External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021.

INTRODUCTION: Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests. METHODS: In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/µL, positive sample B with 5 copies/µL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/µL was prepared using a simulated saliva sample. RESULTS: Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory. CONCLUSIONS: The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results.

The effect of the distraction methods used before the COVID-19 test on the fear and anxiety levels of children: a RCT study.

The current study aimed to investigate the effect of the distraction methods employed before nasopharyngeal swab sampling from children within the scope of the COVID test on their anxiety and fear levels. The study was an RCT with parallel groups conducted according to the CONSORT statement at the pediatric emergency unit of a hospital in Turkey. Children aged 5-10 years were randomized into three groups: Kaleidoscope, Visual Illusion Cards, and control. Data were collected by the researchers using the Descriptive Characteristics Form, the Children's Anxiety Meter-State, and the Children's Fear Scale. According to the reports of the children, the parents, and the nurse, the mean anxiety score and the mean fear score in the experimental groups were significantly lower after the nasopharyngeal swab procedure compared to the control group (p < .05). Fear and anxiety were observed less in the visual illusion cards group and the kaleidoscope group.

Cycle threshold values of SARS-CoV-2 RNA in conjunctival swabs and nasopharyngeal secretions: a comparative study from a tertiary care center in India.

PURPOSE: To detect the viral RNA load of SARS-CoV-2 in conjunctival swabs of COVID-19 patients, and compare with nasopharyngeal swabs. METHODS: Conjunctival swabs of COVID-19 patients (with PCR positive nasopharyngeal swabs) were subjected to quantitative reverse transcription-polymerase chain reaction (RT-PCR) for detection of SARS-CoV-2 RNA. The cycle threshold (Ct) values of Open Reading Frame 1 (ORF 1 Ab gene) and nucleoprotein (N gene) PCRs were used to assess the viral RNA load, and compare them with the baseline values of nasopharyngeal swabs. RESULTS: Of 93 patients, 17 (18.27%) demonstrated SARS-CoV-2 RNA in conjunctival swabs. Baseline nasopharyngeal swabs were collected at a median of 2 days; while, the conjunctival swabs were collected at median 7 days, from onset of illness (p < 0.001). Despite a significant delay in conjunctival swab collection than nasopharyngeal swabs, the Ct values (ORF or N gene PCRs) were comparable between nasopharyngeal swab and conjunctival swab samples. Subsequently, during the recovery period, in four of these 17 patients (with conjunctival swab positivity), when the second nasopharyngeal swab was 'negative', the conjunctival swab was 'positive'. CONCLUSION: The conjunctival swabs demonstrated SARS-CoV-2 RNA in 17 (18.27%) of 93 COVID-19 patients. Our results may suggest a delayed or a prolonged shedding of the virus/viral RNA on the ocular surface than in nasopharyngeal mucosa.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection.

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

Diagnostic test property of transcription-reverse transcription concerted reaction reagent TRCReady® SARS-CoV-2 i using nasopharyngeal swab samples.

TRCReady® SARS-CoV-2 i is a reagent for transcription-reverse transcription concerted reaction (TRC) to detect SARS-CoV-2 N2 gene, used with the automated rapid isothermal nucleic acid amplification test (NAAT) analyzer TRCReady®-80. Sensitivity and specificity of TRCReady® SARS-CoV-2 i was assessed by comparison with the results of real-time reverse transcription-polymerase chain reaction (RT-PCR) using nasopharyngeal swab samples. From November 2020 to March 2021, a total of 441 nasopharyngeal swabs were obtained and analyzed both with TRCReady® SARS-CoV-2 i and RT-PCR. Sensitivity and specificity of TRCReady® SARS-CoV-2 i were 94.6% (53/56) and 99.2% (382/385), respectively. Reaction time to positivity of TRCReady® SARS-CoV-2 i ranged from 1.166 to 9.805 (median: 2.887) min, and minimum detection sensitivity of TRCReady® SARS-CoV-2 i was 9 copies per test, with reaction time as 5.014 min. Detection of SARS-CoV-2 gene from nasopharyngeal swab sample using TRCReady® SARS-CoV-2 i shows comparative diagnostic test accuracy with RT-PCR, and can be used as a useful test to diagnose SARS-CoV-2 infection.

SARS-CoV-2 antigen detection in deceased bodies: implications for infection prevention.

Background & objectives: High transmissibility of the SARS-CoV-2 has significant implications on healthcare workers' safety, preservation, handling, transportation and disposal of the deceased bodies. The objective of this study was to detect SARS-CoV-2 antigen in nasopharyngeal samples and its implications in handling and care of COVID-19 deceased bodies. Methods: A study was conducted at a dedicated COVID-19 centre on deceased individuals from April to December 2020. Rapid antigen test (RAT) and reverse transcription (RT)-PCR was compared on all the SARS-CoV-2 positive cadavers recruited in the study. Results: A total of 115 deceased individuals were included in the study. Of these, 79 (68.7%) were male and 36 (31.3%) were female and majority were in the age group of 51-60 yr [31 (27%)]. SARS-CoV-2 antigen test was positive in 32 (27.8%) and negative in 83 (72.1%) individuals. The mean time interval between deaths to the sample collection was 13.2 h with interquartile range of eight to 20 h. Reverse transcription (RT)-PCR was used as the reference test and 24 (20.9%) cases were true positive; 93.6 per cent [95% confidence interval (CI) 88.8-98.4%] sensitivity, 45.2 per cent (95% CI 35.5-55%) specificity, 60.2 per cent (95% CI 50.6-69.8%) positive predictive value and 88.8 per cent (95% CI 82.7-95%) negative predictive value of antigen test was computed. Interpretation & conclusions: SARS-CoV-2 antigen test was positive beyond 19 h in COVID-19 deceased individuals. Antigen test was found to be highly sensitive in the deceased. Patients, suspected of having died due to COVID-19, can be screened by this method. As infectiousness of the virus in the deceased bodies cannot be directly concluded from either the antigen or RT-PCR test, yet possible transmission cannot be completely ruled out. Strict infection control measures need to be followed during the handling and clearance of COVID-19 cadavers.

Termination of paroxysmal supraventricular tachycardia by intranasal swab insertion.

Paroxysmal supraventricular tachycardia (SVT) is a common emergency department presentation. Vagal maneuvers are commonly tried to terminate SVT but are often unsuccessful in terminating the dysrhythmia. The use of adenosine, while often successful, is associated with a number of side effects and is often disliked by patients with recurrent episodes of SVT. We report on a 44-year-old woman with a past medical history of SVT who presented to the emergency department (ED) due to a recurrence of her SVT. The patient had no intravenous access and preferred not to receive adenosine. The patient received intranasal stimulation with a nasopharyngeal swab used for COVID-19 testing for 5-10 s. After less than 10 s, the patient converted to a sinus rhythm. She was successfully discharged from the ED after 1 h of observation and no recurrence of her SVT.

Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai.

Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.

Deep Neural Network-Based Visual Feedback System for Nasopharyngeal Swab Sampling.

During the 2019 coronavirus disease pandemic, robotic-based systems for swab sampling were developed to reduce burdens on healthcare workers and their risk of infection. Teleoperated sampling systems are especially appreciated as they fundamentally prevent contact with suspected COVID-19 patients. However, the limited field of view of the installed cameras prevents the operator from recognizing the position and deformation of the swab inserted into the nasal cavity, which highly decreases the operating performance. To overcome this limitation, this study proposes a visual feedback system that monitors and reconstructs the shape of an NP swab using augmented reality (AR). The sampling device contained three load cells and measured the interaction force applied to the swab, while the shape information was captured using a motion-tracking program. These datasets were used to train a one-dimensional convolution neural network (1DCNN) model, which estimated the coordinates of three feature points of the swab in 2D X-Y plane. Based on these points, the virtual shape of the swab, reflecting the curvature of the actual one, was reconstructed and overlaid on the visual display. The accuracy of the 1DCNN model was evaluated on a 2D plane under ten different bending conditions. The results demonstrate that the x-values of the predicted points show errors of under 0.590 mm from P0, while those of P1 and P2 show a biased error of about -1.5 mm with constant standard deviations. For the y-values, the error of all feature points under positive bending is uniformly estimated with under 1 mm of difference, when the error under negative bending increases depending on the amount of deformation. Finally, experiments using a collaborative robot validate its ability to visualize the actual swab's position and deformation on the camera image of 2D and 3D phantoms.

Analysis of Bacteriophage Behavior of a Human RNA Virus, SARS-CoV-2, through the Integrated Approach of Immunofluorescence Microscopy, Proteomics and D-Amino Acid Quantification.

SARS-CoV-2, one of the human RNA viruses, is widely studied around the world. Significant efforts have been made to understand its molecular mechanisms of action and how it interacts with epithelial cells and the human microbiome since it has also been observed in gut microbiome bacteria. Many studies emphasize the importance of surface immunity and also that the mucosal system is critical in the interaction of the pathogen with the cells of the oral, nasal, pharyngeal, and intestinal epithelium. Recent studies have shown how bacteria in the human gut microbiome produce toxins capable of altering the classical mechanisms of interaction of viruses with surface cells. This paper presents a simple approach to highlight the initial behavior of a novel pathogen, SARS-CoV-2, on the human microbiome. The immunofluorescence microscopy technique can be combined with spectral counting performed at mass spectrometry of viral peptides in bacterial cultures, along with identification of the presence of D-amino acids within viral peptides in bacterial cultures and in patients' blood. This approach makes it possible to establish the possible expression or increase of viral RNA viruses in general and SARS-CoV-2, as discussed in this study, and to determine whether or not the microbiome is involved in the pathogenetic mechanisms of the viruses. This novel combined approach can provide information more rapidly, avoiding the biases of virological diagnosis and identifying whether a virus can interact with, bind to, and infect bacteria and epithelial cells. Understanding whether some viruses have bacteriophagic behavior allows vaccine therapies to be focused either toward certain toxins produced by bacteria in the microbiome or toward finding inert or symbiotic viral mutations with the human microbiome. This new knowledge opens a scenario on a possible future vaccine: the probiotics vaccine, engineered with the right resistance to viruses that attach to both the epithelium human surface and gut microbiome bacteria.

Detection of coronavirus in tear samples of hospitalized patients with COVID-19.

PURPOSE: To assess the presence of viral RNA in conjunctival secretions and tears of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients in terms of a possible ocular transmission route and also to examine whether a difference between the patients with and without ocular surface positivity existed. METHODS: A prospective cross-sectional study of 70 consecutive patients who were hospitalized in Haseki Training and Research Hospital with SARS-CoV-2 from February 1 to April 1, 2021, was performed. Tears and conjunctival secretions were collected within 24 h of nasopharyngeal sample collection and examined for SARS-CoV-2 using reverse transcription real-time polymerase chain reaction (qPCR). The clinical data, results of blood tests and nasopharyngeal and conjunctival swabs, and CT findings were evaluated for all patients. RESULTS: Seventy patients (37 males, 33 females) were included in this study. Tear-conjunctival samples from eight patients (11.42%) yielded positive PCR results although these eight patients had no eye symptoms or conjunctivitis. In patients with positive conjunctival PCR results, cycle threshold values for conjunctival samples were higher than those for nasopharyngeal samples. All findings (except gender) were similar between patients with either positive or negative conjunctival swab samples. All patients with positive conjunctival swab samples were male; however, the male ratio in patients with negative conjunctival swab samples was only 46.77%. CONCLUSION: In our study, the rate of conjunctival swab PCR positivity was 11.42%. It appears that even in the absence of ocular symptoms, SARS-CoV-2 virus may be present on the ocular surface; therefore, the ocular surface may be a significant viral transmission route.

Analysis of a direct access testing system for the detection of SARS-CoV-2 in the paediatric population attending school.

Background: During the COVID-19 pandemic, the paediatric population plays a minor role in the spread of the SARS-CoV-2 virus. However, in order to keep schools open and reduce SARS-CoV spreading, it is necessary to identify and isolate early SARS-CoV-2 positive paediatric patients even if they are asymptomatic. The aim of this study was to describe a setting for SARS-CoV 2 testing based on the spontaneous presentation of paediatric patients attending school without a medical prescription and explore its appropriateness. Study design: Cross-sectional study. Methods: The study performed between September 2020 and March 2021 among a sample of 13,283 paediatric patients who underwent a swab in four different hospital settings (school hot spot, emergency department, day hospital setting and hospital wards). For each patients we collected: date of swab execution, type of swab, execution setting of the swab, result of the swab, information about community spread of the virus in the 14 days prior to the swab execution, sex and age. Results: In our sample, females accounted for 45.8%. The median age was 6.8 years (IQR 3.0-11.2) and the most frequent age category was between 6 and 11 years (27.9%). At multivariable models with a swab tested positive as outcome. The swabs executed in all the hospital settings had a lower likelihood of resulting positive compared with the school hot spot setting. Compared with adolescents aged between 14 and 19 years old, new-borns below 3 months (adjOR 1.83, 95% C.I. 1.14-3) and patients aged between 11 and 14 years old (adjOR 1.32, 95% C.I. 1.07-1.63) reported a higher probability of a swab tested positive. Instead, children aged between 3 months and 3 years (adjOR 0.77, 95% C.I. 0.61-0.96) and children aged between 3 years and 6 years (adjOR 0.66, 95% C.I. 0.53-0.83) were less likely to result positive. The higher was the mean of pooled Rt in the 14 days preceding the swab, the higher was the likelihood of resulting positive (adjOR 1.75, 95% C.I. 1.53-1.99). Conclusion: In conclusion, we found a high incidence of paediatric patients positive to the test for the detection of SARS-CoV-2 at the school hot spot compared with other settings during the period of observation. The free access modality to the nasopharyngeal swab was effective in identifying patients with COVID-19. Public health authorities should implement these testing modality in order to help reduce the spread of SARS-CoV-2 in school settings.

Identifying novel host-based diagnostic biomarker panels for COVID-19: a whole-blood/nasopharyngeal transcriptome meta-analysis.

BACKGROUND: Regardless of improvements in controlling the COVID-19 pandemic, the lack of comprehensive insight into SARS-COV-2 pathogenesis is still a sophisticated challenge. In order to deal with this challenge, we utilized advanced bioinformatics and machine learning algorithms to reveal more characteristics of SARS-COV-2 pathogenesis and introduce novel host response-based diagnostic biomarker panels. METHODS: In the present study, eight published RNA-Seq datasets related to whole-blood (WB) and nasopharyngeal (NP) swab samples of patients with COVID-19, other viral and non-viral acute respiratory illnesses (ARIs), and healthy controls (HCs) were integrated. To define COVID-19 meta-signatures, Gene Ontology and pathway enrichment analyses were applied to compare COVID-19 with other similar diseases. Additionally, CIBERSORTx was executed in WB samples to detect the immune cell landscape. Furthermore, the optimum WB- and NP-based diagnostic biomarkers were identified via all the combinations of 3 to 9 selected features and the 2-phases machine learning (ML) method which implemented k-fold cross validation and independent test set validation. RESULTS: The host gene meta-signatures obtained for SARS-COV-2 infection were different in the WB and NP samples. The gene ontology and enrichment results of the WB dataset represented the enhancement in inflammatory host response, cell cycle, and interferon signature in COVID-19 patients. Furthermore, NP samples of COVID-19 in comparison with HC and non-viral ARIs showed the significant upregulation of genes associated with cytokine production and defense response to the virus. In contrast, these pathways in COVID-19 compared to other viral ARIs were strikingly attenuated. Notably, immune cell proportions of WB samples altered in COVID-19 versus HC. Moreover, the optimum WB- and NP-based diagnostic panels after two phases of ML-based validation included 6 and 8 markers with an accuracy of 97% and 88%, respectively. CONCLUSIONS: Based on the distinct gene expression profiles of WB and NP, our results indicated that SARS-COV-2 function is body-site-specific, although according to the common signature in WB and NP COVID-19 samples versus controls, this virus also induces a global and systematic host response to some extent. We also introduced and validated WB- and NP-based diagnostic biomarkers using ML methods which can be applied as a complementary tool to diagnose the COVID-19 infection from non-COVID cases.

Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS-CoV-2 variants.

A prospective cohort study was conducted during the Delta and Omicron severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) epidemic waves from paired nasopharyngeal swab (NPS or NP swab) and saliva samples taken from 624 participants. The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any freezing and thawing steps before processing. Nucleic acids from saliva and NPS were prospectively extracted and SARS-CoV-2 was detected using a real-time reverse-transcription polymerase chain reaction. All observed results were statistically analyzed. Although the results obtained with NP and saliva agreed overall, higher viral loads were observed in NP swabs regardless of the day of specimen collection in both SARS-CoV-2 epidemic waves. No significant difference could be observed between the two epidemic waves characterized by Delta or Omicron SARS-CoV-2. To note, Delta infection resulted in higher viral loads both in NP and saliva and more symptoms, including rhinorrhea, cough, and dyspnea, whereas Omicron wave patients more frequently reported sore throat. An increase in the mean log RNA of SARS-CoV-2 was observed with the number of expressed symptoms in both waves, however, the difference was not significant. Data confirmed that results from saliva were concordant with those from NP swabs, although saliva proved to be a challenging sample with frequent inhibitions that required substantial retesting.

Ethmoidal silent sinus syndrome after nasal swab test.

This study reported the case of a healthy male in his 40s who presented with a 3-month history of frontal headache and post-nasal drip, which did not improve with oral antibiotics. One month prior to the onset of the symptoms, he underwent a nasopharyngeal swab testing for SARS-CoV-2 (which yielded a negative result) for a history of malaise and cough. The patient claimed that the swab insertion into the nasal cavity was particularly painful on the left side. Sinus computed tomography (CT) scan showed deformity of the left middle nasal turbinate with occlusion of the osteomeatal complex, resulting in ethmoid silent sinus syndrome. This study makes a significant contribution to the literature because nasopharyngeal, midturbinate and anterior nasal swabs have been recommended as initial diagnostic specimen collection methods by the US Centers for Disease Control and Prevention (CDC) for the coronavirus disease 2019. These methods require introducing an instrument into the nasal cavity, potentially leading to adverse effects due to the delicate and complex nasal anatomy. However, complications related to swab testing for respiratory pathogens have not yet been fully discussed in the literature.

Etiology and the challenge of diagnostic testing of community-acquired pneumonia in children and adolescents.

BACKGROUND: Pneumonia is the leading cause of mortality in pediatric population. The etiology of pneumonia in this population is variable and changes according to age and disease severity and where the study is conducted. Our aim was to determine the etiology of community-acquired pneumonia (CAP) in children aged 1 month to 17 years admitted to 13 Colombian hospitals. METHODS: Prospective cohort study. Hospitalized children with radiologically confirmed CAP and ≤ 15 days of symptoms were included and followed together with a control group. Induced sputum (IS) was submitted for stains and cultures for pyogenic bacteria and Mycobacterium tuberculosis, and multiplex PCR (mPCR) for bacteria and viruses; urinary antigens for pneumococcus and Legionella pneumophila; nasopharyngeal swabs for viruses, and paired serology for atypical bacteria and viruses. Additional cultures were taken at the discretion of primary care pediatricians. RESULTS: Among 525 children with CAP, 71.6% had non-severe pneumonia; 24.8% severe and 3.6% very severe pneumonia, and no fatal cases. At least one microorganism was identified in 84% of children and 61% were of mixed etiology; 72% had at least one respiratory virus, 28% pyogenic bacteria and 21% atypical bacteria. Respiratory syncytial virus, Parainfluenza, Rhinovirus, Influenza, Mycoplasma pneumoniae, Adenovirus and Streptococcus pneumoniae were the most common etiologies of CAP. Respiratory syncytial virus was more frequent in children under 2 years and in severe pneumonia. Tuberculosis was diagnosed in 2.3% of children. IS was the most useful specimen to identify the etiology (33.6%), and blood cultures were positive in 3.6%. The concordance between all available diagnostic tests was low. A high percentage of healthy children were colonized by S. pneumoniae and Haemophilus influenzae, or were infected by Parainfluenza, Rhinovirus, Influenza and Adenovirus. CONCLUSIONS: Respiratory viruses are the most frequent etiology of CAP in children and adolescents, in particular in those under 5 years. This study shows the challenges in making an etiologic diagnosis of CAP in pediatric population because of the poor concordance between tests and the high percentage of multiple microorganisms in healthy children. IS is useful for CAP diagnosis in pediatric population.

Complications of Nasopharyngeal Swabs and Safe Procedures for COVID-19 Testing Based on Anatomical Knowledge.

Nasopharyngeal swabs have been widely to prevent the spread of coronavirus disease 2019 (COVID-19). Nasopharyngeal COVID-19 testing is a generally safe and well-tolerated procedure, but numerous complications have been reported in the media. Therefore, the present study aimed to review and document adverse events and suggest procedural references to minimize preventable but often underestimated risks. A total of 27 articles were selected for the review of 842 related documents in PubMed, Embase, and KoreaMed. The complications related to nasopharyngeal COVID-19 testing were reported to be rarely happened, ranging from 0.0012 to 0.026%. Frequently documented adverse events were retained swabs, epistaxis, and cerebrospinal fluid leakage, often associated with high-risk factors, including severe septal deviations, pre-existing skull base defects, and previous sinus or transsphenoidal pituitary surgery. Appropriate techniques based on sufficient anatomical knowledge are mandatory for clinicians to perform nasopharyngeal COVID-19 testing. The nasal floor can be predicted by the line between the nostril and external ear canal. For safe testing, the angle of swab insertion in the nasal passage should remain within 30° of the nasal floor. The swab was gently inserted along the nasal septum just above the nasal floor to the nasopharynx and remained on the nasopharynx for several seconds before removal. Forceful insertion should be attempted, and alternative examinations should be considered, especially in vulnerable patients. In conclusion, patients and clinicians should be aware of rare but possible complications and associated high-risk factors. The suggested procedural pearls enable more comfortable and safe nasopharyngeal COVID-19 testing for both clinicians and patients.

Discrepancies of SARS-CoV-2 testing results among patients with total laryngectomy.

PURPOSE: Prevention of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is obtained with nasopharyngeal swabs. By the way, there is no consensus regarding sampling in totally laryngectomized subjects (who thus breathe directly by the tracheostomy and, theoretically, may be infected in the trachea). The aim of this study is to evaluate possible differences between swab results in the trachea and in the nasopharynx of this category of patients. METHODS: A retrospective chart review was performed in April 2021 among patients who previously had been operated on for total laryngectomy and who underwent swabs for SARS-CoV-2 research in 3 health-care centers in Northern-Eastern Italy. Data regarding the site of swabbing (trachea or nasopharynx) were analyzed. A comprehensive review of the literature regarding the same topic was then performed. RESULTS: A total of 25 totally laryngectomized subjects underwent swabs. Among them, 5 tested positive in the trachea (1) and in the nasopharynx (4). According to the literature review, 4 more subjects tested positive in the trachea (1) and in the nasopharynx (3). Data were overall divergent and no statistically significant correlations emerged between results of the tests performed in the two sites. CONCLUSION: Due to these discrepancies, both tracheal and nasopharyngeal swabs are recommended in these kinds of patients, to obtain a reliable test and to avoid false negatives.

On the Efficacy of ZnO Nanostructures against SARS-CoV-2.

In 2019, the new coronavirus disease (COVID-19), related to the severe acute respiratory syndrome coronavirus (SARS-CoV-2), started spreading around the word, giving rise to the world pandemic we are still facing. Since then, many strategies for the prevention and control of COVID-19 have been studied and implemented. In addition to pharmacological treatments and vaccines, it is mandatory to ensure the cleaning and disinfection of the skin and inanimate surfaces, especially in those contexts where the contagion could spread quickly, such as hospitals and clinical laboratories, schools, transport, and public places in general. Here, we report the efficacy of ZnO nanoparticles (ZnONPs) against SARS-CoV-2. NPs were produced using an ecofriendly method and fully characterized; their antiviral activity was tested in vitro against SARS-CoV-2, showing a decrease in viral load between 70% and 90%, as a function of the material's composition. Application of these nano-antimicrobials as coatings for commonly touched surfaces is envisaged.