Measure and Maximizing Covid 19 - 2

Measuring Indicators of
Impact in Contact Tracing

Emily S. Gurley, PhD
Johns Hopkins Bloomberg
School of Public Health
Learning Objectives
► Summarize key features of SARS-CoV-2 transmission, including the infectious period,

generation time, and types of contact associated with transmission
► Describe the meaning of the reproductive number and the benefits of using it to measure
the impact of contact tracing programs
► Identify the importance of completeness and timing of case detection and isolation, as
well as contact notification and quarantine, to contact tracing programs
► Calculate metrics of completeness and timing, and explain how they influence the impact
of contact tracing programs
2
Review of SARS-CoV-2 Transmission
Copyright © 2020 Johns Hopkins University. Except where otherwise noted, this work is licensed
under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 license.
SARS-CoV-2 Is the Virus That Causes COVID-19
► There are a wide variety of clinical presentations,

from no symptoms to severe disease and death
► Many never develop fever or respiratory
symptoms
► Approximately 20% of infected people never
develop symptoms (they are asymptomatic)
► The infection fatality ratio (IFR) is the proportion

of infected people who die
► IFR varies dramatically by age
► Population age structure impacts IFR in a
population
SARS = severe acute respiratory syndrome; CoV = coronavirus; COVID-19 = coronavirus disease that emerged in 2019.
Image credit: US Centers for Disease Control and Prevention (CDC) / Alissa Eckert, MS; Dan Higgins, MAMS. 4
SARS-CoV-2: Incubation Period
► The incubation period is the time from when Onset of symptoms

someone is infected until symptoms develop
► The SARS-CoV-2 incubation period ranges from

2 to 14 days
► 50% of people will become ill by 5 days after

they are infected
Image adapted by Center for Teaching and Learning, Johns Hopkins Bloomberg School of Public Health, from:
Bi, Q., et al. (2020). Epidemiology and transmission of COVID-19 in Shenzhen China: analysis of 391 cases and 1,286 of their close
contacts [medRxiv preprint]. Infectious Diseases (except HIV/AIDS). https://doi.org/10.1101/2020.03.03.20028423 5
SARS-CoV-2: Onset of Infectiousness
► People become infectious about 2 days before Onset of infectiousness

symptom onset
► About 50% of people infected will become

infectious 3 days after they are infected
Image adapted by Center for Teaching and Learning, Johns Hopkins Bloomberg School of Public Health, from:
Bi, Q., et al. (2020). Epidemiology and transmission of COVID-19 in Shenzhen China: analysis of 391 cases and 1,286 of their close
contacts [medRxiv preprint]. Infectious Diseases (except HIV/AIDS). https://doi.org/10.1101/2020.03.03.20028423 6
SARS-CoV-2: Infectiousness Over Time—1
► Onset of infectiousness
is, on average, 3 days
after infection
Image source: Center for Teaching and Learning, Johns Hopkins Bloomberg School of Public Health. 7
► Duration of
infectiousness is about
8 to 9 days after illness
onset (but can be longer
for those who are
severely ill)
► Asymptomatic people
likely have a similar
duration of
infectiousness (but are
less infectious than
people who develop
symptoms)
► Infectiousness peaks
around time of onset of
symptoms
Contact During Infectious Period Leads to Transmission
► CDC definition of potentially infectious contact: ► Closest contacts are at

► Physical highest risk for
► Close (within 6 feet for at least 15 minutes) infection
► Proximate (at more than 6 feet but in an enclosed area ► Household members
for at least 1 hour) ► People who spend
significant time
► Risk of transmission is determined by: together (meals,
► Amount of infectious virus (dose) travel, workspaces)
► Opportunities to transmit (how many contacts do they
have?) ► Not all contacts are at
► Intensity of contact (proximity, duration) equal risk for infection
CDC = US Centers for Disease Control and Prevention. 10

Infectious Period and Generation Time
Timeline of Infection: Incubation Period
Timeline of Infection: Signs and Symptoms
Timeline of Infection: Infectious Period
Timeline of Infection: Infected Contact
Infectious Period and Transmission—1
► Curve represents the

infectious period of a
case identified in
surveillance
► This case is called
Generation 0
► Subsequent generations
will be Generation 1, 2,
and so on
Infectious Period and Transmission—2
► Curve represents the

infectious period of a
case identified in
surveillance
► This case is called
Generation 0
► Subsequent generations
will be Generation 1, 2,
and so on
► We want a measure of
how quickly each
successive generation
occurs
Serial Interval as an Approximation of Generation Time—1
► Let’s assume one

contact is infected,
around the first day of
symptoms
► Generation time is the

time from the infection
in one generation to the
time of infection in the
next generation (5 days)
► This is a measure of how
quickly the outbreak will
grow
► Generation time is the

time from the infection
in one generation to the
time of infection in the
next generation (5 days)
► This is a measure of how
quickly the outbreak will
grow
► Serial interval is the
time between onset of
symptoms in one
generation to the next
Timing of Contact Tracing Matters Because of Generation Time
► Think about if, how, and

when contact tracing
happens
► What will be the effect

on transmission?
Reproductive Number as an Indicator of
Impact of Contact Tracing
Basic Reproductive Number (R0 or R-Naught)
► Basic reproductive number—the

number of people one infectious
person will infect if everyone that
person has contact with is
susceptible
► The higher the basic

reproductive number, the more
people will be infected
► R0 of 1 means new cases stay

constant
Image source: Johns Hopkins University. 2

Basic
Reproductive
Number (R0)
Image source: Johns Hopkins University.

Source: Eisenberg, J. (2020 March 17). R0: How scientists quantify the intensity of an outbreak like
coronavirus and predict the pandemic’s spread. The Conversation US. Accessed May 4, 2020. 3
Basic
Reproductive
Number (R0)
for SARS-CoV-2
Image source: Johns Hopkins University.

Source: Eisenberg, J. (2020 March 17). R0: How scientists quantify the intensity of an outbreak like
coronavirus and predict the pandemic’s spread. The Conversation US. Accessed May 4, 2020. 4
R0 Hides Variation in Transmission—1
► If R0 = 2.5, it does not mean that every person infects 2.5 others
5
► Many people never infect anyone else 10 cases, infect average of 2.1 contacts
Cases Number infected

4 0
2 1
1 2
2 3
1 15
10 21
6
► Some infect only 1 other person 10 cases, infect average of 2.1 contacts

4 0
2 1
1 2
2 3
1 15
10 21
7
► Some infect only a couple of people 10 cases, infect average of 2.1 contacts

4 0
2 1
1 2
2 3
1 15
10 21
8
► Some infect only a couple of people 10 cases, infect average of 2.1 contacts

4 0
2 1
1 2
2 3
1 15
10 21
9
► Some transmission results in 10 cases, infect average of 2.1 contacts

superspreading events
► Infect more than 5 people Cases Number infected
► Factors: 4 0
● Biology—shedding a lot of virus 2 1
● Context—close contact with many people
1 2
2 3
1 15
10 21
10

► Factors: 4 0
1 2
2 3
1 15
10 21
11

► Factors: 4 0
1 2
2 3
1 15
10 21
R0 = 21/10 = 2.1
12
Basic Reproductive Number (R0) vs. Reproductive Number (R)
Basic reproductive number (R0) Reproductive number (R)
► R0 is the average number infected if all ► R is an indicator of transmission after

contacts are susceptible interventions
► It is determined by the pathogen and the ► If not everyone is susceptible, it will bring
context down R
► Interventions like contact tracing or social

distancing will bring down R
The difference between R0 and R is a good way to measure

impact of contact tracing programs
13
Change From R0 to R as a Measure of Impact—1
► Interventions can reduce reproductive number R0 = 2
► Let’s assume that each person infects 2 more, on

average

Change From R0 to R as a Measure of Impact—2
► Interventions can reduce reproductive number R=1
► Let’s assume that each person infects 2 more, on

average
► Intervention can reduce 1 new infection at each step
► This changes the overall size of outbreak

Impact of Contact Tracing Measured as Change From R0 to R
R0 = 2 INTERVENTION R=1

Introduction to Performance Metrics
How “Well” Does Contact Tracing Work?
► Is the program able to find cases and their contacts?
► Do cases agree to isolate and contacts to quarantine?

► Do they understand the rationale?
► Do they have logistics and support?
► How quickly are cases identified?
► Are cases isolated quickly enough to prevent transmission?
► Are contacts quarantined before they become infectious?
2
Guidance About Monitoring Contact Tracing Programs
► US Centers for Disease Control and Prevention
► Vital Strategies Contact Tracing Playbook
*See Resources for links to guidance on various performance metrics for contact tracing programs. 3
Two Basic Categories
Day-to-day functioning Program impact
► How many cases called per day ► What proportion of new cases were
already under quarantine?
► How many contacts notified per day
► What proportion of cases are isolated
► Average number of contacts notified per within 24 hours of test result?
case
4
Outcome Metrics Are Required for Estimating Impact on R0
Day-to-day functioning Program impact
► How many cases called per day ► What proportion of new cases were
already under quarantine?
► How many contacts notified per day
► What proportion of cases are isolated
► Average number of contacts notified per within 24 hours of test result?
case
Our metrics are about impact
5
What Is the Impact of Contact Tracing on R0?
Completeness Timing
► What proportion of all infectious people ► Average duration rather than proportion
does surveillance identify? ► What is the average time between
symptom onset and isolation?
► What proportion of infected people are ► What is the average time between
isolated? exposure and quarantine among
contacts?
► What proportion of contacts are ● Does this duration differ for
quarantined? household contacts?
6
Indicators Needed to Estimate Impact on R0
Completeness Timing
► What proportion of all infectious people ► Average duration rather than proportion
does surveillance identify? ► What is the average time between
symptom onset and isolation?
► What proportion of infected people are ► What is the average time between
isolated? exposure and quarantine among
contacts?
► What proportion of contacts are ● Does this duration differ for
quarantined? household contacts?
*For the next section, please refer to the metric calculation worksheet
7
Surveillance: Detection and Isolation
of Infected People
Surveillance: Cornerstone of Prevention
► Contact tracing programs have the “opportunity” to intervene and stop transmission only
from detected cases
► The recognition of a “case” starts the whole chain of events
► For our purposes, a case is a person who is infected

► This includes people who develop symptoms and those who don’t (asymptomatic)
► Both can infect others, although there is some evidence that asymptomatic people are
less infectious
2
The proportion of infections that your surveillance system
detects affects the impact of your contact tracing program
3
These Are All the Infected People in Your Population …
Some May Never Develop Symptoms and So Will Be Harder to Find
Proportion of All Infected People Detected by Surveillance—1
Proportion of All Infected People Detected by Surveillance—2
Completeness of Case Finding
► Goal of surveillance: detect as many new infections as possible
► Indicator of completeness: what proportion of infections (cases) are you finding?
► What you can usually measure: number of new infections detected
► We can estimate the number of infections in the community

► Combining with the number of deaths in the same time period
● Laboratory-confirmed deaths
● Deaths probably from COVID-19 (no testing done)
8
Estimating All Infections in the Community
Troubleshooting Completeness of Case Detection
► Identifying all infections is not necessary to have a big impact on R

► But increasing detections can improve the impact of your contact tracing program
► You must understand how testing works in your population

► Availability of supplies and testing resources
► Restrictions on who can get tested
► Awareness about when and where to seek testing
► Access to testing sites and tests
► Percent of tests positive is an important indicator

► Percent positive should be less than 5%
► Keep in mind that average percent may hide large variation in percent of tests positive
10
Time delays in detecting cases and isolating them
will affect the impact of your contact tracing program
11
Infectiousness Changes Over Time
► Timing of case detection

and isolation matters
because infectiousness
changes over time
Some Transmission May Occur Before Symptoms Start
► Timing of case detection

and isolation matters
because infectiousness
changes over time
► 50% of cases will

develop symptoms
within 5 days of
infection
► Many people are

infectious before
symptom onset
Detection Time Affects Program Impact—1
► Let’s assume that

someone becomes sick
5 days after infection
► Next, 2 days later, they

seek care and have a
sample collected


sample collected
► The results are returned


sample collected
► The results are returned
► The following day, they

are asked to isolate
Calculating Delays: Onset to Sample Collection
► Measuring metrics of
timeliness:
► Average time from
symptom onset to
sample collection
Calculating Delays: Sample Collection to Isolation
timeliness:
symptom onset to
sample collection
sample collection to
isolation
Calculating Delays: Symptom Onset to Isolation
timeliness:
symptom onset to
sample collection
sample collection to
isolation
► Total from symptom
onset to isolation
● 2 + 2 = 4 days
Impact of Quicker Detection and Isolation
► Let’s assume:
► Case seeks care and
is tested 1 day faster
► Test result is
available the same
day, and the case is
asked to isolate
► Case is still very
infectious but no
longer infecting
others, resulting a
larger impact on R
Completeness and Timing of Contact
Tracing and Quarantine
Identifying and Intervening on Contacts Can Stop Transmission
► Among the cases detected, there is an opportunity to identify contacts who may have
been infected
► Contacts who are notified of exposure and asked to self-quarantine will result in fewer
people infected
► Not all contacts the same

► Closest contacts are at highest risk for transmission and easiest to find
► Other contacts may be more difficult to find but are at lower risk for infection
2
The proportion of all contacts notified and quarantined
will affect the impact of the contact tracing program
3
Notifying and Quarantining Contacts
► These are all the

close contacts that
cases tell you about
► Improving trust with

the community can
improve contact
listing; reluctance to
identify contacts will
limit impact of
contact tracing
program
Identifying the Proportion of Contacts That Are Household Members

close contacts that
► Let’s assume most
are household
contacts
Household Contacts May Be Easier to Find and Quarantine

close contacts that
► Let’s assume most
are household
contacts
► Let’s assume you
contact and
quarantine 60%
overall, but 85% of
household contacts
Calculating Metrics of Contact and Quarantine Completeness
► Count all contacts
► Identify number or
proportion that are
household members
► Calculate the
proportion reached
and quarantined by
type of contact
► Household
► Community
The timing of notifying and quarantining contacts
will affect the impact of the contact tracing program
8
Timing of Contact Notification and Quarantine
Linked to Case Detection—1
► Recall our previous
scenario:
► Total time from
symptom onset to
isolation
● 2 + 2 = 4 days
Timing of Contact Notification and Quarantine
Linked to Case Detection—2
► Recall our previous
scenario:
► Total time from
symptom onset to
isolation
● 2 + 2 = 4 days
► Contacts will be
quarantined 2 days after
the case is isolated
► Takes time to find the
contact
Separate Household and Community Contacts
► Let’s assume that …

► Household contacts
are easier to find
High-Risk Contacts Can Be Identified More Quickly

are easier to find
can be quarantined
the same day as the
case is isolated
(quarantined before
peak infectiousness)
Delayed Quarantine of Community Contacts Still Has Impact

are easier to find
can be quarantined
the same day as the
case is isolated
(quarantined before
peak infectiousness)
► Community contacts
are quarantined 2
days later (still have
an impact)
Calculating Timing of Quarantine
► Average time between

onset of case and
quarantine of contacts
► In this example:
► 4 days for household
contacts
Calculating Timeliness of Quarantine
► Average time between

onset of case and
quarantine of contacts
► In this example:
► 4 days for household
contacts
► 6 days for community
contacts
Decreased Delay at Each Step = Big Impact on Transmission
► Now, think back to the

quicker timeline for
identification and
isolation of cases
► Household contacts are

quarantined at the same
time cases are isolated
► Community contacts
quarantined 2 days later
Summary
Metrics of Completeness and Timing Can Estimate Impact
► Surveillance and contact tracing programs need not be perfect to have a major impact on
transmission of SARS-CoV-2
► The completeness and timing of case detection, isolation, contact tracing and quarantine
will all affect the impact of a contact tracing program
► These metrics can be calculated from surveillance and contact tracing data
► Using models, these metrics can be used to estimate the impact of contact tracing
programs on the reproductive number (R)

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Measuring Indicators of

Impact in Contact Tracing

► Summarize key features of SARS-CoV-2 transmission, including the infectious period,

► There are a wide variety of clinical presentations,

► The infection fatality ratio (IFR) is the proportion

► The incubation period is the time from when Onset of symptoms

► The SARS-CoV-2 incubation period ranges from

► 50% of people will become ill by 5 days after

► People become infectious about 2 days before Onset of infectiousness

► About 50% of people infected will become

► CDC definition of potentially infectious contact: ► Closest contacts are at

CDC = US Centers for Disease Control and Prevention. 10

► Curve represents the

► Curve represents the

► Let’s assume one

► Generation time is the

► Generation time is the

► Think about if, how, and

► What will be the effect

► Basic reproductive number—the

► The higher the basic

► R0 of 1 means new cases stay

Image source: Johns Hopkins University. 2

Image source: Johns Hopkins University.

Image source: Johns Hopkins University.

Cases Number infected

Cases Number infected

Cases Number infected

Cases Number infected

► Some transmission results in 10 cases, infect average of 2.1 contacts

► Some transmission results in 10 cases, infect average of 2.1 contacts

► Some transmission results in 10 cases, infect average of 2.1 contacts

Basic reproductive number (R0) Reproductive number (R)

► R0 is the average number infected if all ► R is an indicator of transmission after

► Interventions like contact tracing or social

The difference between R0 and R is a good way to measure

► Interventions can reduce reproductive number R0 = 2

► Let’s assume that each person infects 2 more, on

Image source: Johns Hopkins University. 14

► Interventions can reduce reproductive number R=1

► Let’s assume that each person infects 2 more, on

► Intervention can reduce 1 new infection at each step

► This changes the overall size of outbreak

Image source: Johns Hopkins University. 15

Image source: Johns Hopkins University. 16

► Is the program able to find cases and their contacts?

► Do cases agree to isolate and contacts to quarantine?

► How quickly are cases identified?

► Are cases isolated quickly enough to prevent transmission?

► Are contacts quarantined before they become infectious?

► US Centers for Disease Control and Prevention

► Vital Strategies Contact Tracing Playbook

Day-to-day functioning Program impact

Day-to-day functioning Program impact

Our metrics are about impact

► The recognition of a “case” starts the whole chain of events

► For our purposes, a case is a person who is infected

► Goal of surveillance: detect as many new infections as possible

► Indicator of completeness: what proportion of infections (cases) are you finding?

► What you can usually measure: number of new infections detected

► We can estimate the number of infections in the community

► Identifying all infections is not necessary to have a big impact on R

► You must understand how testing works in your population