasonal Influenza Serology Testing Use reagents from WHO CDC test kit Conduct HAI assay on paired sera (if available)  Positive: 4-fold rise in antibody titer Collect convalescent serum 14 days – 4 weeks after symptom onset Other considerations Important for retrospective analysis of outbreaks

140. Avian influenza A(H5N1) Serology Testing Virus neutralization assay BSL-3 laboratory with BSL-3 standards Positive: 4-fold or greater rise in neutralization antibody titer Paired serum samples Other considerations Single serum samples can be useful for detecting antibodies Used for:  Confirmation when respiratory specimen testing and virus isolation are inconclusive  Retrospective analysis of outbreaks

141. WHO kits and protocols for real time RT-PCR detection of pandemic (H1N1) 2009 In response to the pandemic, WHO CC at CDC has developed and distributed kits for real-time RT-PCR detection of pandemic (H1N1) 2009.

142. Shipment of Specimens

143. Shipment of Specimens to WHO Collaborating Center Logistical support: WHO Global Shipment Project  Covers 2-3 shipments of seasonal viruses per season  Covers novel viruses as necessary  Uses World Courier  Shipment initiated by completing booking form  Requires export permit (standing permit recommended)

144. Shipment Regulations International regulations for air shipment  Technical Instructions for the Safe Transport of Dangerous Goods by Air  Dangerous Goods Regulations (DGR) may add further restrictions Shipping personnel  IATA-certified training available to NIC staff  Certificate valid for 12 months  Encouraged, but not required for personnel shipping seasonal influenza pathogens

145. Shipping Specimens on Ice For fresh isolates  Use ice packs  Use insulated vials  Delivery within 48 hours or refrigerate at 4°C For frozen isolates  Ship on dry ice Include swab form and itemized list of contents between secondary and outer packaging

146. Specimens for WHO CC or WHO H5 Reference Laboratories Forward to WHO CC for virus strain characterization and vaccine strain selection: Representative seasonal viruses from SARI and ILI cases  A(H3N2)  A(H1N1)  Influenza B At beginning, peak and near end of season Dispatch immediately to WHO CC and/or WHO H5 Reference Laboratory: The first specimens found to be positive for H1N1v Low-reacting viruses Specimens with influenza A viruses for which subtype was not identified Specimens with avian influenza or other novel viruses Include swab form and list of contents