The effect of sample site and collection procedure on identification of SARS-CoV-2 infection.
Sample collection is a key driver of accuracy in the diagnosis of SARS-CoV-2 infection. Viral load may vary at different anatomical sampling sites and accuracy may be compromised by difficulties obtaining specimens and the expertise of the person taking the sample. It is important to optimise sampling accuracy within cost, safety and accessibility constraints.
To compare the sensitivity of different sampling collection sites and methods for the detection of current SARS-CoV-2 infection with any molecular or antigen-based test.
Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 22 February 2022. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions.
We included studies of symptomatic or asymptomatic people with suspected SARS-CoV-2 infection undergoing testing. We included studies of any design that compared results from different sample types (anatomical location, operator, collection device) collected from the same participant within a 24-hour period.
Within a sample pair, we defined a reference sample and an index sample collected from the same participant within the same clinical encounter (within 24 hours). Where the sample comparison was different anatomical sites, the reference standard was defined as a nasopharyngeal or combined naso/oropharyngeal sample collected into the same sample container and the index sample as the alternative anatomical site. Where the sample comparison was concerned with differences in the sample collection method from the same site, we defined the reference sample as that closest to standard practice for that sample type. Where the sample pair comparison was concerned with differences in personnel collecting the sample, the more skilled or experienced operator was considered the reference sample. Two review authors independently assessed the risk of bias and applicability concerns using the QUADAS-2 and QUADAS-C checklists, tailored to this review. We present estimates of the difference in the sensitivity (reference sample (%) minus index sample sensitivity (%)) in a pair and as an average across studies for each index sampling method using forest plots and tables. We examined heterogeneity between studies according to population (age, symptom status) and index sample (time post-symptom onset, operator expertise, use of transport medium) characteristics.
This review includes 106 studies reporting 154 evaluations and 60,523 sample pair comparisons, of which 11,045 had SARS-CoV-2 infection. Ninety evaluations were of saliva samples, 37 nasal, seven oropharyngeal, six gargle, six oral and four combined nasal/oropharyngeal samples. Four evaluations were of the effect of operator expertise on the accuracy of three different sample types. The majority of included evaluations (146) used molecular tests, of which 140 used RT-PCR (reverse transcription polymerase chain reaction). Eight evaluations were of nasal samples used with Ag-RDTs (rapid antigen tests). The majority of studies were conducted in Europe (35/106, 33%) or the USA (27%) and conducted in dedicated COVID-19 testing clinics or in ambulatory hospital settings (53%). Targeted screening or contact tracing accounted for only 4% of evaluations. Where reported, the majority of evaluations were of adults (91/154, 59%), 28 (18%) were in mixed populations with only seven (4%) in children. The median prevalence of confirmed SARS-CoV-2 was 23% (interquartile (IQR) 13%-40%). Risk of bias and applicability assessment were hampered by poor reporting in 77% and 65% of included studies, respectively. Risk of bias was low across all domains in only 3% of evaluations due to inappropriate inclusion or exclusion criteria, unclear recruitment, lack of blinding, nonrandomised sampling order or differences in testing kit within a sample pair. Sixty-eight percent of evaluation cohorts were judged as being at high or unclear applicability concern either due to inflation of the prevalence of SARS-CoV-2 infection in study populations by selectively including individuals with confirmed PCR-positive samples or because there was insufficient detail to allow replication of sample collection. When used with RT-PCR • There was no evidence of a difference in sensitivity between gargle and nasopharyngeal samples (on average -1 percentage points, 95% CI -5 to +2, based on 6 evaluations, 2138 sample pairs, of which 389 had SARS-CoV-2). • There was no evidence of a difference in sensitivity between saliva collection from the deep throat and nasopharyngeal samples (on average +10 percentage points, 95% CI -1 to +21, based on 2192 sample pairs, of which 730 had SARS-CoV-2). • There was evidence that saliva collection using spitting, drooling or salivating was on average -12 percentage points less sensitive (95% CI -16 to -8, based on 27,253 sample pairs, of which 4636 had SARS-CoV-2) compared to nasopharyngeal samples. We did not find any evidence of a difference in the sensitivity of saliva collected using spitting, drooling or salivating (sensitivity difference: range from -13 percentage points (spit) to -21 percentage points (salivate)). • Nasal samples (anterior and mid-turbinate collection combined) were, on average, 12 percentage points less sensitive compared to nasopharyngeal samples (95% CI -17 to -7), based on 9291 sample pairs, of which 1485 had SARS-CoV-2. We did not find any evidence of a difference in sensitivity between nasal samples collected from the mid-turbinates (3942 sample pairs) or from the anterior nares (8272 sample pairs). • There was evidence that oropharyngeal samples were, on average, 17 percentage points less sensitive than nasopharyngeal samples (95% CI -29 to -5), based on seven evaluations, 2522 sample pairs, of which 511 had SARS-CoV-2. A much smaller volume of evidence was available for combined nasal/oropharyngeal samples and oral samples. Age, symptom status and use of transport media do not appear to affect the sensitivity of saliva samples and nasal samples. When used with Ag-RDTs • There was no evidence of a difference in sensitivity between nasal samples compared to nasopharyngeal samples (sensitivity, on average, 0 percentage points -0.2 to +0.2, based on 3688 sample pairs, of which 535 had SARS-CoV-2).
When used with RT-PCR, there is no evidence for a difference in sensitivity of self-collected gargle or deep-throat saliva samples compared to nasopharyngeal samples collected by healthcare workers when used with RT-PCR. Use of these alternative, self-collected sample types has the potential to reduce cost and discomfort and improve the safety of sampling by reducing risk of transmission from aerosol spread which occurs as a result of coughing and gagging during the nasopharyngeal or oropharyngeal sample collection procedure. This may, in turn, improve access to and uptake of testing. Other types of saliva, nasal, oral and oropharyngeal samples are, on average, less sensitive compared to healthcare worker-collected nasopharyngeal samples, and it is unlikely that sensitivities of this magnitude would be acceptable for confirmation of SARS-CoV-2 infection with RT-PCR. When used with Ag-RDTs, there is no evidence of a difference in sensitivity between nasal samples and healthcare worker-collected nasopharyngeal samples for detecting SARS-CoV-2. The implications of this for self-testing are unclear as evaluations did not report whether nasal samples were self-collected or collected by healthcare workers. Further research is needed in asymptomatic individuals, children and in Ag-RDTs, and to investigate the effect of operator expertise on accuracy. Quality assessment of the evidence base underpinning these conclusions was restricted by poor reporting. There is a need for further high-quality studies, adhering to reporting standards for test accuracy studies.
Davenport C
，Arevalo-Rodriguez I
，Mateos-Haro M
，Berhane S
，Dinnes J
，Spijker R
，Buitrago-Garcia D
，Ciapponi A
，Takwoingi Y
，Deeks JJ
，Emperador D
，Leeflang MMG
，Van den Bruel A
，Cochrane COVID-19 Diagnostic Test Accuracy Group
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《Cochrane Database of Systematic Reviews》
The value of fractional flow reserve based on coronary computed tomography angiography with low-dose contrast agent in noninvasive diagnosis of coronary artery disease.
The study aimed, using invasive coronary angiography (ICA) as the gold standard, to investigate the noninvasive diagnostic value of flow reserve fraction derived from coronary computed tomography angiography (CCTA) with low-dose contrast agent in coronary artery disease (CAD).
A total of 163 patients with clinical symptoms related to CAD were enrolled between 1 January 2022 and 30 January 2023. The patients received CCTA with a low dose of contrast agent to rule out CAD. If significant (CCTA ≥ 50%) stenosis is suspected, ICA is performed to further evaluate the CCTA for coronary lesions. CT-FFR is calculated from the CCTA dataset using a machine learning-based algorithm. Compared with ICA as a reference standard, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of low-dose contrast agent CT-FFR in the diagnosis of myocardial ischemia were calculated. Coronary lesions with CT-FFR ≤0.80 were defined as hemodynamically significant.
Obstructive CAD was excluded by low-contrast CCTA in 87 of 163 patients (53.7%). In the remaining 75 patients (42.35%), at least one coronary artery stenosis was greater than 50%. The accuracy, sensitivity, specificity, PPV, and NPV of low-dose contrast agent CT-FFR on a patient-based evaluation in diagnosing CAD were 93.06, 93.44, 90.01, 98.28, and 71.43%, respectively (Kappa = 0.759). The accuracy, sensitivity, specificity, PPV, and NPV of low-dose contrast agent CT-FFR on a vessel-based evaluation in diagnosing CAD were 86.72, 82.76, 91.58, 92.31, and 81.31%, respectively (Kappa = 0.735). Pearson correlation analysis showed that the ICA examination had a good correlation with CT-FFR value of low-dose contrast media ( r = 0.731, P < 0.01). Moreover, in 81.31% of cases, additional analysis of CT-FFR correctly excluded the hemodynamic significance of stenosis.
CT-FFR based on low-dose contrast agent CCTA is a very promising noninvasive approach to exclude hemodynamically significant coronary artery stenosis in patients with suspected coronary heart disease while reducing renal burden and helping to reduce the rate of ICA in this high-risk population.
Wang Z
，Luan X
，Zhang Q
，Chu C
，Xu X
，Chai H
，Song P
... -
《-》
Invasive fractional-flow-reserve prediction by coronary CT angiography using artificial intelligence vs. computational fluid dynamics software in intermediate-grade stenosis.
Coronary computed angiography (CCTA) with non-invasive fractional flow reserve (FFR) calculates lesion-specific ischemia when compared with invasive FFR and can be considered for patients with stable chest pain and intermediate-grade stenoses according to recent guidelines. The objective of this study was to compare a new CCTA-based artificial-intelligence deep-learning model for FFR prediction (FFRAI) to computational fluid dynamics CT-derived FFR (FFRCT) in patients with intermediate-grade coronary stenoses with FFR as reference standard. The FFRAI model was trained with curved multiplanar-reconstruction CCTA images of 500 stenotic vessels in 413 patients, using FFR measurements as the ground truth. We included 37 patients with 39 intermediate-grade stenoses on CCTA and invasive coronary angiography, and with FFRCT and FFR measurements in this retrospective proof of concept study. FFRAI was compared with FFRCT regarding the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy for predicting FFR ≤ 0.80. Sensitivity, specificity, PPV, NPV, and diagnostic accuracy of FFRAI in predicting FFR ≤ 0.80 were 91% (10/11), 82% (23/28), 67% (10/15), 96% (23/24), and 85% (33/39), respectively. Corresponding values for FFRCT were 82% (9/11), 75% (21/28), 56% (9/16), 91% (21/23), and 77% (30/39), respectively. Diagnostic accuracy did not differ significantly between FFRAI and FFRCT (p = 0.12). FFRAI performed similarly to FFRCT for predicting intermediate-grade coronary stenoses with FFR ≤ 0.80. These findings suggest FFRAI as a potential non-invasive imaging tool for guiding therapeutic management in these stenoses.
Peters B
，Paul JF
，Symons R
，Franssen WMA
，Nchimi A
，Ghekiere O
... -
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ResearchGate
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