Capstone Exercise
“Influenza Sentinel Surveillance in the
Country of Tranquilidad”
PARTICIPANT GUIDE
Objectives



Recognize the different types of measures used in statistical reporting of laboratory
data for influenza surveillance
Collect and report key influenza measures
Present weekly data on key measures in graphical form
Instructions
This activity puts into practice the concepts from classroom training, including data analysis,
data aggregation, data display and presentation. There are four parts to this activity. In the
first part, you will assume the role of a local laboratory professional for an ILI sentinel
surveillance system in a fictional country, Tranquilidad. You will analyze electronic data
from a local laboratory database and present weekly and annual data in graphical and tabular
form. In the second part of the activity, you will present your analysis results to a local
epidemiology office. In the third part of the activity, you will analyze and summarize weekly
and annual data for the entire country of Tranquilidad. In the fourth and final part of the
activity, you will present national influenza trends in oral and written forms; this section of
the activity is to be completed at home and submitted online.
To complete this activity, you will need the following:
 Activity Student Guide (this document)
o A document with activity instructions and questions to complete.
 Appendix I: Description of Tranquilidad’s Influenza-Like Illness Sentinel
Surveillance System: Tranquilidad Highlands
 Database I: “InfluenzaLabData_Highlands.xls”
o Laboratory surveillance data from a local sentinel laboratory in the highlands,
one region of Tranquilidad. This database contains data for the entire
epidemiologic year. It has two tabs: one which arranges data in line listing
format (e.g. one entry for each respiratory specimen), and one which provides
summary data for each epidemiologic week.
 Appendix II: Microsoft Excel Database Codebook
o A list of all the variables, potential responses and manner of coding for both
the
“InfluenzaLabData_Highlands”
database
as
well
as
the
“InfluenzaLabData_AllTranquilidad” database.
 Microsoft Excel Guide: “Capstone_MicrosoftExcelGuide.doc”
o A guide to using Microsoft Excel 2007 or Excel 2003 for data analysis and
Capstone Exercise
Epidemiologic Analyses of Influenza Laboratory Data Page 1

presentation.
OPTIONAL:PowerPointTemplateSlides:
“Capstone_Part2AlternateActivity_PptTemplate.ppt”
o Power Point slide templates to be used as part of an alternate activity for Part
2 of the Capstone activity.
Time allotted:
Part I:
20 minutes
Part II:
2 hours
Part III:
40 minutes
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Epidemiologic Analyses of Influenza Laboratory Data Page 2
Part 1: Demonstration and tutorial of Excel
The Excel file used for this demonstration is Capstone Part 1.xls.
Time allotted: 20 minutes
Part 2: Influenza-Like Illness (ILI) Sentinel Surveillance in the Highlands Region,
Tranquilidad
Background
The country of Tranquilidad initiated an influenza-like illness (ILI) sentinel
surveillance system in January 2009. You are a laboratory professional of a regional
branch of this national surveillance system, based in the highlands of Tranquilidad.
As part of your responsibilities in this position, you prepare weekly reports which are
submitted to the local epidemiology office.
At this time, you are preparing a weekly report for the last week of the epidemiologic
year (epidemiologic week 52).
Directions: Before you begin, review the description of the surveillance system in Appendix I
of this document. After you have read the description of the surveillance system, open
Database I, which contains a line listing of regional laboratory results for the Highlands
region of Tranquilidad (“InfluenzaLabData_Highlands.xls”). You will use this database to
answer the questions below; these answers will help you prepare your weekly laboratory
report to the local epidemiology office. Where indicated, please refer to the supplementary
materials to help you answer the questions.
1. You will be including several basic descriptive measures in your weekly laboratory
report. These measures will be captured through tables and charts/graphs. In
general, what are the main differences between tables and charts/graphs? Name one
advantage and disadvantage of presenting influenza laboratory surveillance data
using each.
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Epidemiologic Analyses of Influenza Laboratory Data Page 3
2. During epidemiologic week 52, how many ILI samples were received and tested?
NOTE: You can assume that all records in the database represent those received
(e.g. no missing data in the database), and that all received samples were tested. Use
the information in Appendix II to help you with interpreting the database.
3. In order to meet the case definition, all ILI patients must report having a sudden
onset of fever. In addition, to ensure data quality, the symptom onset cannot be
more than 3 days prior to the lab test. All data up to week 52 have already been
reviewed, and records inconsistent with these criteria were deleted from the
database. Review the current ILI samples for week 52. Do any of the records not
meet these criteria? If so, how many? To help you calculate the number of days
between onset of symptoms and the testing date, there are empty cells in the Days
column of Database I for week 52 where you can add a simple formula. (NOTE:
Exclude any records that don’t meet these criteria from all future analyses).
4. Of the total eligible samples received and tested for ILI during epidemiologic week
52, how specimens were positive for respiratory pathogens? How many positive tests
were there? (Note: count only the type, for influenza, since the subtype is captured
in this number)
5. To complete your weekly influenza laboratory report, create a table showing counts
of total respiratory specimens tested, both overall and by agent. In addition to
counts, include percents of the total number of specimens and the total number of
positive tests in your table. Put the appropriate column headings in the first row of
the table below, listing the agents in the first column. Don’t forget to include rows
with the total numbers of positive and negative specimens. NOTE: You have already
reported some of the counts necessary for this table in the previous two questions.
Also note that respiratory specimens may be positive for multiple etiologic agents.
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Epidemiologic Analyses of Influenza Laboratory Data Page 4
Table 1. __________________________________________________________
Characteristic
Number
Percentage of Percentage of
Specimens
Positive Specimens
Total Specimens Processed
-
Total positive specimens
-
Total negative specimens
-
Total Positive Tests
-
Influenza A
-
Influenza B
-
Parainfluenza
-
Adenovirus
-
Respiratory Syncytial Virus
-
Source:
6. You would now like to create a table of weekly counts of specimens that tested
positive for influenza by type and subtype. Using the data in your local laboratory
database for this final week in the epidemiologic year and the empty table shell
below, complete a table with this information. Your table should also include the
total number of specimens tested. Do not forget to provide a descriptive title for
your table. NOTE: There is no single “correct” way of presenting data in this table;
depending on how you format your rows and columns, you may find that you have
empty cells. Also note that you may use the Microsoft Excel Guide as a reference
for how to summarize the data necessary for this table.
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Epidemiologic Analyses of Influenza Laboratory Data Page 5
Table 2. ______________________________________________________
Influenza Type/subtype
Total respiratory samples tested
Number
Total positive tests
Influenza A
Pandemic Influenza H1N1
Influenza A H3N2
Influenza B
Source:
Directions: Use Tables 1-2 to answer the following questions:
7. During epidemiologic week 52, what proportion of specimens was positive for
influenza A?
8. In epidemiologic week 52, which respiratory pathogen was most common? Does
influenza appear to be a leading cause of ILI in this sample?
9. Next, you are curious to know about the distribution of ILI-associated respiratory
pathogens for the entire year (e.g. epidemiologic weeks 1 through 52). Create a table
summarizing the count, proportions of respiratory specimens positive, and
proportion of total positive tests, by each respiratory pathogen. This means that we
will use the total number of specimens in the denominator for one column, and the
total number of positive tests as the denominator in another column. Be sure to
count influenza A tests as positive only once (don’t count subtypes). Provide a
descriptive title for your table. HINT: It may be helpful to use the COUNTIFS
function in Excel. See the Microsoft Excel Guide for further instructions.
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Epidemiologic Analyses of Influenza Laboratory Data Page 6
Table 3. ______________________________________________________
Pathogen Tested
Number
Percent of total
Tested
Percent of
Positive Tests
Total respiratory specimens tested
Total respiratory pathogen,
positive
Total negative specimens
Total pathogens detected
Influenza A
Influenza B
Parainfluenza
Adenovirus
Respiratory Syncytial Virus
10. A colleague in the local epidemiology office asks if you could create an additional
table, showing the number and percent positive ILI cases by respiratory pathogen
and by age group. She would like an aggregated summary for the entire year of
laboratory surveillance data. Your colleague provides a template of the table she
would like completed, below. Complete this table with the information requested
from your colleague in the local epidemiology office. HINT: Use the COUNTIFS
function. See the Microsoft Excel guide for further instructions. NOTE: Verify that
your total numbers for each respiratory pathogen are the same as the total counts
you calculated in Table 3.
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Epidemiologic Analyses of Influenza Laboratory Data Page 7
Table 4. ______________________________________________________
Age group
Total number of
respiratory
specimens
tested
Influenza
A
Influenza
B
Parainfluenza
Adenovirus
RSV
Total
Positive
< 2 years
2-4 years
5-14 years
15-49 years
50-60 years
Over 60
Total
Source:
11. Looking at Table 4, which type of respiratory infection is most common in each age
group? Complete the table below summarizing your observations.
Age group
Most common respiratory infection
< 2 years
2-4 years
5-14 years
15-49 years
50-60 years
Over 60
Source:
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Epidemiologic Analyses of Influenza Laboratory Data Page 8
12. In the 2009 sentinel surveillance data, which respiratory pathogen was most
common? Does influenza A/B appear to be a leading cause of ILI in this sample?
Directions: For the following questions, use the Highlands laboratory surveillance database
to answer the following questions about circulating respiratory infections for ILI cases for
the entire epidemiologic year. In the spreadsheet “InfluenzaLabData_Highlands.xlsx”the tab
named “Highlands_Subtotals” contains counts of positive respiratory pathogens for each
epidemiologic week.
13. You are curious to know how the distribution of each type of infection for
epidemiologic week 52 compared with the rest of the year. Create a stacked bar
chart to show the number positive specimens for each infection in the Highlands
district of Tranquilidad over the year. Add a line to the chart to show the total
number of specimens collected for each week. Be sure to provide appropriate axes
for your graph as well as labels and a legend. NOTE: Refer to the Microsoft Excel
guide for instructions on how to create graphs and charts in Excel. NOTE: Your
database contains a tab with weekly counts of influenza cases, by week on the tab
“Region 1 Highlands_Subtotals.” However, if you would like to know how to
generate these weekly summary data in the spreadsheet, please see the Microsoft
Excel guide section, “Using subtotals to get weekly summary data from line
listings.”
14. In general, does it appear that influenza A and B constitute a large proportion of
ILI respiratory specimens in the Highlands region of Tranquilidad? Does this graph
confirm your observations in Question 12?
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Epidemiologic Analyses of Influenza Laboratory Data Page 9
Part 3: Presenting Results to Officials in the Highlands Region
An Invitation to Present Surveillance Results
You have been asked by the regional epidemiology office to prepare a brief oral
presentation regarding yearly influenza-like illness surveillance trends in the
Highlands region of Tranquilidad. You will be presenting to 5-10 regional
epidemiologists working on Tranquilidad influenza surveillance.
Specifically, you are asked to present on year-long trends in circulating strains of
influenza and influenza-related pathogens.
1. Would you describe this as an internal or external audience? Briefly explain your
answer.
2. Name 2-3 considerations for presenting to the type of audience you specified in the
previous question.
3. List 2-3 major points you would like to communicate in your presentation.
4. The regional epidemiologist who invited you to speak encourages you to use
PowerPoint to communicate your presentation, and asks you to please limit your
presentation to three slides. Using the PowerPoint slide template provided below,
create a title slide and two content slides containing major points you would like to
communicate in your presentation. How you organize your content slides is up to
you. Remember to keep the considerations you listed in Part 2 Question 2 in mind as
you design your slides. NOTE: Generally, full PowerPoint presentation should
contain a title slide, overview slide, content slides, conclusion slide, and references.
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Epidemiologic Analyses of Influenza Laboratory DataPage 10
Title Slide Notes:
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
Content Slide Notes:
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
Content Slide Notes:
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
_________________________________________
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Epidemiologic Analyses of Influenza Laboratory DataPage 11
Responding to E-mails
You gave your presentation at the regional epidemiology office, and provided your
e-mail address so that epidemiologists could contact you with questions. Now less
than 24 hours later, you find two e-mails with questions from regional epidemiology
office personnel in your inbox.
Directions: Read each of the e-mails with questions from local epidemiology office
personnel and craft response e-mails using the space provided. NOTE: Where indicated, you
may have to go back to your database to find answers.
Email 1:
From:
To:
Subject:
tm412@tranquilidad.moh.gov
highlands_laboratory@tranquilidad.moh.gov
Vaccination in the Highlands
Hello,
Since influenza A was not a prominent circulating strain, I wonder to what extent influenza
vaccination occurred in this region of Tranquilidad. Are you able to provide data on how
many people were vaccinated, and among those vaccinated with the influenza vaccine, how
many had laboratory-confirmed influenza?
NOTE: Refer to your laboratory database in order to provide the statistics necessary to
answer this email. To respond to this email, comment, in general terms, about the number of
those vaccinated and the pathogenic status of their respiratory specimens.
From:
To:
Subject:
highlands_laboratory@tranquilidad.moh.gov
tm412@tranquilidad.moh.gov
RE: Vaccination in the Highlands
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
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Epidemiologic Analyses of Influenza Laboratory DataPage 12
Email 2:
From:
To:
Subject:
ds717@tranquilidad.moh.gov
highlands_laboratory@tranquilidad.moh.gov
Influenza vs. ILI surveillance
Thank you for your presentation!
I am wondering why sentinel surveillance captures influenza-like illness? Why can’t we test
all suspect cases for pandemic influenza?
From:
To:
Subject:
highlands_laboratory@tranquilidad.moh.gov
ds717@tranquilidad.moh.gov
RE: Influenza vs. ILI surveillance
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
___________________________________________________________________________
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Epidemiologic Analyses of Influenza Laboratory DataPage 13
Appendix I:
Description of Tranquilidad’s Influenza-Like Illness Sentinel Surveillance
System: Tranquilidad Highlands
Case Definition for Influenza-Like Illness (ILI):
Any person with a sudden onset of a fever over 38° C; AND Cough or sore throat, AND the
absence of other diagnoses
Source of Information and Specimens:
All data for ILI surveillance are obtained from a combination of sentinel hospitals and
clinics, sentinel laboratories, and the national reference laboratory. Sentinel clinics and
hospitals were selected as a nationally representative sample of patients residing in each of
four Tranquilidad regions (North, South, Central, and Highlands). Sentinel hospitals and
clinics collect basic demographic data and respiratory specimens for all patients meeting ILI
case criterion. Sentinel laboratories and the national laboratory process these specimens, and
submit data on laboratory results to local and national epidemiology offices, respectively.
Information flow in Tranquilidad’s ILI Sentinel Surveillance System:
Sentinel Hospitals/Clinics: Collects respiratory specimens from patients meeting surveillance
eligibility, and send to local sentinel laboratory.
Local Sentinel Laboratory: Local laboratory uses immunofluorescence testing; sends all
positive influenza specimens and 10% of influenza-negative specimens to national influenza
center for further virus characterization, and sub-typing of influenza A samples; analyzes
laboratory data and sends weekly reports to local epidemiology office.
Local Epidemiology Office: Collates and analyzes information from sentinel hospitals/clinics
as well as local sentinel laboratory; submits weekly reports to National Epidemiology Office
and back to local sentinel hospitals/clinics.
National Influenza Center: Processes respiratory specimens from local sentinel laboratories;
performs sub-typing, virus isolation and characterization; creates and submits weekly reports
to National Epidemiology Office.
Demographic data obtained for ILI cases:
Sex of patient
Age of patient
Lost work or school days
Influenza vaccination status
Military base employee/ civilian status
Laboratory analysis
Nasopharyngeal swab and oropharyngeal swabs are collected from all cases.
In the local sentinel laboratory, immunofluorescence testing is performed in order to
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Epidemiologic Analyses of Influenza Laboratory DataPage 14
ascertain infection status by the following respiratory pathogens:
Influenza A
Influenza B
Respiratory syncytial virus (RSV)
Adenovirus
Parainfluenza
All influenza positive and 10% of influenza-negative respiratory specimens are then sent to
the national influenza center (e.g. national laboratory) to further characterize respiratory
specimens and sub-type influenza A specimens.
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Epidemiologic Analyses of Influenza Laboratory DataPage 15
Appendix II:
Microsoft Excel Database Codebook
Variable Name
Description
Region*
Local surveillance region
Numeric
NoSpec
EpiWeek
Age
Number of specimens
Epidemiologic Week
Age of patient, in years
Numeric
Numeric
Numeric
Sex
Sex of patient
VaccHistory
History of influenza vaccination
Numeric
LostDays
Numeric
Hospitalized
Number of work days lost due to
illness
Hospitalization of ILI patient
Military
Stationed at military base
Numeric
Civilian
Not stationed at military base
Numeric
RespPos
Respiratory
specimen
tested
positive for any type of respiratory
pathogen
Respiratory
specimen
tested
positive for Influenza A
Respiratory
specimen
tested
positive for Influenza B
Respiratory
specimen
tested
positive for Influenza A, subtype
H1N1
Respiratory
specimen
tested
positive for Influenza A, subtype
H3N2
Respiratory
specimen
tested
positive for Parainfluenza
Respiratory
specimen
tested
positive for Adenovirus
Respiratory
specimen
tested
positive for respiratory syncytial
virus
Patient reported sudden onset of
fever as a symptom
Date of symptom onset
Numeric
InfluenzaA
InfluenzaB
Pandemic Influenza
H1N1
Influenza A H3N2
Parainfluenza
Adenovirus
RSV
Fever
DSO
SampleDate
Days
*
Date biological sample was
obtained from patient
Number of days between DSO
and SampleDate
Variable Type
Character
Numeric
Numeric
Numeric
Numeric
Response Options**
1 = Highlands
2 = Central
3 = South
4 = North
1-99
1-52
0-99
M = Male
F = Female
0 = No
1= Yes
1-99
0 = No
1= Yes
0 = No
1= Yes
0 = No
1= Yes
0 = No
1= Yes
0 = No
1= Yes
0 = No
1= Yes
0 = No
1= Yes
Numeric
0 = No
1= Yes
Numeric
0 = No
1= Yes
0 = No
1= Yes
0 = No
1= Yes
Numeric
Numeric
Numeric
Numeric
(dd/mm/yyyy)
Numeric
(dd/mm/yyyy)
Numeric
0 = No
1= Yes
04/01/2009 – 02/01/2010
04/01/2009 – 02/01/2010
0-3
These variables are presented in the aggregated datasets for all regions.
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Epidemiologic Analyses of Influenza Laboratory DataPage 16
**
For ease in examining trends in number of cases over time, if there were no
specimens collected in a given epidemiologic week, a row was entered for that week
with blank data. Thus, in this dataset, missing data only occurs in epidemiologic
weeks where no specimens were collected.
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Epidemiologic Analyses of Influenza Laboratory DataPage 17