Point of care testing for respiratory virusesJen KokMedical VirologistCentre for Infectious Diseases and Microbiology Laboratory ServicesPathology West ICPMR Westmead [email protected]
Outline
• rationale for testing, testing methods and
impact of testing
• factors affecting performance of tests
– sample, transport, age of patient, novel virus
• examples of platforms
• surveillance
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Why test those meeting clinical case
definition of ILI (fever + cough/sore throat)?
• individual patient management
– antivirals
– obviates unnecessary tests and treatments
– infection control measures
• epidemiological purposes
– emerging pathogens
– monitoring of secular trends of existing pathogens
– pandemic preparedness planning
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Respiratory virus diagnostic methods
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Type of test Sensitivity
Turn
around
time
Advantages Disadvantages
POCT/RIDT 18-77%15-30
mins
Rapid
Simple
No need for
specialised
laboratory
Influenza A and
B typing
possible
Expensive
Limited shelf life
Lower sensitivity
False positives
and negatives
Specimen quality
important
Nucleic acid
detection ~98 - 100% ~4 hours
Sensitive
Typing and
subtyping
possible
Can detect
viable and non-
viable virus
Requires
technical
expertise and
specialised
equipment
Expensive
Clinician’s perspective: which diagnostic
method?
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
24/7
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Accurate
TAT
Cost
Laboratory’s perspective: which diagnostic
method?
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
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Workflow
Automation
Throughput
Random access
TAT
Complexity
Expertise
Instruments
Cost*
*reagents, labor,
instruments, QAP,
transport
A positive RIDT alters outpatient
pediatrician practices in ILIs
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Jennings IORV 2009
Clearview Exact Influenza A + Bo increase antiviral therapyo reduce antibiotic therapy
Impact of RIDT in EDs
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Bonner Pediatrics 2003
MD aware RIDT positive (n=96)
MD unaware RIDT positive
(n=106)P value
CBC 0 13 (12%) <0.001
BC 0 11 (13%) <0.001
Urinalysis 2 (2%) 12 (11%) 0.011
CXR 7 (7%) 26 (25%) 0.001
Charge/patient $15.65 $92.37 <0.001
Antibioticprescription
7 (7%) 26 (25%) <0.001
Antiviralprescription
18 (19%) 7 (7%) 0.02
Mean time from exam to discharge
25 minutes 49 minutes <0.001
Impact of RIDT on hospital inpatients
RIDT negative (n=80)
RIDT positive (n=86)
P value
Antibiotic use 79 (99%) 74 (86%) 0.002
Antiviral use 6 (8%) 63 (73%) <0.001
Antibiotics ceased because of influenza
2 (2%) 12 (14%) 0.004
Discharged from hospital whilst on
antibiotics51 (64%) 38 (44%) 0.006
Length of stay 7.9 ± 4.2 days 9.6 ± 10 days 0.16
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital Falsey Arch Intern Med 2007
multivariate analysis for discontinuing antibioticspositive RIDT OR of 6.90 (95% CI 2.0 – 32.70) p=0.005
Detection of influenza virus in samples collected, stored
and transported using media at different temperatures
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital Druce J Clin Microbiol 2012
4OC 22OC
37OC
Liquid Amies
Rate of detection of respiratory viruses differs
according to age and samples tested
Recoveryusing flocked
swabs
Recoveryusing
comparator
p values andΔ in CT values
(flocked swab –comparator)
DeByleJ Virol Methods 2012 (n=314 children < 3 years)
79 – 89% (nasopharyngeal)
69 – 94% (nasal wash)
p=0.069 – 1.00.6 – 7.0
MunywokiJ Clin Microbiol2011 (n=299 children < 13 years)
89.6% (nasopharyngeal)
79.2% (nasal wash)
p=0.0043-1 – -2
HernesEur J Clin MicrobiolInfect Dis 2011 (n=223 adults)
78% (nasopharyngeal)
63% (oropharyngealflocked swabs)
p <0.01-5.75
Sensitivity of antigen tests stratified according to
age groups in 2009 (n=2274)
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Unpublished data
Age group
RIDTpH1N1 Non-pH1N1
IFApH1N1 Non-pH1N1
0-1 years (n=65 RIDT, 46 IFA)
87.5% 100% 86.7% 90%
2-5 years (n=61 RIDT, 25 IFA)
70% 87.5% 100% 100%
6-15 years (n=160 RIDT, 25 IFA)
69.3% 71.9% 86.7% 83.3%
≥16 years (n=1503 RIDT, 389 IFA)
42.4% 72.1% 39.8% 56.7%
Kok ASID 2010
Important to test lower respiratory tract in critically
ill (adult) patients with influenza
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
RIDT (QuickVue) and IFA vs NAT
• 21 patients with severe A(H1N1)pdm09 infection requiring
respiratory support with paired URT / LRT samples
• Nose and/or throat swabs: RIDT
• BAL/mini BAL: IFA
• All samples: NAT
*** ***p < 0.01
Blyth N Engl J Med 2009
***
Reduced sensitivity of RIDT (QuickVue) for newly
circulating pandemic influenza virus
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Kok J Clin Microbiol 2010
Should RIDT be performed “in the lab”
or “in the field”?
• parallel testing of RIDT using NAT/viral
culture as gold standard (n=124 samples)
• transported at 4OC, tested within 24h
• inter-operator variability (WYD 2008)
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
OperatorSensitivity
(%)
Specificity
(%)PPV (%) NPV (%)
Trained
(n=59)60* 96.6 94.7 70
Untrained
(n=65)34.6* 89.7 69.2 67.3
Foo J Clin Virol 2009
*p > 0.05
RIDT : Rapid (15 - 20 minutes)
Rapid respiratory virus diagnostic tests
Turnaround times (minutes)
Sensitivity Specificity
Lateral flow immunochromatography (BinaxNOW)
15 minutesInfluenza A: 44%Influenza B: 25%
RSV: 63 – 65%
Influenza A: 100%Influenza B: 100%
RSV: 100%
Fluorescent immunoassay(Sofia)
15 minutesInfluenza A: 71.4%Influenza B: 33.3%
RSV: 92.9%
Influenza A: 98.2%Influenza B: 99.5%
RSV: 100%
Loop mediated isothermalamplification (Alere i)
15 minutesInfluenza A: 77.8%Influenza B: 75%
Influenza A: 100%Influenza B: 99%
Photon fluorescent excitation(mariPOC)
20 minutesInfluenza A: 71%Influenza B: 86%
RSV: 89%
Influenza A: 100%Influenza B: 98%
RSV: 100%
Hazelton J Med Virol 2014, IORV 2015; Ivaska J Clin Virol 2013
PPV and NPV of RIDT depends on
prevalence of flu
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
If flu prevalence is…
and specificity is…
then PPV is…
very low (2.5%) good (98%) poor (39 – 56%)
moderate (20%) good (98%) good (86 - 93%)
If flu prevalence is…
and sensitivity is…
then NPV is…
moderate (20%) poor (50%) moderate (86 –89%)
high (40%) poor (50%) very good (93 –94%)
RIDT : Rapid (20 minutes – 4 hours)
Rapid respiratory virus diagnostic tests
Turnaround times (minutes)
Sensitivity Specificity
Cobas Liat Influenza A/B (Roche Diagnostics)
20 minutesInfluenza A: 99.2%Influenza B: 100%
Influenza A: 100%Influenza B: 100%
Xpert Flu (Cepheid) 40 – 75 minutesInfluenza A: 97.8%Influenza B: 100%
RSV: 90.6%
Influenza A: 100%Influenza B: 99.4%
RSV: 99.4%
FilmArray RP (BioFire/bioMerieux)
1 hour17 viruses
Up to 100%17 viruses
Up to 100%
Simplexa Flu A/B + RSV Direct (Focus Diagnostics)
1 – 4 hours
Influenza A: 91.7 -100%
Influenza B: 97.5 -100%
Influenza A: 99.4 -100%
Influenza B: 98.1 -99.4%
Binnicker J Clin Microbiol 2015, Popowitch J Clin Microbiol 2015, Babady Expert Rev Mol Diagn 2013, KoJ Med Virol 2013
San Diego
Wireless transmission of influenza
surveillance data
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital courtesy of John Tamerius
San Diego
CDC, Atlanta
WI
Daily at midnight (optional)
Daily
Dept. of Hygiene, Madison
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Feedback of data to Wisconsin State Department of
Hygiene and CDC Atlanta
courtesy of John Tamerius
Laboratory surveillance of influenza
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital NSW Health 2015
Novel antiviral agents for respiratory viruses
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Virus Existing agentsNovel agents in development
Influenza
Amantadine, Rimantidine
Zanamivir, Laninamivir, Oseltamivir, Peramivir
Favipiravir
DAS181 (Fludase®)CR6261CR8020
AVI-7100VX-787
RSVRibavirin
PalivizumabMotavizumab
GS-5806ALS-008176
RI-001ALN-RSV01TMC353121
MDT-637ALX-0171
Novel antiviral agents for respiratory viruses
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
Virus Existing agents Novel agents in development
Parainfluenza virus - DAS181 (Fludase®)
Rhinovirus -Vapendavir
(BTA798)SNG001 (IFN-β)
Adenovirus CidofovirBrincidofovir
(CMX001)
Conclusions
• laboratory diagnosis of viral infections
important
– impact of availability of rapid test result
– novel antivirals for specific viruses
• technological advances
– multi-analyte rapid molecular based tests
– real-time surveillance
• quality and regulatory aspects
• costs
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital
icpmrCentre for Infectious Diseases and Microbiology, Westmead Hospital