COVID-19 Specimen Collection & Diagnostic Tests
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MODULE3:
DIAGNOSIS
OF COVID-19:
Specimen Collection, Transportation &
Diagnostic
Tests
Learning
objectives
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At the end
of
this
session
,
you
will be able
to:
•
Describe when and what specimens
to
collect for
L
aboratory
diagnosis
of COVID-19
.
•
To describe the Optimal conditions for transportation of samples for
COVID-19.
•
To describe the
characteristics
of
diffrenet
diagnostic
tests
used
for
the
diagnosis of COVID-19.
•
Rapid collection and testing of appropriate specimens from
suspected cases is a priority and should be guided by a laboratory
expert.
•
As extensive testing is still needed to confirm the COVID-19 virus
and the role of mixed infection has not been verified, multiple tests
may need to be performed and sampling sufficient clinical material is
recommended.
•
Local guidelines established by the testing Lab (UVRI) should be
followed regarding patient or guardian’s informed consent for
specimen collection, testing and potentially future research.
•
Ensure that SOPs are available, and the appropriate staff is trained
and available for appropriate collection, specimen storage, packaging
and transport.
•
There is still limited information on the risk posed by the reported
coronavirus found in Wuhan, but it would appear samples prepared
for molecular testing could be handled as would samples for
influenza of with maximum biosafety precautions as appropriate.
•
Attempts to culture the virus may require heightened biosafety
control measures.
Specimen
collection
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Collect correct biological
Specimens
•
Respiratory material*
•
(nasopharyngeal and oropharyngeal swab in ambulatory patients
•
sputum (if produced)
•
and/or endotracheal aspirate or bronchoalveolar lavage in patients with
more severe respiratory disease)
•
Serum for serological testing, acute sample and convalescent sample
(this is additional to respiratory materials and can support the
identification of the true agent, once serologic assay is available)
Collect correct biological
specimens
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•
Guided by differential diagnosis
and laboratory
capacity:
–
collect
samples before antimicrobial therapy provided
it
does
not
delay the administration of antimicrobial therapy by
> 45
minutes
–
notify laboratory and public health authorities
if
concerns regarding
emerging or high risk pathogens
–
use results for better and focused
clinical
management
–
use results to influence public health
interventions
.
Upper respiratory tract
samples
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•
Use
appropriate
PPE
during collection procedure (gown,
mask,
gloves and eye
protection).
•
Nasal or
nasopharyngeal samples
have
highest yield
for
detection
of
the
virus.
•
Also collect throat swabs
to
improve
the yield
for
suspected emerging
C
O
V
ID-19
.
–
Collect samples
as soon as
possible
.
–
Ideally samples should be collected less
than 4 days from
illness
onset for seasonal
influenza
A or B, as
yield
goes down as viral
shedding
decreases.. This may also be
true for COVID-19
Minimize
direct
unprotected
exposure to blood and
body
fluids.
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Risk assessment
for
appropriate use
of
PPE
Nasopharyngeal
swabs
Throat
swabs
✓
U
s
e
s
t
e
r
i
l
e
d
a
c
r
o
n
o
r
r
a
y
o
n
s
w
a
b
s
.
D
o
n
o
t
u
s
e
c
o
t
t
o
n
s
w
a
b
s
o
r
w
o
o
d
s
h
a
f
t
s
a
s
c
a
n
i
n
t
e
r
f
e
r
e
w
i
t
h
R
T
-
P
C
R
a
s
s
a
y
s
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Lower respiratory tract
samples
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•
Also collect
lower respiratory tract
samples in
patients
with
radiographic evidence or clinical
diagnosis of lower respiratory
tract
disease,
in certain
situations, if
results will impact clinical
interventions:
–
expectorated
sputum
–
tracheal aspirates
–
bronchoalveolar
lavage.
•
Can generate aerosols, thus
use
airborne precautions
during
procedure.
I
n
i
n
t
u
b
a
t
e
d
p
a
t
i
e
n
t
,
c
a
n
c
o
l
l
e
c
t
t
r
a
c
h
e
a
l
a
s
p
i
r
a
t
e
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•
Collection
can generate
aerosols, thus use
airborne
precautions.
•
Using sterile collection
trap.
•
Do not send
suction
catheter
tip
to
laboratory.
Benefits
of
lower respiratory tract
samples
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•
Higher
sensitivity
than upper respiratory specimens
for
zoonotic
influenza
virus,
MERS-CoV and
Probably for COVID-19.
•
Increases diagnostic yield
for seasonal
in if upper samples
are
negative
or
tested
late
and may be the same for COVID-19.
•
Can
also
be
used to
tested
for
other pathogens such
bacterial,
fungal and parasitic infections
if suspected as co-infection.
–
e.g.
M. tuberculosis,
PjP.
Sample Transportation
•
There must be ready means of transport to take the sample to lab immediately upon collection.
•
All specimens collected for laboratory investigations should be regarded as potentially infectious, and HCWs
who collect, or transport clinical specimens should adhere rigorously to infection prevention and control
guidelines and national or international regulations for the transport of dangerous goods (infectious
substances) to minimize the possibility of exposure to pathogens.
•
Implement the appropriate infection prevention and control precautions during transportation.
*
Good communication with the laboratory and provide needed information*
•
To ensure proper and fast processing of samples and to assure adequate biosafety measures in the
laboratory, communication and information sharing is essential.
•
Be sure you have alerted the laboratory of the urgency and situation before sending the sample.
•
Also assure that specimens are correctly labelled, and diagnostic request forms are filled out properly and
clinical information is provided (see box: information to be recorded)
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Collection time
and
site
matter
EMERGENCIES
Virology
Journal
2019:16,
Article
number:
88
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•
Collect
samples
as
soon
as
possible:
–
Ideally less
than 4 days of
illness
onset for seasonal
influenza
A or B, as
yield
goes
down as viral
shedding
decreases.
–
In
patients
with respiratory
failure
diagnosis may still be made by sampling the lower
respiratory tract
at any
time.
–
In
children,
oropharyngeal swabs may be
alternative.*
•
Collect lower tract
samples
for
zoonotic influenza
and
MERS:
–
If you sample the
upper
respiratory
tract
at
illness
day 6 you might miss
detection
of
these viruses, and still make the diagnosis
by
testing
endotracheal
aspirate
.
*Le
Wang,
Shuo
Yang,
Xiaotong
Yan, Teng
Liu, Zhishan
Feng
&
Guixia
Li.
Comparing
the yield
of
oropharyngeal
swabs
and
sputum
for
detection of
11
common
pathogens
in
hospitalized
children
with
lower respiratory
tract
infection.
Information to be recorded for the sample
•
Patient information –
name, date of birth, sex and residential address, unique identification number,
other useful information (e.g. patient hospital number, surveillance identification number, name of hospital,
hospital address, room number, physicians’ name and contact information, name and address for report
recipient),
•
Date and time of sample collection,
•
Anatomical site and location of specimen collection,
•
Tests requested,
•
Clinical symptoms and relevant patient history (including vaccination and
antimicrobial therapies received, epidemiological information, risk factors).
A
dditional specimens
to consider
for
L
aboratory
diagnosis
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Complete blood cell count
for
white blood
cells.
•
Sputum
for
bacteriology:
–
including TB
if in
high prevalence country
or
fungus
if
immunosuppressed,
etc.
•
Specimens
from
other
sites
that
may
be infected and can
yield pathogens,
as
clinically
indicated:
–
urine, cerebrospinal fluid,
stool,
pleural fluid, peritoneal fluid,
etc.
•
Two sets of blood cultures for bacteriology from two
different
sites
(where possible) for patients
with
sepsis
.
Additional
specimens
for
public health and research
purposes
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•
Discuss
with
local public health officials need for
additional
samples and
interval of
repeat testing, if suspect emerging
infection:
–
collection of blood for virus detection may
aid in
prognosis and
IPC
implementation
–
repeated specimens
can
enhance understanding of viral
replication
patterns and response to experimental treatments for research
purposes
(use
standard
protocol)
–
serial collection should be part of standardized protocol (e.g. ISARIC
protocol).
Laboratory testing
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Diagnostic tests for C
0
V
ID-19
EMERGENCIES
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r
og
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•
This
is a
rapidly evolving area of work.
•
Real time (RT-PCR)
is
currently recommended for diagnosis of
patients
with
suspected
C
O
V
ID-19
.
–
As sequence information from the C
O
V
ID-19
has recently been made
available, PCR
assays can
be designed to detect these
sequences.
•
For latest information refer to your national laboratory and health ministry
recommendations and to the C
O
V
ID-19
website.
https://
www.who.int/emergencies/diseases/novel-coronavirus-2019
https://
www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-
guidance
Diagnostic tests for
2019-nCoV
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•
Laboratories may desire to use
a
pan-coronavirus
assay
for amplification
followed by sequencing of amplicons from non-conserved regions for
characterization and
confirmation.
•
The importance of the need for confirmation of results of testing
with
pan-
coronavirus primers
is
underscored by the
fact
that four human coronaviruses
(HcoVs)
are endemic globally: HCoV-229E, HCoV-NL63,
HCoV-HKU1 as
well
as
HCoV-OC43.
–
The
latter two are.
betacoronaviruses. Two other betacoronaviruses
that
cause
zoonotic
infection in
humans
are
MERS-CoV, acquired by.
contact with
dromedary camels and
SARS
arising from civets
and cave-dwelling horseshoe
bats
Diagnostic tests for
2019-nCoV
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•
Alternatively, amplification and detection of 2019-nCoV specific sequences
can
be diagnostic without the necessity for further
sequencing.
•
If
testing does not
occur in an
expert/reference laboratory
it is
encouraged to
send the sample for confirmation to
a
regional, national or international.
reference laboratory
with
pan-coronavirus or specific 2019-nCoV detection
capacity.
–
WHO
can assist
Member States to identify laboratories able to provide this
support
•
If case
management requires, screen
also
for other common causes
of
respiratory illness according to
local
guidelines,
as
co-infections
can
occur.
•
In hospitalized patients with confirmed nCoV infection, repeat URT and
LRT samples should be collected to demonstrate viral clearance.
•
The frequency of specimen collection will depend on local
circumstances but should be at least every 2 to 4 days until there are
two consecutive negative results (both URT and LRT samples if
both are collected) in a clinically recovered patient at least 24
hours apart.
•
If local infection control practice requires two negative results before
removal of droplet precautions, specimens may be collected as often as
daily.
Laboratory Crterion for Cure
Su
mm
a
ry
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•
Sample for diagnosis of COVID should be collected as soon as possible and
delivered to laboratory to get a good diagnostic yield.
•
It is important to apply appropriate IPC precautions during the sample
collection.
•
It important to use to the correct sample collection container and to use a viral
transport medium and at the right tempearure during the sample transportation
to get a good diagnostic yield.
•
Lower tract samples
can
be useful when upper samples are not diagnostic
and
usually provided a better diagnostic yield.
Contributors
Dr Cheryl
Cohen,
National
Institute
for
Communicable
Diseases (NICD), Johannesburg,
South
Africa
Dr Shabir Madhi,
University of the
Witwatersrand, Johannesburg,
South
Africa
Dr Niranjan
Bhat, Johns Hopkins University, Baltimore,
USA
Dr
Tim Uyeki,
Centers for Disease
Control and Prevention,
Atlanta,
USA
Dr Fred Hayden,
University of
Virginia,
USA
Dr
Owen Tsang, Hospital Authority,
Princess Margaret
Hospital, Hong Kong,
SAR, China
Dr
Leo Yee Sin, Tan Tock Seng Hospital, Communicable
Disease Centre,
Singapore
Dr Janet
Diaz, WHO Consultant, San
Francisco CA,
USA
Dr
Vu Quoc
Dat,
Hanoi
Medical
University and
National
Hospital of
Tropical Diseases,
Hanoi, Viet
Nam
Dr Natalia
Pshenichnaya,
Rostov
State
Medical
University,
Russian
Federation
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Acknowledgements
Rapid and accurate specimen collection is crucial for diagnosing COVID-19. Learn about optimal transportation conditions, different diagnostic tests, and specimen collection guidelines to combat health emergencies effectively.
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Presentation Transcript
MODULE3: DIAGNOSIS OF COVID-19: Specimen Collection, Transportation & Diagnostic Tests HEALTH EMERGENCIES programme
Learning objectives At the end of this session, you will be able to: Describe when and what specimens to collect for Laboratory diagnosis of COVID-19. To describe the Optimal conditions for transportation of samples for COVID-19. To describe the characteristics of diffrenet diagnostic tests used for the diagnosis of COVID-19. HEALTH EMERGENCIES programme
Rapid collection and testing of appropriate specimens from suspected cases is a priority and should be guided by a laboratory expert. As extensive testing is still needed to confirm the COVID-19 virus and the role of mixed infection has not been verified, multiple tests may need to be performed and sampling sufficient clinical material is recommended. Local guidelines established by the testing Lab (UVRI) should be followed regarding patient or guardian s informed consent for specimen collection, testing and potentially future research.
Ensure that SOPs are available, and the appropriate staff is trained and available for appropriate collection, specimen storage, packaging and transport. There is still limited information on the risk posed by the reported coronavirus found in Wuhan, but it would appear samples prepared for molecular testing could be handled as would samples for influenza of with maximum biosafety precautions as appropriate. Attempts to culture the virus may require heightened biosafety control measures.
Specimen collection HEALTH EMERGENCIES programme
Collect correct biological Specimens Respiratory material* (nasopharyngeal and oropharyngeal swab in ambulatory patients sputum (if produced) and/or endotracheal aspirate or bronchoalveolar lavage in patients with more severe respiratory disease) Serum for serological testing, acute sample and convalescent sample (this is additional to respiratory materials and can support the identification of the true agent, once serologic assay is available)
Upper respiratory tract samples Use appropriate PPE during collection procedure (gown, mask, gloves and eye protection). Nasal or nasopharyngeal samples have highest yield for detection of the virus. Also collect throat swabs to improve suspected emerging COVID-19. the yield for Collect samples as soon as possible. Ideally samples should be collected less than 4 days from illness onset for seasonal influenza A or B, as yield goes down as viral shedding decreases.. This may also be true for COVID-19 HEALTH EMERGENCIES programme
Risk assessment for appropriate use of PPE Minimize direct unprotected exposure to blood and body fluids. SCENARIO GLOVES GOWN HAND HYGIENE MEDICAL MASK EYE- WEAR Always before and after patient contact, and after contaminated environment If direct contact with blood and body fluids, secretions, excretions, mucous membranes, non-intact skin If there is risk of splashes onto the health care worker s body If there is a risk of splashes onto the body and face x x x x x x x x x x x HEALTH programme EMERGENC IES
Use sterile dacron or rayon swabs. Do not use cotton swabs or wood shafts as can interfere with RT-PCR assays Nasopharyngeal swabs Throat swabs HEALTH EMERGENCIES programme
Lower respiratory tract samples Also collect lower respiratory tract samples in patients with radiographic evidence or clinical diagnosis of lower respiratory tract disease, in certain situations, if results will impact clinical interventions: expectorated sputum tracheal aspirates bronchoalveolar lavage. Can generate aerosols, thus use airborne precautions during procedure. HEALTH EMERGENCIES programme
In intubated patient, can collect tracheal aspirate Collection can generate aerosols, thus use airborne precautions. Using sterile collection trap. Do not send suction catheter tip to laboratory. HEALTH EMERGENCIES programme
Benefits of lower respiratory tract samples Higher sensitivity than upper respiratory specimens for zoonotic influenza virus, MERS-CoV and Probably for COVID-19. Increases diagnostic yield for seasonal in if upper samples are negative or tested late and may be the same for COVID-19. Can also be used to tested for other pathogens such bacterial, fungal and parasitic infections if suspected as co-infection. e.g. M. tuberculosis, PjP. HEALTH EMERGENCIES programme
Sample Transportation There must be ready means of transport to take the sample to lab immediately upon collection. All specimens collected for laboratory investigations should be regarded as potentially infectious, and HCWs who collect, or transport clinical specimens should adhere rigorously to infection prevention and control guidelines and national or international regulations for the transport of dangerous goods (infectious substances) to minimize the possibility of exposure to pathogens. Implement the appropriate infection prevention and control precautions during transportation. *Good communication with the laboratory and provide needed information* To ensure proper and fast processing of samples and to assure adequate biosafety measures in the laboratory, communication and information sharing is essential. Be sure you have alerted the laboratory of the urgency and situation before sending the sample. Also assure that specimens are correctly labelled, and diagnostic request forms are filled out properly and clinical information is provided (see box: information to be recorded)
Specimen type Collection materials Dacron or polyester flocked swabs* Transport to Laboratory 4 C Storage till testing Comment Nasopharyngeal and oropharyngeal swab 5 days: 4 C >5 days: -70 C The nasopharyngeal andoropharyngeal swabs should be placed in the same tube toincrease the viral load. There may be some dilutionof pathogen, but still a worthwhile specimen Broncoalveolar Lavage sterile container 4 C 48 hours: 4 C >48 hours: -70 C (Endo)tracheal aspirate, nasopharyngeal aspirate or nasal wash Sputum Sterile Container 4 oC 48 hours: 4 C >48 hours: -70 C Sterile container 4 C 48 hours: 4 C >48 hours: -70 C 24 hours: 4 C >24 hours: 70 C Ensure the material is from the lower respiratory tract Tissue from biopsy or autopsy including from lung Serum (2 samples acute and convalscent possibly 2-4 weeks after acute phase. Whole blood sterile container with saline Serum separator tubes (adults: collect 3-5mls whole blood) 4 C collection tube 4 C Collect paired samples: Acute-first week of illness; Convalscent-2-3weeks later For antigen detection particularly in the first week of illness 5 days: 4 C >5days:- 70 C 5 days: 4 C >5days:- 70 C 5 days: 4 C >5days:- 70 C 4 C Urine Collectin container Urine 4 C
Information to be recorded for the sample Patient information name, date of birth, sex and residential address, unique identification number, other useful information (e.g. patient hospital number, surveillance identification number, name of hospital, hospital address, room number, physicians name and contact information, name and address for report recipient), Date and time of sample collection, Anatomical site and location of specimen collection, Tests requested, Clinical symptoms and relevant patient history (including vaccination and antimicrobial therapies received, epidemiological information, risk factors).
Laboratory testing HEALTH EMERGENCIES programme
Diagnostic tests for C0VID-19 This is a rapidly evolving area of work. Real time (RT-PCR) is currently recommended for diagnosis of patients with suspected COVID-19. As sequence information from the COVID-19 has recently been made available, PCR assays can be designed to detect these sequences. For latest information refer to your national laboratory and health ministry recommendations and to the COVID-19 website. https://www.who.int/emergencies/diseases/novel-coronavirus-2019 https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical- guidance HEALTH EMERGENCIES programme
Diagnostic tests for 2019-nCoV Laboratories may desire to use a pan-coronavirus assay for amplification followed by sequencing of amplicons from non-conserved regions for characterization and confirmation. The importance of the need for confirmation of results of testing with pan- coronavirus primers is underscored by the fact that four human coronaviruses (HcoVs) are endemic globally: HCoV-229E, HCoV-NL63, HCoV-HKU1 as well as HCoV-OC43. The latter two are. betacoronaviruses. Two other betacoronaviruses that cause zoonotic infection in humans are MERS-CoV, acquired by. contact with dromedary camels and SARS arising from civets and cave-dwelling horseshoe bats HEALTH EMERGENCIES programme
Diagnostic tests for 2019-nCoV Alternatively, amplification and detection of 2019-nCoV specific sequences can be diagnostic without the necessity for further sequencing. If testing does not occur in an expert/reference laboratory it is encouraged to send the sample for confirmation to a regional, national or international. reference laboratory with pan-coronavirus or specific 2019-nCoV detection capacity. WHO can assist Member States to identify laboratories able to provide this support If case management requires, screen also for other common causes of respiratory illness according to local guidelines, as co-infections can occur. HEALTH EMERGENCIES programme
Laboratory Crterion for Cure In hospitalized patients with confirmed nCoV infection, repeat URT and LRT samples should be collected to demonstrate viral clearance. The frequency of specimen collection will depend on local circumstances but should be at least every 2 to 4 days until there are two consecutive negative results (both URT and LRT samples if both are collected) in a clinically recovered patient at least 24 hours apart. If local infection control practice requires two negative results before removal of droplet precautions, specimens may be collected as often as daily.
Summary Sample for diagnosis of COVID should be collected as soon as possible and delivered to laboratory to get a good diagnostic yield. It is important to apply appropriate IPC precautions during the sample collection. It important to use to the correct sample collection container and to use a viral transport medium and at the right tempearure during the sample transportation to get a good diagnostic yield. Lower tract samples can be useful when upper samples are not diagnostic and usually provided a better diagnostic yield. HEALTH EMERGENCIES programme
Acknowledgements Contributors Dr Cheryl Cohen, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa Dr Shabir Madhi, University of the Witwatersrand, Johannesburg, South Africa Dr Niranjan Bhat, Johns Hopkins University, Baltimore, USA Dr Tim Uyeki, Centers for Disease Control and Prevention, Atlanta, USA Dr Fred Hayden, University of Virginia, USA Dr Owen Tsang, Hospital Authority, Princess Margaret Hospital, Hong Kong, SAR, China Dr Leo Yee Sin, Tan Tock Seng Hospital, Communicable Disease Centre, Singapore Dr Janet Diaz, WHO Consultant, San Francisco CA, USA Dr Vu Quoc Dat, Hanoi Medical University and National Hospital of Tropical Diseases, Hanoi, Viet Nam Dr Natalia Pshenichnaya, Rostov State Medical University, Russian Federation HEALTH EMERGENCIES programme
