Diagnosis of SARS-CoV-2 in children: accuracy of nasopharyngeal swab compared to nasopharyngeal aspirate

The effect of sample site and collection procedure on identification of SARS-CoV-2 infection

BACKGROUND

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.

OBJECTIVES

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.

SEARCH METHODS

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.

SELECTION CRITERIA

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.

DATA COLLECTION AND ANALYSIS

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.

MAIN RESULTS

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).

AUTHORS' CONCLUSIONS

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.

Epidemiology and Clinical Features of COVID-19 among 4,015 Neonates in Iran: Results of the National Study from the Iranian Maternal and Neonatal Network

OBJECTIVE

The coronavirus disease 2019 (COVID-19) pandemic had a significant impact on pregnant women and neonates in Iran. This retrospective study describes the national experience among neonates having suspected and confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection following hospital admission to examine the epidemiology, demographic, and clinical features.

STUDY DESIGN

All nationwide cases of suspected and confirmed neonatal SARS-CoV-2 infection were drawn from the Iranian Maternal and Neonatal Network (IMaN) between February 2020 and February 2021. IMaN registers demographic, maternal, and neonatal health data throughout Iran. Statistical analysis of demographic, epidemiological, and clinical data were performed.

RESULTS

There were 4,015 liveborn neonates having suspected or confirmed SARS-CoV-2 infection that fulfilled the study inclusion criteria identified in the IMaN registry from 187 hospitals throughout Iran. There were 1,392 (34.6%) neonates that were preterm, including 304 (7.6%) less than 32 weeks' gestation. Among the 2,567 newborns admitted to the hospital immediately after birth, the most common clinical problems were respiratory distress (1,095 cases; 42.6%), sepsis-like syndrome (355; 13.8%), and cyanosis (300 cases; 11.6%). Of 683 neonates transferred from another hospital, the most frequent problems were respiratory distress (388; 56.8%), sepsis-like syndrome (152; 22.2%), and cyanosis (134; 19.6%). Among 765 neonates discharged home after birth and subsequently admitted to the hospital, sepsis-like syndrome (244 cases; 31.8%), fever (210; 27.4%), and respiratory distress (185; 24.1%) were most frequent. A total of 2,331 (58%) of neonates required respiratory care, with 2,044 surviving and 287 having a neonatal death. Approximately 55% of surviving neonates received respiratory support, compared with 97% of neonates who expired. Laboratory abnormalities included elevations of white blood cell count, creatine phosphokinase, liver enzymes, and C-reactive protein.

CONCLUSION

This report adds the national experience of Iran to the list of reports from multiple countries describing their experience with COVID-19 in neonates, demonstrating that newborns are not exempt from COVID-19-morbidity and mortality.

KEY POINTS

· Most common clinical problem was respiratory distress.. · Sepsis-like syndrome was also frequently present.. · A total of 58% of all neonates required respiratory care..

SARS-CoV-2 infection in children: A 24 months experience with focus on risk factors in a pediatric tertiary care hospital in Milan, Italy

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children is characterized by a wide variety of expressions ranging from asymptomatic to, rarely, critical illness. The basis of this variability is not yet fully understood. The aim of this study was to identify clinical and genetic risk factors predisposing to disease susceptibility and progression in children.

METHODS

We enrolled 181 consecutive children aged less than 18 years hospitalized with or for SARS-CoV-2 infection during a period of 24 months. Demographic, clinical, laboratory, and microbiological data were collected. The development of coronavirus disease 2019 (COVID-19)-related complications and their specific therapies were assessed. In a subset of 79 children, a genetic analysis was carried out to evaluate the role of common COVID-19 genetic risk factors (chromosome 3 cluster; ABO-blood group system; FUT2, IFNAR2, OAS1/2/3, and DPP9 loci).

RESULTS

The mean age of hospitalized children was 5.7 years, 30.9% of them being under 1 year of age. The majority of children (63%) were hospitalized for reasons different than COVID-19 and incidentally tested positive for SARS-CoV-2, while 37% were admitted for SARS-CoV-2 infection. Chronic underlying diseases were reported in 29.8% of children. The majority of children were asymptomatic or mildly symptomatic; only 12.7% developed a moderate to critical disease. A concomitant pathogen, mainly respiratory viruses, was isolated in 53.3%. Complications were reported in 7% of children admitted for other reasons and in 28.3% of those hospitalized for COVID-19. The respiratory system was most frequently involved, and the C-reactive protein was the laboratory test most related to the development of critical clinical complications. The main risk factors for complication development were prematurity [relative risk (RR) 3.8, 95% confidence interval (CI) 2.4-6.1], comorbidities (RR 4.5, 95% CI 3.3-5.6), and the presence of coinfections (RR 2.5, 95% CI 1.1-5.75). The OAS1/2/3 risk variant was the main genetic risk factor for pneumonia development [Odds ratio (OR) 3.28, 95% CI 1-10.7; p value 0.049].

CONCLUSION

Our study confirmed that COVID-19 is generally less severe in children, although complications can develop, especially in those with comorbidities (chronic diseases or prematurity) and coinfections. Variation at the OAS1/2/3 genes cluster is the main genetic risk factor predisposing to COVID-19 pneumonia in children.

[The nasal and pharyngeal swab techniques during the COVID-19-pandemic - the ENT-perspective - SARS-CoV-2, Coronavirus, nasal swab, pharyngeal swab, complications]

Since the beginning of the SARS-CoV-2 pandemic, swabs or other samples have increasingly been taken from the upper aero-digestive tract, since high viral loads exist here, especially in the early stages of the disease. As diagnostic options, swabs from the anterior nose, from the nasopharynx, from the oropharynx or the extraction of throat rinse water or saliva are possible. The laboratory methods available are antigen tests that can be read in a few minutes or more lengthy RT-PCR methods in a lab. Swabs are carried out by physicians, medical staff, laypeople and in the self-test, in each case according to prior instructions. Many of these factors therefore have an influence on the informative value and the sensitivity of the entire diagnostic process. The PCR laboratory method is more sensitive than the antigen method; the swabs from the nasopharynx are considered the most valid smear site; correct execution of a test can be achieved even with non-professional individuals with good instructions. Complications with such swabs are reported very rarely, given the assumed number of procedures performed. Short-term nosebleeds after traumatic smears can be assumed without publications about it being found. Broken parts of swabs had to be removed by an ENT doctor. There are only very few reports on injuries to the skullbase with CSF-leaks, including 2 times with anomalies such as meningoceles. The choice of a suitable diagnostic medium depends on many parameters such as availability, the timing of the result, a smear test by knowledgeable staff or a self-test, and a number of other practical considerations.

Intussusception in an Infant With SARS-CoV-2 Infection: A Case Report and a Review of the Literature

Coronavirus disease 2019 (COVID-19) is caused by acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Even if predominantly considered a respiratory pathogen, it could be associated with gastrointestinal involvement, generally in mild forms. Recent reports highlight the association between SARS-CoV-2 and intussusception in infants. A case of intussusception is hereby described in a previously healthy infant in whom the diagnosis of SARS-CoV-2 was made after the analysis of bronchoalveolar lavage and intraoperative specimens following surgical procedures. Accordingly, a review of infant cases with intussusception and SARS-CoV-2 infection is also reported.